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Supplementary Figure 2 from RASSF1C, an Isoform of the Tumor Suppressor RASSF1A, Promotes the Accumulation of β-Catenin by Interacting with βTrCP

The Ras-association domain family 1 (RASSF1) gene has seven different isoforms; isoform A is a tumor-suppressor gene (RASSF1A). The promoter of RASSF1A is inactivated in many cancers, whereas the expression of another major isoform, RASSF1C, is not affected. Here, we show that RASSF1C, but not RASSF1A, interacts with βTrCP. Binding of RASSF1C to βTrCP involves serine 18 and serine 19 of the SS18GYXS19 motif present in RASSF1C but not in RASSF1A. This motif is reminiscent of the canonical phosphorylation motif recognized by βTrCP; however, surprisingly, the association between RASSF1C and βTrCP does not occur via the βTrCP substrate binding domain, the WD40 repeats. Overexpression of RASSF1C, but not of RASSF1A, resulted in accumulation and transcriptional activation of the β-catenin oncogene, due to inhibition of its βTrCP-mediated degradation. Silencing of RASSF1A by small interfering RNA was sufficient for β-catenin to accumulate, whereas silencing of both RASSF1A and RASSF1C had no effect. Thus, RASSF1A and RASSF1C have opposite effects on β-catenin degradation. Our results suggest that RASSF1C expression in the absence of RASSF1A could play a role in tumorigenesis. [Cancer Res 2007;67(3):1054–61]

Supplementary Figure 3 from RASSF1C, an Isoform of the Tumor Suppressor RASSF1A, Promotes the Accumulation of β-Catenin by Interacting with βTrCP

Supplementary Figure 1 from RASSF1C, an Isoform of the Tumor Suppressor RASSF1A, Promotes the Accumulation of β-Catenin by Interacting with βTrCP

Age-related macular degeneration is a prevalent neuroinflammatory condition and a major cause of blindness driven by genetic and environmental factors such as obesity. In diseases of aging, modifiable factors can be compounded over the life span. We report that diet-induced obesity earlier in life triggers persistent reprogramming of the innate immune system, lasting long after normalization of metabolic abnormalities. Stearic acid, acting through Toll-like receptor 4 (TLR4), is sufficient to remodel chromatin landscapes and selectively enhance accessibility at binding sites for activator protein-1 (AP-1). Myeloid cells show less oxidative phosphorylation and shift to glycolysis, ultimately leading to proinflammatory cytokine transcription, aggravation of pathological retinal angiogenesis, and neuronal degeneration associated with loss of visual function. Thus, a past history of obesity reprograms mononuclear phagocytes and predisposes to neuroinflammation.

National audience; Hypernetworks appeared in many fields and uses including combinatorics problems, the theory of complex systems, the systems biology and deep learning with different semantics. It is important to understand the uses of the term hypernetwork in the literature to avoid confusion. The objective of this article to make a state of the art of the definitions of the hypernetwork according to the field of use. In particular, we will try to situate hypernetworks in our research context on artificial intelligence.; Les hyper-réseaux apparaissaient dans de nombreux domaines et usages dont des problèmes de combinatoire, la théorie des systèmes complexes, la biologie des systèmes et l’apprentissage profond avec une sémantique différente. Il est important de comprendre les utilisations du terme hyper-réseau dans la littérature afin d’éviter toute confusion. L’objectif de cet article est de faire un état de l’art des définitions de l’hyper-réseau suivant le domaine d’utilisation. Nous nous attacherons notamment à situer les hyper-réseaux dans notre contexte de recherche sur l’intelligence artificielle.

