Distribution of RTX toxin genes in strains of [Actinobacillus] rossii and [Pasteurella] mairii

Strains of [Actinobacillus] rossii, [Pasteurella] mairii and [Pasteurella] aerogenes can be isolated from abortion in swine. The RTX toxin Pax has previously been found only in those [P.] aerogenes strains isolated from abortion. Nothing is known about RTX toxins in field isolates of the other two species. To gain insight into the distribution of selected RTX toxin genes and their association with abortion, PCR screening for the pax, apxII and apxIII operons on 21 [A.] rossii and seven [P.] mairii isolates was done. Since species can be phenotypically misidentified, the study was backed up by a phylogenetic analysis of all strains based on 16S rRNA, rpoB and infB genes. The pax gene was detected in all [P.] mairii but not in [A.] rossii strains. No apx genes were found in [P.] mairii but different gene combinations for apx were detected in [A.] rossii strains. Most of these strains were positive for apxIII, either alone or in combination with apxII. Whereas pax was found to be associated to strains from abortion no such indication could be found with apx in [A.] rossii strains. Phylogenetically [A.] rossii strains formed a heterogeneous cluster separated from Actinobacillus sensu stricto. [P.] mairii strains clustered with [P.] aerogenes but forming a separate branch. The fact that [P.] aerogenes, [P.] mairii and [A.] rossii can phylogenetically clearly be identified and might contain distinct RTX toxin genes allows their proper diagnosis and will further help to investigate their role as pathogens.

Species-level selection reduces selfishness through competitive exclusion

Adaptation does not necessarily lead to traits which are optimal for the population. This is because selection is often the strongest at the individual or gene level. The evolution of selfishness can lead to a 'tragedy of the commons', where traits such as aggression or social cheating reduce population size and may lead to extinction. This suggests that species-level selection will result whenever species differ in the incentive to be selfish. We explore this idea in a simple model that combines individual-level selection with ecology in two interacting species. Our model is not influenced by kin or trait-group selection. We find that individual selection in combination with competitive exclusion greatly increases the likelihood that selfish species go extinct. A simple example of this would be a vertebrate species that invests heavily into squabbles over breeding sites, which is then excluded by a species that invests more into direct reproduction. A multispecies simulation shows that these extinctions result in communities containing species that are much less selfish. Our results suggest that species-level selection and community dynamics play an important role in regulating the intensity of conflicts in natural populations.

Characterization of the CopR regulon of Lactococcus lactis IL1403

To identify components of the copper homeostatic mechanism of Lactococcus lactis, we employed two-dimensional gel electrophoresis to detect changes in the proteome in response to copper. Three proteins upregulated by copper were identified: glyoxylase I (YaiA), a nitroreductase (YtjD), and lactate oxidase (LctO). The promoter regions of these genes feature cop boxes of consensus TACAnnTGTA, which are the binding site of CopY-type copper-responsive repressors. A genome-wide search for cop boxes revealed 28 such sequence motifs. They were tested by electrophoretic mobility shift assays for the interaction with purified CopR, the CopY-type repressor of L. lactis. Seven of the cop boxes interacted with CopR in a copper-sensitive manner. They were present in the promoter region of five genes, lctO, ytjD, copB, ydiD, and yahC; and two polycistronic operons, yahCD-yaiAB and copRZA. Induction of these genes by copper was confirmed by real-time quantitative PCR. The copRZA operon encodes the CopR repressor of the regulon; a copper chaperone, CopZ; and a putative copper ATPase, CopA. When expressed in Escherichia coli, the copRZA operon conferred copper resistance, suggesting that it functions in copper export from the cytoplasm. Other member genes of the CopR regulon may similarly be involved in copper metabolism.

Income Insecurity and Youth Emancipation: A Theoretical Approach

n this paper, we propose a theoretical model to study the effect of income insecurity of parents and offspring on the child's residential choice. Parents are partially altruistic toward their children and will provide financial help to an independent child when her income is low relative to the parents'. We find that children of more altruistic parents are more likely to become independent. However, first-order stochastic dominance (FOSD) shifts in the distribution of the child's future income (or her parents') have ambiguous effects on the child's residential choice. Parental altruism is the very source of ambiguity in the results. If parents are selfish or the joint income distribution of parents and child places no mass on the region where transfers are provided, a FOSD shift in the distribution of the child's (parents') future income will reduce (raise) the child's current income threshold for independence.

