Structural studies of the bacterial Type II secretion system

The type II secretion system is a multiprotein machine that extends from the inner membrane to the outer membrane in Gram-negative bacteria; it transports folded proteins from the periplasm to the extracellular space. The type II secretion system comprises 12 core proteins arranged in 4 main parts: a cytoplasmic secretion ATPase, an inner membrane platform with domains that extend into the periplasm, a periplasmic pseudopilus, and an outer membrane pore formed by the secretin complex. Different species present different sets of accessory proteins. GspB, found in the plant pathogen Dickeya dadantii, reaches from the inner membrane to the periplasm anchoring and stabilizing the secretin. GspS is a lipoprotein pilotin found in both D. dadantii and the human pathogen Escherichia coli IHE3034 and it is involved in the correct localization of the secretin in the outer membrane. The correct localization of the secretin pore is of utmost importance for a fully functional system. The first part of this study explores the architecture of the outer membrane secretin complex of D. dadantii in association with GspB, and the secretin complex of E. coli IHE3034 in association with GspS, using negative stain TEM and cryo-EM. The second part of the work characterizes the interaction between the periplasmic domains of the inner membrane proteins GspL and GspM of E. coli IHE3034. Both possess a ferredoxin-like domain in the periplasmic belt followed by an alpha-helix domain that extends through the inner membrane and then connects to an N-terminal cytoplasmic domain. These proteins are the links between the substrate sensing 6 periplasmic region and the ATPase in the cytoplasm, therefore are key in the activation of the system. I propose a binding model between the ferredoxin-like domains of GspL and GspM based on NMR studies and computational modelling

Social norms of cooperation in small-scale societies

Indirect reciprocity, besides providing a convenient framework to address the evolution of moral systems, offers a simple and plausible explanation for the prevalence of cooperation among unrelated individuals. By helping someone, an individual may increase her/his reputation, which may change the pre-disposition of others to help her/him in the future. This, however, depends on what is reckoned as a good or a bad action, i.e., on the adopted social norm responsible for raising or damaging a reputation. In particular, it remains an open question which social norms are able to foster cooperation in small-scale societies, while enduring the wide plethora of stochastic affects inherent to finite populations. Here we address this problem by studying the stochastic dynamics of cooperation under distinct social norms, showing that the leading norms capable of promoting cooperation depend on the community size. However, only a single norm systematically leads to the highest cooperative standards in small communities. That simple norm dictates that only whoever cooperates with good individuals, and defects against bad ones, deserves a good reputation, a pattern that proves robust to errors, mutations and variations in the intensity of selection.This research was supported by Fundacao para a Ciencia e Tecnologia (FCT) through grants SFRH/BD/94736/2013, PTDC/EEI-SII/5081/2014, PTDC/MAT/STA/3358/2014 and by multi-annual funding of CBMA and INESC-ID (under the projects UID/BIA/04050/2013 and UID/CEC/50021/2013 provided by FCT). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Identification of a novel zinc metalloprotease through a global analysis of clostridium difficile extracellular proteins

Clostridium difficile is a major cause of infectious diarrhea worldwide. Although the cell surface proteins are recognized to be important in clostridial pathogenesis, biological functions of only a few are known. Also, apart from the toxins, proteins exported by C. difficile into the extracellular milieu have been poorly studied. In order to identify novel extracellular factors of C. difficile, we analyzed bacterial culture supernatants prepared from clinical isolates, 630 and R20291, using liquid chromatography-tandem mass spectrometry. The majority of the proteins identified were non-canonical extracellular proteins. These could be largely classified into proteins associated to the cell wall (including CWPs and extracellular hydrolases), transporters and flagellar proteins. Seven unknown hypothetical proteins were also identified. One of these proteins, CD630_28300, shared sequence similarity with the anthrax lethal factor, a known zinc metallopeptidase. We demonstrated that CD630_28300 (named Zmp1) binds zinc and is able to cleave fibronectin and fibrinogen in vitro in a zinc-dependent manner. Using site-directed mutagenesis, we identified residues important in zinc binding and enzymatic activity. Furthermore, we demonstrated that Zmp1 destabilizes the fibronectin network produced by human fibroblasts. Thus, by analyzing the exoproteome of C. difficile, we identified a novel extracellular metalloprotease that may be important in key steps of clostridial pathogenesis

Psychological interventions delivered as a single component intervention for children and adolescents with overweight or obesity aged 6 to 17 years

Objectives This is a protocol for a Cochrane Review (intervention). The objectives are as follows: To assess the effects of psychological interventions delivered as a single component intervention on the management of overweight or obesity in children and adolescents aged 6 to 17 years