Muller glial cells (MGCs) are responsible for the homeostatic and metabolic support of the retina. Despite the importance of MGCs in retinal disorders, reliable and accessible human cell sources to be used to model MGC‐associated diseases are lacking. Although primary human MGCs (pMGCs) can be purified from post‐mortem retinal tissues, the donor scarcity limits their use. To overcome this problem, we developed a protocol to generate and bank human induced pluripotent stem cell‐derived MGCs (hiMGCs). Using a transcriptome analysis, we showed that the three genetically independent hiMGCs generated were homogeneous and showed phenotypic characteristics and transcriptomic profile of pMGCs. These cells expressed key MGC markers, including Vimentin, CLU, DKK3, SOX9, SOX2, S100A16, ITGB1, and CD44 and could be cultured up to passage 8. Under our culture conditions, hiMGCs and pMGCs expressed low transcript levels of RLPB1, AQP4, KCNJ1, KCJN10, and SLC1A3. Using a disease modeling approach, we showed that hiMGCs could be used to model the features of diabetic retinopathy (DR)‐associated dyslipidemia. Indeed, palmitate, a major free fatty acid with elevated plasma levels in diabetic patients, induced the expression of inflammatory cytokines found in the ocular fluid of DR patients such as CXCL8 (IL‐8) and ANGPTL4. Moreover, the analysis of palmitate‐treated hiMGC secretome showed an upregulation of proangiogenic factors strongly related to DR, including ANG2, Endoglin, IL‐1β, CXCL8, MMP‐9, PDGF‐AA, and VEGF. Thus, hiMGCs could be an alternative to pMGCs and an extremely valuable tool to help to understand and model glial cell involvement in retinal disorders, including DR., Main Points We developed a protocol to generate and bank human iPSC‐derived Müller Glial cells (hiMGCs).hiMGCs showed phenotypic characteristics and transcriptomic profile of primary MGCs.hiMGCs can be used to model the features of diabetic retinopathy.

Summary The classical aortic ring model is well suited for deciphering pro-angiogenic processes. Here, we propose simple modifications of the standard protocol to study various anti-angiogenic processes from growth arrest to capillary degeneration. Aortic rings are cultured under basal conditions for 6 days to allow physiological vessel sprouting and then split into treatment groups to follow capillary growth or degeneration for an additional 2 days., Graphical Abstract, Highlights • Aortic rings sprout under basal conditions until day 5 and are treated on day 6 only • Growth rate analysis allows evaluation of vascular degeneration • The protocol can distinguish angiostatic from vascular degenerative processes • Paired statistical analysis confers additional power to the analysis, The classical aortic ring model is well suited for deciphering pro-angiogenic processes. Here, we propose simple modifications of the standard protocol to study various anti-angiogenic processes from growth arrest to capillary degeneration. Aortic rings are cultured under basal conditions for 6 days to allow physiological vessel sprouting and then split into treatment groups to follow capillary growth or degeneration for an additional 2 days.

Background Rhegmatogenous retinal detachment (RD) involving the macula is a major cause of visual impairment despite high surgical success rate, mainly because of cone death. We and others have shown that cone loss occurs secondary to chronic inflammation in many retinal diseases, including age-related macular degeneration and retinitis pigmentosa. We here investigated the yet unknown mechanisms of inflammation-induced cone death in RD.Methods Vitreous samples from patients with RD and from control patients with macular hole were analyzed to characterize the inflammatory response to RD. A mouse model of RD and retinal explants culture were then used to explore the mechanisms leading to cone death.Results Analysis of vitreous samples shows that RD induces a marked inflammatory response with increased cytokine and chemokine expression in humans, which is closely mimicked by experimental murine RD. In this model, we demonstrate that myeloid cells and T-lymphocytes directly contribute to cone loss, as the inhibition of their accumulation by Thrombospondin 1 increased cone survival. We show that cones are highly dependent on glucose and insulin signaling for survival in vitro and that insulin, and the insulin sensitizers rosiglitazone and metformin, prevent RD-induced cone loss in vivo, despite the persistence of inflammation.Conclusion Our results describe a new mechanism by which inflammation, likely through a combination of competition for glucose and the inhibition of insulin signaling, promotes cone death in RD. Therapeutic inhibition of inflammation and stimulation of insulin signaling might prevent RD-associated cone death until the RD can be surgically repaired and improve visual outcome after RD.Trial registration: ClinicalTrials.gov Identifier NCT03318588

We present the leading experiment that helps designing the Rhythm Network. The model diverges from typical time graphs and is not explicitly helpful for longitudinal studies. However, the objective...

Retroviral integrase (IN) proteins catalyze the permanent integration of the viral genome into host DNA. They can productively recruit cellular proteins, and the human Bromodomain and Extra-Terminal domain (hBET) proteins have been shown to be co-factors for integration of gamma-retroviruses such as Murine Leukemia Virus (MLV) into human cells. By using two-hybrid, co-immunoprecipitation and in vitro interaction assays, we showed that IN of the gamma- Porcine Endogenous Retrovirus-A/C (PERV IN) interacts through its C-terminal domain (CTD) with hBET proteins. We observed that PERV IN interacts with the BRD2, BRD3 and BRD4 proteins in vitro and that the BRD2 protein specifically binds and co-localizes with PERV IN protein in the nucleus of cells. We further mapped the interaction sites to the conserved Extra-Terminal (ET) domain of the hBET proteins and to several amino acids of the of the C-terminal tail of the PERV IN CTD. Finally, we determined the first experimental structure of an IN CTD - BET ET complex from small-angle X-ray scattering data (SAXS). We showed that the two factors assemble as two distinct modules linked by a short loop which confers partial flexibility. The SAXS-restrained model is structurally compatible with the binding of the PERV intasome to BRD2. Altogether, these data confirm the important role of host BET proteins in the gamma-retroviruses' targeting site and efficiency of integration.