Apx toxins in Pasteurellaceae species from animals

Pasteurellaceae species particularly of porcine origin which are closely related to Actinobacillus pleuropneumoniae were analyzed for the presence of analogues to the major A. pleuropneumoniae RTX toxin genes, apxICABD, apxIICA and apxIIICABD and for their expression. Actinobacillus suis contains both apxICABD(var.suis) and apxIICA(var. suis) operons and was shown to produce ApxI and ApxII toxin. Actinobacillus rossii contained the operons apxIICA(var.rossii) and apxIIICABD(var.rossii). However, only the toxin ApxII and not ApxIII could be detected in cultures of A. rossii. The Apx toxins found in A. suis and A. rossi may play a role in virulence of these pathogens. Actinobacillus lignieresii, which was included since it is phylogenetically very closely related to A. pleuropneumoniae, was found to contain a full apxICABD(var.lign.) operon which however lacks the -35 and -10 boxes in the promoter sequences. As expected from these results, no expression of ApxI was detected in A. lignieresii grown under standard culture conditions. Actinobacillus seminis, Actinobacillus equuli, Pasteurella aerogenes, Pasteurella multocida, Haemophilus parasuis, and also Mannheimia (Pasteurella) haemolytica, which is known to secrete leukotoxin, were all shown to be devoid of any of the apx toxin genes and did not produce ApxI, ApxII or ApxIII toxin proteins. However, proteins of slightly lower molecular mass than ApxI, ApxII and ApxIII which showed limited cross-reactions with monospecific, polyclonal anti-ApxI, anti-ApxII and anti-ApxIII were detected on immunoblot analysis of A. equuli, A. seminis and P. aerogenes. The presence of Apx toxins and proteins that imunologically cross react with Apx toxins in porcine Actinobacillus species other than A. pleuropneumoniae can be expected to interfere with serodiagnosis of porcine pleuropneumonia.

Characterization of PaxA and its operon: a cohemolytic RTX toxin determinant from pathogenic Pasteurella aerogenes

Pasteurella aerogenes is known as a commensal bacterium or as an opportunistic pathogen, as well as a primary pathogen found to be involved in abortion cases of humans, swine, and other mammals. Using broad-range DNA probes for bacterial RTX toxin genes, we cloned and subsequently sequenced a new operon named paxCABD encoding the RTX toxin PaxA in P. aerogenes. The pax operon is organized analogous to the classical RTX operons containing the activator gene paxC upstream of the structural toxin gene paxA, which is followed by the secretion protein genes paxB and paxD. The highest sequence similarity of paxA with known RTX toxin genes is found with apxIIIA (82%). PaxA is structurally similar to ApxIIIA and also shows functional analogy to ApxIIIA, since it shows cohemolytic activity with the sphingomyelinase of Staphylococcus aureus, known as the CAMP effect, but is devoid of direct hemolytic activity. In addition, it shows to some extent immunological cross-reactions with ApxIIIA. P. aerogenes isolated from various specimens showed that the pax operon was present in about one-third of the strains. All of the pax-positive strains were specifically related to swine abortion cases or septicemia of newborn piglets. These strains were also shown to produce the PaxA toxin as determined by the CAMP phenomenon, whereas none of the pax-negative strains did. This indicated that the PaxA toxin is involved in the pathogenic potential of P. aerogenes. The examined P. aerogenes isolates were phylogenetically analyzed by 16S rRNA gene (rrs) sequencing in order to confirm their species. Only a small heterogeneity (<0.5%) was observed between the rrs genes of the strains originating from geographically distant farms and isolated at different times.

Draft Genome Sequence of the Virulent Avibacterium paragallinarum Serotype A Strain JF4211 and Identification of Two Toxins

Avibacterium paragallinarum is an important pathogen of chicken livestock causing infectious coryza. Here, we report the draft genome sequence of the virulent A. paragallinarum serotype A strain JF4211 (2.8 Mbp and G+C content of 41%) and the two toxin operons discovered from the annotation of the genome.