The Origin of Malarial Parasites in Orangutans

Background Recent findings of Plasmodium in African apes have changed our perspectives on the evolution of malarial parasites in hominids. However, phylogenetic analyses of primate malarias are still missing information from Southeast Asian apes. In this study, we report molecular data for a malaria parasite lineage found in orangutans. Methodology/Principal Findings We screened twenty-four blood samples from Pongo pygmaeus (Kalimantan, Indonesia) for Plasmodium parasites by PCR. For all the malaria positive orangutan samples, parasite mitochondrial genomes (mtDNA) and two antigens: merozoite surface protein 1 42 kDa (MSP-142) and circumsporozoite protein gene (CSP) were amplified, cloned, and sequenced. Fifteen orangutans tested positive and yielded 5 distinct mitochondrial haplotypes not previously found. The haplotypes detected exhibited low genetic divergence among them, indicating that they belong to one species. We report phylogenetic analyses using mitochondrial genomes, MSP-142 and CSP. We found that the orangutan malaria parasite lineage was part of a monophyletic group that includes all the known non-human primate malaria parasites found in Southeast Asia; specifically, it shares a recent common ancestor with P. inui (a macaque parasite) and P. hylobati (a gibbon parasite) suggesting that this lineage originated as a result of a host switch. The genetic diversity of MSP-142 in orangutans seems to be under negative selection. This result is similar to previous findings in non-human primate malarias closely related to P. vivax. As has been previously observed in the other Plasmodium species found in non-human primates, the CSP shows high polymorphism in the number of repeats. However, it has clearly distinctive motifs from those previously found in other malarial parasites. Conclusion The evidence available from Asian apes indicates that these parasites originated independently from those found in Africa, likely as the result of host switches from other non-human primates

Co-evolutionary dynamics of collective action with signaling for a quorum

Collective signaling for a quorum is found in a wide range of organisms that face collective action problems whose successful solution requires the participation of some quorum of the individuals present. These range from humans, to social insects, to bacteria. The mechanisms involved, the quorum required, and the size of the group may vary. Here we address the general question of the evolution of collective signaling at a high level of abstraction. We investigate the evolutionary dynamics of a population engaging in a signaling N-person game theoretic model. Parameter settings allow for loners and cheaters, and for costly or costless signals. We find a rich dynamics, showing how natural selection, operating on a population of individuals endowed with the simplest strategies, is able to evolve a costly signaling system that allows individuals to respond appropriately to different states of Nature. Signaling robustly promotes cooperative collective action, in particular when coordinated action is most needed and difficult to achieve. Two different signaling systems may emerge depending on Nature's most prevalent states.Funding: This research was supported by FEDER through POFC - COMPETE, FCT-Portugal through grants SFRH/BD/86465/2012, PTDC/MAT/122897/2010, EXPL/EEI-SII/2556/2013, and by multi-annual funding of CMAF-UL, CBMA-UM and INESC-ID (under the projects PEst-OE/BIA/UI4050/2014 and UID/CEC/50021/2013) provided by FCT-Portugal, and by Fundacao Calouste Gulbenkian through the "Stimulus to Research" program for young researchers. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Cooperative dynamics in the penetration of a group of intruders in a granular medium

An object moving in a fluid experiences a drag force that depends on its velocity, shape and the properties of the medium. From this simplest case to the motion of a flock of birds or a school of fish, the drag forces and the hydrodynamic interactions determine the full dynamics of the system. Similar drag forces appear when a single projectile impacts and moves through a granular medium, and this case is well studied in the literature. On the other hand, the case in which a group of intruders impact a granular material has never been considered. Here, we study the simultaneous penetration of several intruders in a very low-density granular medium. We find that the intruders move through it in a collective way, following a cooperative dynamics, whose complexity resembles flocking phenomena in living systems or the movement of reptiles in sand, wherein changes in drag are exploited to efficiently move or propel

Signal-Regulated Pre-mRNA Occupancy by the General Splicing Factor U2AF

Alternative splicing of transcripts in a signal-dependent manner has emerged as an important concept to ensure appropriate expression of splice variants under different conditions. Binding of the general splicing factor U2AF to splice sites preceding alternatively spliced exons has been suggested to be an important step for splice site recognition. For splicing to proceed, U2AF has to be replaced by other factors. We show here that U2AF interacts with the signal-dependent splice regulator Sam68 and that forced expression of Sam68 results in enhanced binding of the U2AF65 subunit to an alternatively spliced pre-mRNA sequence in vivo. Conversely, the rapid signal-induced and phosphorylation-dependent interference with Sam68 binding to RNA was accompanied by reduced pre-mRNA occupancy of U2AF in vivo. Our data suggest that Sam68 can affect splice site occupancy by U2AF in signal-dependent splicing. We propose that the induced release of U2AF from pre-mRNA provides a regulatory step to control alternative splicing