Halfway between music analysis and graph visualization, we propose tonal pitch representations from the chromatic scale. On the first part of the experiment, a 12-node graph is connected as a Rhythm Network and visualized with a Circular Layout, commonly known as Pitch constellation. This particular graph topology focuses on node structure and gives strength to weak edges. At this occasion, we unveil the Singularity Threshold, giving an opportunity to isolate structure from singular parts of melodies. Where usual Pitch constellations focus on chords, we focus on successive pitch intervals. On the second part, we propose a rhythm representation using a Force-Directed layout. In addition to structural information, our second technique shows proximal and peripheral elements. This experiment features 6 melodies that we propose to visualize using Gephi.

EU annual serosurveillance programs show that domestic duck flocks have the highest seroprevalence of H5 antibodies, demonstrating the circulation of notifiable avian influenza virus (AIV) according to OIE, likely low pathogenic (LP). Therefore, transmission characteristics of LPAIV within these flocks can help to understand virus circulation and possible risk of propagation. This study aimed at estimating transmission parameters of four H5 LPAIV (three field strains from French poultry and decoy ducks, and one clonal reverse-genetics strain derived from one of the former), using a SIR model to analyze data from experimental infections in SPF Muscovy ducks. The design was set up to accommodate rearing on wood shavings with a low density of 1.6 ducks/m 2 : 10 inoculated ducks were housed together with 15 contact-exposed ducks. Infection was monitored by RNA detection on oropharyngeal and cloacal swabs using real-time RT-PCR with a cutoff corresponding to 2–7 EID50. Depending on the strain, the basic reproduction number ( R 0 ) varied from 5.5 to 42.7, confirming LPAIV could easily be transmitted to susceptible Muscovy ducks. The lowest R 0 estimate was obtained for a H5N3 field strain, due to lower values of transmission rate and duration of infectious period, whereas reverse-genetics derived H5N1 strain had the highest R 0 . Frequency and intensity of clinical signs were also variable between strains, but apparently not associated with longer infectious periods. Further comparisons of quantitative transmission parameters may help to identify relevant viral genetic markers for early detection of potentially more virulent strains during surveillance of LPAIV.

Nowadays, wireless communication technologies have high influence on our daily lives. The vehicular ad hoc networks (VANETs) is now evolving quickly and attract attention from road operators, car manufacturers and governments. We unveil a fine traffic flow optimization method with VANETs. On the macroscopic level, our model identifies road segment profiles. On the microscopic level, vehicles send and receive alerts using low-level-of-details data. This paper gives workflows for both vehicle and infrastructure sides.

The Ras-association domain family 1 (RASSF1) gene has seven different isoforms; isoform A is a tumor-suppressor gene (RASSF1A). The promoter of RASSF1A is inactivated in many cancers, whereas the expression of another major isoform, RASSF1C, is not affected. Here, we show that RASSF1C, but not RASSF1A, interacts with βTrCP. Binding of RASSF1C to βTrCP involves serine 18 and serine 19 of the SS18GYXS19 motif present in RASSF1C but not in RASSF1A. This motif is reminiscent of the canonical phosphorylation motif recognized by βTrCP; however, surprisingly, the association between RASSF1C and βTrCP does not occur via the βTrCP substrate binding domain, the WD40 repeats. Overexpression of RASSF1C, but not of RASSF1A, resulted in accumulation and transcriptional activation of the β-catenin oncogene, due to inhibition of its βTrCP-mediated degradation. Silencing of RASSF1A by small interfering RNA was sufficient for β-catenin to accumulate, whereas silencing of both RASSF1A and RASSF1C had no effect. Thus, RASSF1A and RASSF1C have opposite effects on β-catenin degradation. Our results suggest that RASSF1C expression in the absence of RASSF1A could play a role in tumorigenesis. [Cancer Res 2007;67(3):1054–61]