DAT1 polymorphism determines L-DOPA effects on learning about others' prosociality.

Despite that a wealth of evidence links striatal dopamine to individualś reward learning performance in non-social environments, the neurochemical underpinnings of such learning during social interaction are unknown. Here, we show that the administration of 300 mg of the dopamine precursor L-DOPA to 200 healthy male subjects influences learning about a partners' prosocial preferences in a novel social interaction task, which is akin to a repeated trust game. We found learning to be modulated by a well-established genetic marker of striatal dopamine levels, the 40-bp variable number tandem repeats polymorphism of the dopamine transporter (DAT1 polymorphism). In particular, we found that L-DOPA improves learning in 10/10R genoype subjects, who are assumed to have lower endogenous striatal dopamine levels and impairs learning in 9/10R genotype subjects, who are assumed to have higher endogenous dopamine levels. These findings provide first evidence for a critical role of dopamine in learning whether an interaction partner has a prosocial or a selfish personality. The applied pharmacogenetic approach may open doors to new ways of studying psychiatric disorders such as psychosis, which is characterized by distorted perceptions of others' prosocial attitudes.

Diminishing reciprocal fairness by disrupting the right prefrontal cortex.

Humans restrain self-interest with moral and social values. They are the only species known to exhibit reciprocal fairness, which implies the punishment of other individuals' unfair behaviors, even if it hurts the punisher's economic self-interest. Reciprocal fairness has been demonstrated in the Ultimatum Game, where players often reject their bargaining partner's unfair offers. Despite progress in recent years, however, little is known about how the human brain limits the impact of selfish motives and implements fair behavior. Here we show that disruption of the right, but not the left, dorsolateral prefrontal cortex (DLPFC) by low-frequency repetitive transcranial magnetic stimulation substantially reduces subjects' willingness to reject their partners' intentionally unfair offers, which suggests that subjects are less able to resist the economic temptation to accept these offers. Importantly, however, subjects still judge such offers as very unfair, which indicates that the right DLPFC plays a key role in the implementation of fairness-related behaviors.

Generosity is a sign of trustworthiness—the punishment of selfishness is not

Peer-punishment is an important determinant of cooperation in human groups. It has been suggested that, at the proximate level of analysis, punitive preferences can explain why humans incur costs to punish their deviant peers. How punitive preferences could have evolved in humans is still not entirely understood. A possible explanation at the ultimate level of analysis comes from signaling theory. It has been argued that the punishment of defectors can be a type-separating signal of the punisher's cooperative intent. As a result, punishers are selected more often as interaction partners in social exchange and are partly compensated for the costs they incur when punishing defectors. A similar argument has been made with regard to acts of generosity. In a laboratory experiment, we investigate whether the punishment of a selfish division of money in a dictator game is a sign of trustworthiness and whether punishers are more trustworthy interaction partners in a trust game than non-punishers. We distinguish between second-party and third-party punishment and compare punitive acts with acts of generosity as signs of trustworthiness. We find that punishers are not more trustworthy than non-punishers and that punishers are not trusted more than non-punishers, both in the second-party and in the third-party punishment condition. To the contrary, second-party punishers are trusted less than their non-punishing counterparts. However, participants who choose a generous division of money are more trustworthy and are trusted more than participants who choose a selfish division or participants about whom no information is available. Our results suggest that, unlike for punitive acts, the signaling benefits of generosity are to be gained in social exchange.

Monetary Policy Delegation, Contract Costs, and Contract Targets

We reconsider the optimal central banker contract derived in Walsh (1995). We show that if the government's objective function places weight (value) on the cost of the contract, then the optimal inflation contract does not completely neutralize the inflation bias. That is, a fraction of the inflation bias emerges in the resulting inflation rate after the central banker's monetary policy decision. Furthermore, the more concerned the government is about the cost of the contract or the less selfish (more benevolent) is the central banker, the smaller is the share of the inflation bias eliminated by the contract. No matter how concerned the government is about the cost of the contract or how unselfish (benevolent) the central banker is, the contract always reduces the inflationary bias by at least half. Finally, a central banker contract written in terms of output (i.e., incorporating an output target) can completely eradicate the inflationary bias, regardless of concerns about contract costs.

