Browsing by Issue Date, starting with "2015-02"
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- Genomics and the challenging translation into conservation practicePublication . Shafer, Aaron B.A.; Wolf, Jochen B.W.; Alves, Paulo C.; Bergström, Linnea; Bruford, Michael W.; Brännström, Ioana; Colling, Guy; Dalén, Love; De Meester, Luc; Ekblom, Robert; Fawcett, Katie D.; Fior, Simone; Hajibabaei, Mehrdad; Hill, Jason A.; Hoezel, A. Rus; Höglund, Jacob; Jensen, Evelyn L.; Krause, Johannes; Kristensen, Torsten N.; Krützen, Michael; McKay, John K.; Norman, Anita J.; Ogden, Rob; Österling, E. Martin; Ouborg, N. Joop; Piccolo, John; Popović, Danijela; Primmer, Craig R.; Reed, Floyd A.; Roumet, Marie; Salmona, Jordi; Schenekar, Tamara; Schwartz, Michael K.; Segelbacher, Gernot; Senn, Helen; Thaulow, Jens; Valtonen, Mia; Veale, Andrew; Vergeer, Philippine; Vijay, Nagarjun; Vilà, Carles; Weissensteiner, Matthias; Wennerström, Lovisa; Wheat, Christopher W.; Zieliński, PiotrThe global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.
- Dissection of miRNA Pathways Using Arabidopsis Mesophyll ProtoplastsPublication . Martinho, Cláudia; Confraria, Ana; Elias, Carlos Alexandre; Crozet, Pierre; Rubio-Somoza, Ignacio; Weigel, Detlef; Baena-González, ElenaMicroRNAs (miRNAs) control gene expression mostly post-transcriptionally by guiding transcript cleavage and/or translational repression of complementary mRNA targets, thereby regulating developmental processes and stress responses. Despite the remarkable expansion of the field, the mechanisms underlying miRNA activity are not fully understood. In this article, we describe a transient expression system in Arabidopsis mesophyll protoplasts, which is highly amenable for the dissection of miRNA pathways. We show that by transiently overexpressing primary miRNAs and target mimics, we can manipulate miRNA levels and consequently impact on their targets. Furthermore, we developed a set of luciferase-based sensors for quantifying miRNA activity that respond specifically to both endogenous and overexpressed miRNAs and target mimics. We demonstrate that these miRNA sensors can be used to test the impact of putative components of the miRNA pathway on miRNA activity, as well as the impact of specific mutations, by either overexpression or the use of protoplasts from the corresponding mutants. We further show that our miRNA sensors can be used for investigating the effect of chemicals on miRNA activity. Our cell-based transient expression system is fast and easy to set up, and generates quantitative results, being a powerful tool for assaying miRNA activity in vivo.
- To err is robotic, to tolerate immunological: fault detection in multirobot systemsPublication . Tarapore, Danesh; Lima, Pedro U; Carneiro, Jorge; Christensen, Anders LyhneFault detection and fault tolerance represent two of the most important and largely unsolved issues in the field of multirobot systems (MRS). Efficient, long-term operation requires an accurate, timely detection, and accommodation of abnormally behaving robots. Most existing approaches to fault-tolerance prescribe a characterization of normal robot behaviours, and train a model to recognize these behaviours. Behaviours unrecognized by the model are consequently labelled abnormal or faulty. MRS employing these models do not transition well to scenarios involving temporal variations in behaviour (e.g., online learning of new behaviours, or in response to environment perturbations). The vertebrate immune system is a complex distributed system capable of learning to tolerate the organism's tissues even when they change during puberty or metamorphosis, and to mount specific responses to invading pathogens, all without the need of a genetically hardwired characterization of normality. We present a generic abnormality detection approach based on a model of the adaptive immune system, and evaluate the approach in a swarm of robots. Our results reveal the robust detection of abnormal robots simulating common electro-mechanical and software faults, irrespective of temporal changes in swarm behaviour. Abnormality detection is shown to be scalable in terms of the number of robots in the swarm, and in terms of the size of the behaviour classification space.
- Coordinating morphology with behavior during development: an integrative approach from a fly perspectivePublication . Carvalho, Maria João A.; Mirth, Christen K.Animals in the wild live in highly variable and unpredictable environments. This variation in their habitat induces animals, at all stages of their development, to make decisions about what to eat, where to live, and with whom to associate. Additionally, animals like insects show dramatic restructuring of their morphology across life stages, which is accompanied by alterations in their behavior to match stage-specific functions. Finally, in a process called developmental plasticity, environmental conditions feed back onto developmental mechanisms producing animals with stage-specific variation in both morphological and behavioral traits. In this review, we use examples from insects to explore the idea that animals are integrated units where stage-specific morphological and neurological traits develop together to increase individual fitness within their natural environments. We hypothesize that the same mechanisms act to alter both morphological and behavioral traits in response to the environment in which an organism develops. For example, in insects the steroid hormone ecdysone orchestrates the restructuring of the body from larva to adult form during metamorphosis at the same time as it rebuilds the central nervous system. The remodeling of both body form and nervous system structure results in behavioral alterations that match the morphological functions of the emerging adult. We review relevant findings from the fruit fly Drosophila melanogaster, combining insights from different fields like developmental biology, neurobiology and developmental plasticity. Finally, we highlight how insights drawn from D. melanogaster can be used as a model in future efforts to understand how developmental processes modify behavioral responses to environmental change in a stage-specific manner in other animals.