One often thinks that the use of Information Technologies brings an infinity of choices. However, Popularity still influences people in our free, pervasive and connected world. It is a reality: popular items keep power and weak items tend to be forgotten. Several studies demonstrated that this natural phenomenon is accentuated today with recommender engines. In this article we present a comparative study of 8 recommendation techniques. We also present a personal recommendation approach, based on items timeline. We unveil a Popularity Influence index, which evaluates the way recommender engines are influenced by the phenomenon. This experiment is led by a pool of interdisciplinary researchers, either or both epistemologists and computer scientists. It includes diverse examples and references from e-business, cultural studies or participatory democracy along with others. We believe that Popularity belongs to a wide set of fields. Therefore, we chose to run this experiment in an E-learning context, where we observe pieces of knowledge popularity.

Dendritic cells (DCs) are essential components of the early events of HIV infection. Here, we characterized the trafficking pathways that HIV-1 follows during its capture by DCs and its subsequent presentation to CD4(+) T cells via an infectious synapse. Immunofluorescence microscopy indicates that the virus-containing compartment in mature DCs (mDCs) co-labels for the tetraspanins CD81, CD82, and CD9 but contains little CD63 or LAMP-1. Using ratio imaging of pH-reporting fluorescent virions in live DCs, we show that HIV-1 is internalized in an intracellular endocytic compartment with a pH of 6.2. Significantly, we demonstrate that the infectivity of cell-free virus is more stable at mildly acidic pH than at neutral pH. Using electron microscopy, we confirm that HIV-1 accumulates in intracellular vacuoles that contain CD81 positive internal membranes but overlaps only partially with CD63. When allowed to contact T cells, HIV-1-loaded DCs redistribute CD81, and CD9, as well as internalized HIV-1, but not the immunological synapse markers MHC-II and T-cell receptor to the infectious synapse. Together, our results indicate that HIV-1 is internalized into a non-conventional, non-lysosomal, endocytic compartment in mDCs and further suggest that HIV-1 is able to selectively subvert components of the intracellular trafficking machinery required for formation of the DC-T-cell immunological synapse to facilitate its own cell-to-cell transfer and propagation.

Here, we report that human immunodeficiency virus type 1 (HIV-1) Env glycoprotein is located mainly in the trans- Golgi network (TGN) due to determinants present in the cytoplasmic domain of the transmembrane gp41 glycoprotein (TMgp41). Internalization assays demonstrated that Env present at the cell surface returns to the TGN. We found that the cytoplasmic domain of TMgp41 binds to TIP47, a protein required for the transport of mannose-6-phosphate receptors from endosomes to the TGN. Overexpression of a mutant of TIP47 affected the transport of Env from endosomes to the TGN. Retrograde transport of Env to the TGN requires a Y 802 W 803 diaromatic motif present in the TMgp41 cytoplasmic domain. Mutation of this motif abolished both targeting to the TGN as well as interaction with TIP47. These data support the view that binding of TIP47 to HIV-1 Env facilitates its delivery to the TGN. Lastly, we show that virus mutated in the Y 802 W 803 motif is poorly infectious and presents a defect in Env incorporation, supporting a model in which retrograde transport of Env is implicated in the optimization of fully infectious HIV-1 production.

“For what else is this collection but a disorder to which habit has accommodated itself to such an extent that it can appear as order?”. Unpacking his library, Walter Benjamin describes how a collection is singular [2]. Collections are not unified wholes, but rather chains of undefined objects. Classify, search, arrange or browse collections are personal processes influenced by internal reflexions. Working on figural and non-figural collections, Piaget and Inhelder explain how space and time influence the way a collector looks to his collection [13]. As a result, representing collections is an issue for computer scientists. Here, we propose a time-based method, which consideres chronological events and draws a time-weighted graph defining patterns of items. We therefore show how this graph outputs different results depending on when it is requested. This work is based on an architecture, designed by Openrendezvous.com, a collaborative web-based application helping to make appointments. Our goal is to adapt a social graph used to define the perfect moment for two people to meet, to the collection case. We discuss how we can build a structure that helps to compute the ideal moment for an item to meet a collector.