Is Altruism Feasible? Interdependent Preferences Provide the Answer

Is it possible to be altruistic in the face of altruism? With a naive definition of altruism, the answer is no. If an altruistic consumer is defined to be one whose preferences over allocations satisfy an appropriate interdependence condition, then the answer is yes. However, altruism in the face of malice is impossible. One of our findings is that if two consumers are mutually altruistic, exactly one of them should adopt selfish preferences over allocations.

MOLECULAR AND GENOMIC BASED INSIGHTS INTO THE EVOLUTION OF ENTEROCOCCUS FAECIUM FROM COMMENSAL TO HOSPITAL-ADAPTED PATHOGEN

The basis for the recent transition of Enterococcus faecium from a primarily commensal organism to one of the leading causes of hospital-acquired infections in the United States is not yet understood. To address this, the first part of my project assessed isolates from early outbreaks in the USA and South America using sequence analysis, colony hybridizations, and minimal inhibitory concentrations (MICs) which showed clinical isolates possess virulence and antibiotic resistance determinants that are less abundant or lacking in community isolates. I also revealed that the level of ampicillin resistance increased over time in clinical strains. By sequencing the pbp5 gene, I demonstrated an ~5% difference in the pbp5 gene between strains with MICs <4ug/ml and those with MICs >4µg/ml, but no specific sequence changes correlated with increases in MICs within the latter group. A 3-10% nucleotide difference was also seen in three other genes analyzed, which suggested the existence of two distinct subpopulations of E. faecium. This led to the second part of my project analyzing concatenated core gene sequences, SNPs, the 16S rRNA, and phylogenetics of 21 E. faecium genomes confirming two distinct clades; a community-associated (CA) clade and hospital-associated (HA) clade. Molecular clock calculations indicate that these two clades likely diverged ~ 300,000 to > 1 million years ago, long before the modern antibiotic era. Genomic analysis also showed that, in addition to core genomic differences, HA E. faecium harbor specific accessory genetic elements that may confer selection advantages over CA E. faecium. The third part of my project discovered 6 E. faecium genes with the newly identified “WxL” domain. My analyses, using RT-PCR, western blots, patient sera, whole-cell ELISA, and immunogold electron microscopy, indicated that E. faecium WxL genes exist in operons, encode bacterial cell surface localized proteins, that WxL proteins are antigenic in humans, and are more exposed on the surface of clinical isolates versus community isolates (even though they are ubiquitous in both clades). ELISAs and BIAcore analyses also showed that proteins encoded by these operons bind several different host extracellular matrix proteins, as well as to each other, suggesting a novel cell-surface complex. In summary, my studies provide new insights into the evolution of E. faecium by showing that there are two distantly related clades; one being more successful in the hospital setting. My studies also identified operons encoding WxL proteins whose characteristics could also contribute to colonization and virulence within this species.