- Drosophilasessile hemocyte clusters are true hematopoietic tissues that regulate larval blood cell differentiationPublication . Sucena, ÉlioVirtually all species of coelomate animals contain blood cells that display a division of labor necessary for homeostasis. This functional partition depends upon the balance between proliferation and differentiation mostly accomplished in the hematopoietic organs. In Drosophila melanogaster, the lymph gland produces plasmatocytes and crystal cells that are not released until pupariation. Yet, throughout larval development, both hemocyte types increase in numbers. Mature plasmatocytes can proliferate but it is not known if crystal cell numbers increase by self-renewal or by de novo differentiation. We show that new crystal cells in third instar larvae originate through a Notch-dependent process of plasmatocyte transdifferentiation. This process occurs in the sessile clusters and is contingent upon the integrity of these structures. The existence of this hematopoietic tissue, relying on structure-dependent signaling events to promote blood homeostasis, creates a new paradigm for addressing outstanding questions in Drosophila hematopoiesis and establishing further parallels with vertebrate systems.
- In Vivo Approaches Reveal a Key Role for DCs in CD4+ T Cell Activation and Parasite Clearance during the Acute Phase of Experimental Blood-Stage MalariaPublication . Borges da Silva, Henrique; Fonseca, Raíssa; Cassado, Alexandra dos Anjos; Machado de Salles, Érika; de Menezes, Maria Nogueira; Langhorne, Jean; Perez, Katia Regina; Cuccovia, Iolanda Midea; Ryffel, Bernhard; Barreto, Vasco M.; Marinho, Cláudio Romero Farias; Boscardin, Silvia Beatriz; Álvarez, José Maria; D’Império-Lima, Maria Regina; Tadokoro, Carlos EduardoDendritic cells (DCs) are phagocytes that are highly specialized for antigen presentation. Heterogeneous populations of macrophages and DCs form a phagocyte network inside the red pulp (RP) of the spleen, which is a major site for the control of blood-borne infections such as malaria. However, the dynamics of splenic DCs during Plasmodium infections are poorly understood, limiting our knowledge regarding their protective role in malaria. Here, we used in vivo experimental approaches that enabled us to deplete or visualize DCs in order to clarify these issues. To elucidate the roles of DCs and marginal zone macrophages in the protection against blood-stage malaria, we infected DTx (diphtheria toxin)-treated C57BL/6.CD11c-DTR mice, as well as C57BL/6 mice treated with low doses of clodronate liposomes (ClLip), with Plasmodium chabaudi AS (Pc) parasites. The first evidence suggesting that DCs could contribute directly to parasite clearance was an early effect of the DTx treatment, but not of the ClLip treatment, in parasitemia control. DCs were also required for CD4+ T cell responses during infection. The phagocytosis of infected red blood cells (iRBCs) by splenic DCs was analyzed by confocal intravital microscopy, as well as by flow cytometry and immunofluorescence, at three distinct phases of Pc malaria: at the first encounter, at pre-crisis concomitant with parasitemia growth and at crisis when the parasitemia decline coincides with spleen closure. In vivo and ex vivo imaging of the spleen revealed that DCs actively phagocytize iRBCs and interact with CD4+ T cells both in T cell-rich areas and in the RP. Subcapsular RP DCs were highly efficient in the recognition and capture of iRBCs during pre-crisis, while complete DC maturation was only achieved during crisis. These findings indicate that, beyond their classical role in antigen presentation, DCs also contribute to the direct elimination of iRBCs during acute Plasmodium infection.