Short amino acid sequences in the cytosolic domains of transmembrane proteins are recognized by specialized adapter proteins which are part of coated vesicles utilized to transport membrane proteins between the trans-Golgi network (TGN) and the plasma membrane (forward and backward). Previously, we and others reported that the membrane-proximal tyrosine residues Y712 (human immunodeficiency virus [HIV]) and Y721 (simian immunodeficiency virus [SIV]) in the envelope glycoprotein (Env) of the primate lentiviruses are crucial for the association of Env with clathrin-associated adapter complex AP-2. The same tyrosine-based endocytosis motifs in the cytosolic domains (EnvCD) of transmembrane gp41 of HIV type 1 (HIV-1) and SIV, respectively, were also shown to modulate the interaction with TGN- and endosome-based clathrin-associated complex AP-1. Our findings suggested that EnvCD binding to AP-1, unlike the association of EnvCD with AP-2, is dependent largely on residues other than Y712 and Y721. Here, we tested if motifs downstream of Y712 affect HIV-1 EnvCD–AP-1 binding and Env trafficking. Mutational analysis revealed that the C-terminal leucine-based motif in Env was crucial for the recruitment of AP-1 in vitro and in Env-expressing cells. In addition to affecting Env–AP-1 association, mutations at the C terminus of Env also altered the subcellular localization of Env, suggesting that proper post-Golgi routing of Env depends on its recruitment of AP-1. Finally, the C-terminal dileucine was shown to assist the membrane-proximal Y712 motif in restricting the cell surface expression of Env.

Dendritic cells (DCs) are essential components of the early events of HIV infection. Here, we characterized the trafficking pathways that HIV-1 follows during its capture by DCs and its subsequent presentation to CD4(+) T cells via an infectious synapse. Immunofluorescence microscopy indicates that the virus-containing compartment in mature DCs (mDCs) co-labels for the tetraspanins CD81, CD82, and CD9 but contains little CD63 or LAMP-1. Using ratio imaging of pH-reporting fluorescent virions in live DCs, we show that HIV-1 is internalized in an intracellular endocytic compartment with a pH of 6.2. Significantly, we demonstrate that the infectivity of cell-free virus is more stable at mildly acidic pH than at neutral pH. Using electron microscopy, we confirm that HIV-1 accumulates in intracellular vacuoles that contain CD81 positive internal membranes but overlaps only partially with CD63. When allowed to contact T cells, HIV-1-loaded DCs redistribute CD81, and CD9, as well as internalized HIV-1, but not the immunological synapse markers MHC-II and T-cell receptor to the infectious synapse. Together, our results indicate that HIV-1 is internalized into a non-conventional, non-lysosomal, endocytic compartment in mDCs and further suggest that HIV-1 is able to selectively subvert components of the intracellular trafficking machinery required for formation of the DC-T-cell immunological synapse to facilitate its own cell-to-cell transfer and propagation.

Rift Valley fever virus (RVFV) nonstructural protein NSs acts as the major determinant of virulence by antagonizing interferon β (IFN-β) gene expression. We demonstrate here that NSs interacts with the host protein SAP30, which belongs to Sin3A/NCoR/HDACs repressor complexes and interacts with the transcription factor YY1 that regulates IFN-β gene expression. Using confocal microscopy and chromatin immunoprecipitation, we show that SAP30, YY1, and Sin3A-associated corepressor factors strongly colocalize with nuclear NSs filaments and that NSs, SAP30 and Sin3A-associated factors are recruited on the IFN-β promoter through YY1, inhibiting CBP recruitment, histone acetylation, and transcriptional activation. To ascertain the role of SAP30, we produced, by reverse genetics, a recombinant RVFV in which the interacting domain in NSs was deleted. The virus was unable to inhibit the IFN response and was avirulent for mice. We discuss here the strategy developed by the highly pathogenic RVFV to evade the host antiviral response, affecting nuclear organization and IFN-β promoter chromatin structure., Author Summary Rift Valley fever is a viral mosquito-borne disease affecting ruminants and humans. The disease occurs in Africa and recently it spread to the Arabian Peninsula. In humans, infection can progress to fatal hemorrhagic fever and in ruminants it leads to hepatitis, abortions, or deaths of young lambs. It has been previously shown that the RVFV protein NSs is the major factor of virulence and that pathogenicity is associated with the lack of interferon production. In this study, we analyzed the interaction of NSs with SAP30, a subunit of complexes intervening in gene transcription regulation. We show that SAP30 through its binding to NSs on one hand and to YY1 (the activator/repressor of interferon transcription) on the other hand, forms a multiprotein repression complex on the interferon β promoter. As a consequence, interferon expression is blocked, allowing virus to invade the whole organism. The relevance of the NSs–SAP30 interaction was ascertained by constructing a recombinant virus in which the interacting domain is disrupted. This virus is able to induce interferon expression and when inoculated to the mouse model it was found nonpathogenic.