Cognitive strategies for reducing energy consumption in wireless sensor networks

El consumo energético de las Redes de Sensores Inalámbricas (WSNs por sus siglas en inglés) es un problema histórico que ha sido abordado desde diferentes niveles y visiones, ya que no solo afecta a la propia supervivencia de la red sino que el creciente uso de dispositivos inteligentes y el nuevo paradigma del Internet de las Cosas hace que las WSNs tengan cada vez una mayor influencia en la huella energética. Debido a la tendencia al alza en el uso de estas redes se añade un nuevo problema, la saturación espectral. Las WSNs operan habitualmente en bandas sin licencia como son las bandas Industrial, Científica y Médica (ISM por sus siglas en inglés). Estas bandas se comparten con otro tipo de redes como Wi-Fi o Bluetooth cuyo uso ha crecido exponencialmente en los últimos años. Para abordar este problema aparece el paradigma de la Radio Cognitiva (CR), una tecnología que permite el acceso oportunista al espectro. La introducción de capacidades cognitivas en las WSNs no solo permite optimizar su eficiencia espectral sino que también tiene un impacto positivo en parámetros como la calidad de servicio, la seguridad o el consumo energético. Sin embargo, por otra parte, este nuevo paradigma plantea algunos retos relacionados con el consumo energético. Concretamente, el sensado del espectro, la colaboración entre los nodos (que requiere comunicación adicional) y el cambio en los parámetros de transmisión aumentan el consumo respecto a las WSN clásicas. Teniendo en cuenta que la investigación en el campo del consumo energético ha sido ampliamente abordada puesto que se trata de una de sus principales limitaciones, asumimos que las nuevas estrategias deben surgir de las nuevas capacidades añadidas por las redes cognitivas. Por otro lado, a la hora de diseñar estrategias de optimización para CWSN hay que tener muy presentes las limitaciones de recursos de estas redes en cuanto a memoria, computación y consumo energético de los nodos. En esta tesis doctoral proponemos dos estrategias de reducción de consumo energético en CWSNs basadas en tres pilares fundamentales. El primero son las capacidades cognitivas añadidas a las WSNs que proporcionan la posibilidad de adaptar los parámetros de transmisión en función del espectro disponible. La segunda es la colaboración, como característica intrínseca de las CWSNs. Finalmente, el tercer pilar de este trabajo es teoría de juegos como algoritmo de soporte a la decisión, ampliamente utilizado en WSNs debido a su simplicidad. Como primer aporte de la tesis se presenta un análisis completo de las posibilidades introducidas por la radio cognitiva en materia de reducción de consumo para WSNs. Gracias a las conclusiones extraídas de este análisis, se han planteado las hipótesis de esta tesis relacionadas con la validez de usar capacidades cognitivas como herramienta para la reducción de consumo en CWSNs. Una vez presentada las hipótesis, pasamos a desarrollar las principales contribuciones de la tesis: las dos estrategias diseñadas para reducción de consumo basadas en teoría de juegos y CR. La primera de ellas hace uso de un juego no cooperativo que se juega mediante pares de jugadores. En la segunda estrategia, aunque el juego continúa siendo no cooperativo, se añade el concepto de colaboración. Para cada una de las estrategias se presenta el modelo del juego, el análisis formal de equilibrios y óptimos y la descripción de la estrategia completa donde se incluye la interacción entre nodos. Con el propósito de probar las estrategias mediante simulación e implementación en dispositivos reales hemos desarrollado un marco de pruebas compuesto por un simulador cognitivo y un banco de pruebas formado por nodos cognitivos capaces de comunicarse en tres bandas ISM desarrollados en el B105 Lab. Este marco de pruebas constituye otra de las aportaciones de la tesis que permitirá el avance en la investigación en el área de las CWSNs. Finalmente, se presentan y discuten los resultados derivados de la prueba de las estrategias desarrolladas. La primera estrategia proporciona ahorros de energía mayores al 65% comparados con una WSN sin capacidades cognitivas y alrededor del 25% si la comparamos con una estrategia cognitiva basada en el sensado periódico del espectro para el cambio de canal de acuerdo a un nivel de ruido fijado. Este algoritmo se comporta de forma similar independientemente del nivel de ruido siempre que éste sea espacialmente uniformemente. Esta estrategia, a pesar de su sencillez, nos asegura el comportamiento óptimo en cuanto a consumo energético debido a la utilización de teoría de juegos en la fase de diseño del comportamiento de los nodos. La estrategia colaborativa presenta mejoras respecto a la anterior en términos de protección frente al ruido en escenarios de ruido más complejos donde aporta una mejora del 50% comparada con la estrategia anterior. ABSTRACT Energy consumption in Wireless Sensor Networks (WSNs) is a known historical problem that has been addressed from different areas and on many levels. But this problem should not only be approached from the point of view of their own efficiency for survival. A major portion of communication traffic has migrated to mobile networks and systems. The increased use of smart devices and the introduction of the Internet of Things (IoT) give WSNs a great