FAM161A, associated with retinitis pigmentosa, is a component of the cilia-basal body complex and interacts with proteins involved in ciliopathies.

Retinitis pigmentosa (RP) is a retinal degenerative disease characterized by the progressive loss of photoreceptors. We have previously demonstrated that RP can be caused by recessive mutations in the human FAM161A gene, encoding a protein with unknown function that contains a conserved region shared only with a distant paralog, FAM161B. In this study, we show that FAM161A localizes at the base of the photoreceptor connecting cilium in human, mouse and rat. Furthermore, it is also present at the ciliary basal body in ciliated mammalian cells, both in native conditions and upon the expression of recombinant tagged proteins. Yeast two-hybrid analysis of binary interactions between FAM161A and an array of ciliary and ciliopathy-associated proteins reveals direct interaction with lebercilin, CEP290, OFD1 and SDCCAG8, all involved in hereditary retinal degeneration. These interactions are mediated by the C-terminal moiety of FAM161A, as demonstrated by pull-down experiments in cultured cell lines and in bovine retinal extracts. As other ciliary proteins, FAM161A can also interact with the microtubules and organize itself into microtubule-dependent intracellular networks. Moreover, small interfering RNA-mediated depletion of FAM161A transcripts in cultured cells causes the reduction in assembled primary cilia. Taken together, these data indicate that FAM161A-associated RP can be considered as a novel retinal ciliopathy and that its molecular pathogenesis may be related to other ciliopathies.

Corticosterone mediates the condition-dependent component of melanin-based coloration

The handicap principle of sexual selection theory states that colourful phenotypic traits signal aspects of individual quality because only individuals in prime condition can afford to produce and bear conspicuous traits. Melanin-based pigments participate in the elaboration of many secondary sexual characters and, given their role in sexual selection, melanin-based coloration may therefore honestly reject individual quality. Although the expression of melanism is usually under genetic control, in some species it is condition dependent. However, the underlying physiological mechanism is yet unknown. Based on the negative feedback link between corticosterone and melanogenesis ( melanocortins, tyrosinase) in response to stressful environmental factors, we hypothesize that corticosterone mediates the condition-dependent component of melanism. This hypothesis predicts that stressful factors induce a rise in circulating corticosterone which inhibits the secretion of melanocortins and tyrosinase and in turn melanin production. We tested this prediction by manipulating the level of corticosterone at the time of melanin production in nestling barn owls, Tyto alba, a species showing heritable variation in the degree of phaeomelanism from reddish-brown to white. The finding that corticosterone-implanted nestlings produced feathers with less phaeomelanic coloration than placebo-implanted nestlings is consistent with the hypothesis that the environment-mediated reduction in the degree of melanism is, at least in part, caused by a rise in corticosterone. In species in which the expression of melanin-based coloration is condition dependent, we now need a test showing that individuals with less corticosterone and more melanin-based signals are individuals in better condition.

An architecture for adaptive replication-based multimedia streaming in P2P networks

This PhD thesis addresses the issue of scalable media streaming in large-scale networking environments. Multimedia streaming is one of the largest sink of network resources and this trend is still growing as testified by the success of services like Skype, Netflix, Spotify and Popcorn Time (BitTorrent-based). In traditional client-server solutions, when the number of consumers increases, the server becomes the bottleneck. To overcome this problem, the Content-Delivery Network (CDN) model was invented. In CDN model, the server copies the media content to some CDN servers, which are located in different strategic locations on the network. However, they require heavy infrastructure investment around the world, which is too expensive. Peer-to-peer (P2P) solutions are another way to achieve the same result. These solutions are naturally scalable, since each peer can act as both a receiver and a forwarder. Most of the proposed streaming solutions in P2P networks focus on routing scenarios to achieve scalability. However, these solutions cannot work properly in video-on-demand (VoD) streaming, when resources of the media server are not sufficient. Replication is a solution that can be used in these situations. This thesis specifically provides a family of replication-based media streaming protocols, which are scalable, efficient and reliable in P2P networks. First, it provides SCALESTREAM, a replication-based streaming protocol that adaptively replicates media content in different peers to increase the number of consumers that can be served in parallel. The adaptiveness aspect of this solution relies on the fact that it takes into account different constraints like bandwidth capacity of peers to decide when to add or remove replicas. SCALESTREAM routes media blocks to consumers over a tree topology, assuming a reliable network composed of homogenous peers in terms of bandwidth. Second, this thesis proposes RESTREAM, an extended version of SCALESTREAM that addresses the issues raised by unreliable networks composed of heterogeneous peers. Third, this thesis proposes EAGLEMACAW, a multiple-tree replication streaming protocol in which two distinct trees, named EAGLETREE and MACAWTREE, are built in a decentralized manner on top of an underlying mesh network. These two trees collaborate to serve consumers in an efficient and reliable manner. The EAGLETREE is in charge of improving efficiency, while the MACAWTREE guarantees reliability. Finally, this thesis provides TURBOSTREAM, a hybrid replication-based streaming protocol in which a tree overlay is built on top of a mesh overlay network. Both these overlays cover all peers of the system and collaborate to improve efficiency and low-latency in streaming media to consumers. This protocol is implemented and tested in a real networking environment using PlanetLab Europe testbed composed of peers distributed in different places in Europe.

Hidden branches: developments in root system architecture.

The root system is fundamentally important for plant growth and survival because of its role in water and nutrient uptake. Therefore, plants rely on modulation of root system architecture (RSA) to respond to a changing soil environment. Although RSA is a highly plastic trait and varies both between and among species, the basic root system morphology and its plasticity are controlled by inherent genetic factors. These mediate the modification of RSA, mostly at the level of root branching, in response to a suite of biotic and abiotic factors. Recent progress in the understanding of the molecular basis of these responses suggests that they largely feed through hormone homeostasis and signaling pathways. Novel factors implicated in the regulation of RSA in response to the myriad endogenous and exogenous signals are also increasingly isolated through alternative approaches such as quantitative trait locus analysis.

Secretory component delays the conversion of secretory IgA into antigen-binding competent F(ab')2: a possible implication for mucosal defense.

Secretory component (SC) represents the soluble ectodomain of the polymeric Ig receptor, a membrane protein that transports mucosal Abs across epithelial cells. In the protease-rich environment of the intestine, SC is thought to stabilize the associated IgA by unestablished molecular mechanisms. To address this question, we reconstituted SC-IgA complexes in vitro by incubating dimeric IgA (IgAd) with either recombinant human SC (rSC) or SC isolated from human colostral milk (SCm). Both complexes exhibited an identical degree of covalency when exposed to redox agents, peptidyl disulfide isomerase, and temperature changes. In cross-competition experiments, 50% inhibition of binding to IgAd was achieved at approximately 10 nM SC competitor. Western blot analysis of IgAd digested with intestinal washes indicated that the alpha-chain in IgAd was primarily split into a 40-kDa species, a phenomenon delayed in rSC- or SCm-IgAd complexes. In the same assay, either of the SCs was resistant to degradation only if complexed with IgAd. In contrast, the kappa light chain was not digested at all, suggesting that the F(ab')2 region was left intact. Accordingly, IgAd and SC-IgAd digestion products retained functionality as indicated by Ag reactivity in ELISA. Size exclusion chromatography under native conditions of digested IgAd and rSC-IgAd demonstrates that SC exerts its protective role in secretory IgA by delaying cleavage in the hinge/Fc region of the alpha-chain, not by holding together degraded fragments. The function of integral secretory IgA and F(ab')2 is discussed in terms of mucosal immune defenses.