- Mutualism Breakdown by Amplification of Wolbachia GenesPublication . Chrostek, Ewa; Teixeira, LuisMost insect species are associated with vertically transmitted endosymbionts. Because of the mode of transmission, the fitness of these symbionts is dependent on the fitness of the hosts. Therefore, these endosymbionts need to control their proliferation in order to minimize their cost for the host. The genetic bases and mechanisms of this regulation remain largely undetermined. The maternally inherited bacteria of the genus Wolbachia are the most common endosymbionts of insects, providing some of them with fitness benefits. In Drosophila melanogaster, Wolbachia wMelPop is a unique virulent variant that proliferates massively in the hosts and shortens their lifespan. The genetic bases of wMelPop virulence are unknown, and their identification would allow a better understanding of how Wolbachia levels are regulated. Here we show that amplification of a region containing eight Wolbachia genes, called Octomom, is responsible for wMelPop virulence. Using Drosophila lines selected for carrying Wolbachia with different Octomom copy numbers, we demonstrate that the number of Octomom copies determines Wolbachia titers and the strength of the lethal phenotype. Octomom amplification is unstable, and reversion of copy number to one reverts all the phenotypes. Our results provide a link between genotype and phenotype in Wolbachia and identify a genomic region regulating Wolbachia proliferation. We also prove that these bacteria can evolve rapidly. Rapid evolution by changes in gene copy number may be common in endosymbionts with a high number of mobile elements and other repeated regions. Understanding wMelPop pathogenicity and variability also allows researchers to better control and predict the outcome of releasing mosquitoes transinfected with this variant to block human vector-borne diseases. Our results show that transition from a mutualist to a pathogen may occur because of a single genomic change in the endosymbiont. This implies that there must be constant selection on endosymbionts to control their densities.
- Species differential regulation of COX2 can be described by an NFκB-dependent logic AND gatePublication . Nguyen, Lan K; Cavadas, Miguel A S; Kholodenko, Boris N; Frank, Till D; Cheong, AlexCyclooxygenase 2 (COX2), a key regulatory enzyme of the prostaglandin/eicosanoid pathway, is an important target for anti-inflammatory therapy. It is highly induced by pro-inflammatory cytokines in a Nuclear factor kappa B (NFκB)-dependent manner. However, the mechanisms determining the amplitude and dynamics of this important pro-inflammatory event are poorly understood. Furthermore, there is significant difference between human and mouse COX2 expression in response to the inflammatory stimulus tumor necrosis factor alpha (TNFα). Here, we report the presence of a molecular logic AND gate composed of two NFκB response elements (NREs) which controls the expression of human COX2 in a switch-like manner. Combining quantitative kinetic modeling and thermostatistical analysis followed by experimental validation in iterative cycles, we show that the human COX2 expression machinery regulated by NFκB displays features of a logic AND gate. We propose that this provides a digital, noise-filtering mechanism for a tighter control of expression in response to TNFα, such that a threshold level of NFκB activation is required before the promoter becomes active and initiates transcription. This NFκB-regulated AND gate is absent in the mouse COX2 promoter, most likely contributing to its differential graded response in promoter activity and protein expression to TNFα. Our data suggest that the NFκB-regulated AND gate acts as a novel mechanism for controlling the expression of human COX2 to TNFα, and its absence in the mouse COX2 provides the foundation for further studies on understanding species-specific differential gene regulation.
- Social odors conveying dominance and reproductive information induce rapid physiological and neuromolecular changes in a cichlid fishPublication . Simões, José M; Barata, Eduardo N; Harris, Rayna M; O’Connell, Lauren A; Hofmann, Hans A; Oliveira, Rui FSocial plasticity is a pervasive feature of animal behavior. Animals adjust the expression of their social behavior to the daily changes in social life and to transitions between life-history stages, and this ability has an impact in their Darwinian fitness. This behavioral plasticity may be achieved either by rewiring or by biochemically switching nodes of the neural network underlying social behavior in response to perceived social information. Independent of the proximate mechanisms, at the neuromolecular level social plasticity relies on the regulation of gene expression, such that different neurogenomic states emerge in response to different social stimuli and the switches between states are orchestrated by signaling pathways that interface the social environment and the genotype. Here, we test this hypothesis by characterizing the changes in the brain profile of gene expression in response to social odors in the Mozambique Tilapia, Oreochromis mossambicus. This species has a rich repertoire of social behaviors during which both visual and chemical information are conveyed to conspecifics. Specifically, dominant males increase their urination frequency during agonist encounters and during courtship to convey chemical information reflecting their dominance status.
- The importance of iron in pathophysiologic conditionsPublication . Gozzelino, Raffaella; Arosio, PaoloBiological iron is necessary for vital functions and also potentially toxic to the organisms. This dual effect raised the interest of many investigators to study the mechanisms controlling its homeostasis that are altered in many pathologic conditions. Recently the understanding of iron metabolism significantly improved with the discovery of genes responsible for genetic disorders, such as hemochromatosis, the IRE/IRPs machinery and the hepcidin-ferroportin axis, which allowed to elucidate the basis of cellular and systemic iron homeostasis. In addition, these advances disclosed a causal link between deregulation of iron homeostasis, inflammation and oxidative stress, often induced by the iron accumulation that is commonly observed in many pathologic conditions.