influence on the carbon footprint. Thus, optimizing the energy consumption of wireless networks could reduce their environmental impact considerably. In recent years, another problem has been added to the equation: spectrum saturation. Wireless Sensor Networks usually operate in unlicensed spectrum bands such as Industrial, Scientific, and Medical (ISM) bands shared with other networks (mainly Wi-Fi and Bluetooth). To address the efficient spectrum utilization problem, Cognitive Radio (CR) has emerged as the key technology that enables opportunistic access to the spectrum. Therefore, the introduction of cognitive capabilities to WSNs allows optimizing their spectral occupation. Cognitive Wireless Sensor Networks (CWSNs) do not only increase the reliability of communications, but they also have a positive impact on parameters such as the Quality of Service (QoS), network security, or energy consumption. These new opportunities introduced by CWSNs unveil a wide field in the energy consumption research area. However, this also implies some challenges. Specifically, the spectrum sensing stage, collaboration among devices (which requires extra communication), and changes in the transmission parameters increase the total energy consumption of the network. When designing CWSN optimization strategies, the fact that WSN nodes are very limited in terms of memory, computational power, or energy consumption has to be considered. Thus, light strategies that require a low computing capacity must be found. Since the field of energy conservation in WSNs has been widely explored, we assume that new strategies could emerge from the new opportunities presented by cognitive networks. In this PhD Thesis, we present two strategies for energy consumption reduction in CWSNs supported by three main pillars. The first pillar is that cognitive capabilities added to the WSN provide the ability to change the transmission parameters according to the spectrum. The second pillar is that the ability to collaborate is a basic characteristic of CWSNs. Finally, the third pillar for this work is the game theory as a decision-making algorithm, which has been widely used in WSNs due to its lightness and simplicity that make it valid to operate in CWSNs. For the development of these strategies, a complete analysis of the possibilities is first carried out by incorporating the cognitive abilities into the network. Once this analysis has been performed, we expose the hypotheses of this thesis related to the use of cognitive capabilities as a useful tool to reduce energy consumption in CWSNs. Once the analyses are exposed, we present the main contribution of this thesis: the two designed strategies for energy consumption reduction based on game theory and cognitive capabilities. The first one is based on a non-cooperative game played between two players in a simple and selfish way. In the second strategy, the concept of collaboration is introduced. Despite the fact that the game used is also a non-cooperative game, the decisions are taken through collaboration. For each strategy, we present the modeled game, the formal analysis of equilibrium and optimum, and the complete strategy describing the interaction between nodes. In order to test the strategies through simulation and implementation in real devices, we have developed a CWSN framework composed by a CWSN simulator based on Castalia and a testbed based on CWSN nodes able to communicate in three different ISM bands. We present and discuss the results derived by the energy optimization strategies. The first strategy brings energy improvement rates of over 65% compared to WSN without cognitive techniques. It also brings energy improvement rates of over 25% compared with sensing strategies for changing channels based on a decision threshold. We have also seen that the algorithm behaves similarly even with significant variations in the level of noise while working in a uniform noise scenario. The collaborative strategy presents improvements respecting the previous strategy in terms of noise protection when the noise scheme is more complex where this strategy shows improvement rates of over 50%.

The RIIβ regulatory subunit of protein kinase A binds to cAMP response element: An alternative cAMP signaling pathway

cAMP, through the activation of cAMP-dependent protein kinase (PKA), is involved in transcriptional regulation. In eukaryotic cells, cAMP is not considered to alter the binding affinity of CREB/ATF to cAMP-responsive element (CRE) but to induce serine phosphorylation and consequent increase in transcriptional activity. In contrast, in prokaryotic cells, cAMP enhances the DNA binding of the catabolite repressor protein to regulate the transcription of several operons. The structural similarity of the cAMP binding sites in catabolite repressor protein and regulatory subunit of PKA type II (RII) suggested the possibility of a similar role for RII in eukaryotic gene regulation. Herein we report that RIIβ subunit of PKA is a transcription factor capable of interacting physically and functionally with a CRE. In contrast to CREB/ATF, the binding of RIIβ to a CRE was enhanced by cAMP, and in addition, RIIβ exhibited transcriptional activity as a Gal4-RIIβ fusion protein. These experiments identify RIIβ as a component of an alternative pathway for regulation of CRE-directed transcription in eukaryotic cells.