An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination

Several pathogenic strains of Escherichia coli exploit type III secretion to inject effector proteins into human cells, which then subvert eukaryotic cell biology to the bacterium's advantage. We have exploited bioinformatics and experimental approaches to establish that the effector repertoire in the Sakai strain of enterohemorrhagic E. coli (EHEC) O157:H7 is much larger than previously thought. Homology searches led to the identification of > 60 putative effector genes. Thirteen of these were judged to be likely pseudogenes, whereas 49 were judged to be potentially functional. In total, 39 proteins were confirmed experimentally as effectors: 31 through proteomics and 28 through translocation assays. At the protein level, the EHEC effector sequences fall into > 20 families. The largest family, the NleG family, contains 14 members in the Sakai strain alone. EHEC also harbors functional homologs of effectors from plant pathogens (HopPtoH, HopW, AvrA) and from Shigella (OspD, OspE, OspG), and two additional members of the Map/IpgB family. Genes encoding proven or predicted effectors occur in > 20 exchangeable effector loci scattered throughout the chromosome. Crucially, the majority of functional effector genes are encoded by nine exchangeable effector loci that lie within lambdoid prophages. Thus, type III secretion in E. coli is linked to a vast phage metagenome, acting as a crucible for the evolution of pathogenicity.

Clusters of internally primed transcripts reveal novel long noncoding RNAs

Non- protein- coding RNAs ( ncRNAs) are increasingly being recognized as having important regulatory roles. Although much recent attention has focused on tiny 22- to 25- nucleotide microRNAs, several functional ncRNAs are orders of magnitude larger in size. Examples of such macro ncRNAs include Xist and Air, which in mouse are 18 and 108 kilobases ( Kb), respectively. We surveyed the 102,801 FANTOM3 mouse cDNA clones and found that Air and Xist were present not as single, full- length transcripts but as a cluster of multiple, shorter cDNAs, which were unspliced, had little coding potential, and were most likely primed from internal adenine- rich regions within longer parental transcripts. We therefore conducted a genome- wide search for regional clusters of such cDNAs to find novel macro ncRNA candidates. Sixty- six regions were identified, each of which mapped outside known protein- coding loci and which had a mean length of 92 Kb. We detected several known long ncRNAs within these regions, supporting the basic rationale of our approach. In silico analysis showed that many regions had evidence of imprinting and/ or antisense transcription. These regions were significantly associated with microRNAs and transcripts from the central nervous system. We selected eight novel regions for experimental validation by northern blot and RT- PCR and found that the majority represent previously unrecognized noncoding transcripts that are at least 10 Kb in size and predominantly localized in the nucleus. Taken together, the data not only identify multiple new ncRNAs but also suggest the existence of many more macro ncRNAs like Xist and Air.

The abundance of short proteins in the mammalian proteome

Short proteins play key roles in cell signalling and other processes, but their abundance in the mammalian proteome is unknown. Current catalogues of mammalian proteins exhibit an artefactual discontinuity at a length of 100 aa, so that protein abundance peaks just above this length and falls off sharply below it. To clarify the abundance of short proteins, we identify proteins in the FANTOM collection of mouse cDNAs by analysing synonymous and nonsynonymous substitutions with the computer program CRITICA. This analysis confirms that there is no real discontinuity at length 100. Roughly 10% of mouse proteins are shorter than 100 aa, although the majority of these are variants of proteins longer than 100 aa. We identify many novel short proteins, including a dark matter'' subset containing ones that lack detectable homology to other known proteins. Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway.

AVALIAÇÃO DAS ALTERAÇÕES DENTOESQUELÉTICAS DE PACIENTES COM MÁ OCLUSÃO DE CLASSE II DE ANGLE, TRATADOS COM O APARELHO REGULADOR DE FUNÇÃO DE FRÄNKEL (RF-2).

Esta pesquisa objetivou estudar retrospectivamente por meio de radiografias em norma frontal e modelos de gesso as alterações dentoesqueléticas de pacientes com má oclusão de Classe II, 1ª divisão, divididos em dois grupos: Grupo Tratado, constituído de 28 pacientes, sendo 13 pacientes do sexo masculino e 15 do sexo feminino, tratados com aparelho regulador de função de Fränkel - 2 (RF-2), por um período ativo de 1,5 anos; Grupo Controle: constituído de 28 pacientes, sendo 12 do sexo masculino e 16 do sexo feminino, sem nenhum tipo de tratamento durante o acompanhamento longitudinal de 1,5 anos. A amostra deste estudo consistiu de 112 telerradiografias em norma frontal e 112 pares de modelos de gesso, 56 obtidos ao início (T1) e 56 ao final da observação (T2). Após a análise estatística das mensurações obtidas, concluiu- se que houve como resultado alterações estatisticamente significantes em todas as medidas analisadas e o aparelho RF-2 teve atuação direta nas variáveis: distância intermolares superio res e inferiores (radiografias e modelos),profundidade palatina, largura maxilar e altura facial ântero-inferior.

AVALIAÇÃO CEFALOMÉTRICA DA ESTABILIDADE DO TRATAMENTO COM O REGULADOR DE FUNÇÃO FRÄNKEL-2

O objetivo desta pesquisa consistiu em comparar as alterações dentárias, esqueléticas e tegumentares promovidas pelo aparelho de Fränkel-2 com um grupo controle, além de observar a estabilidade desses efeitos promovidos pelo tratamento, num período médio de 7,11 anos pós-tratamento. A amostra compreendeu um total de 90 telerradiografias em norma lateral, sendo 54 telerradiografias provenientes de 18 pacientes tratados com o RF-2 avaliados em três fases (T1:início de tratamento;T2: final de tratamento e T3: pós-tratamento) e 36 telerradiografias de 18 pacientes-controle, observados em dois tempos. Para comparação entre os grupos tratado e controle foi utilizado o teste t de Student não pareado. Já para a análise dos valores do grupo tratado nos três tempos (T1, T2 e T3) foi utilizada a Análise de Variância (ANOVA) a um critério e o teste de Tukey (p<0,05). As principais alterações proporcionadas pelo aparelho RF-2 observadas a partir da comparação do grupo tratado com o controle envolveram efeitos mandibulares, principalmente a protrusão e aumento do comprimento mandibular associado com uma rotação horária, que resultou em uma maior altura facial total (N-Me) e ântero-inferior (AFAI), além de suave rotação anti-horária do plano palatino (SN.PP). Os incisivos superiores retruíram e o inferior vestibularizou. Houve uma distalização relativa dos molares superiores juntamente com a diminuição do overjet , desta forma a convexidade do perfil facial tegumentar melhorou. No período pós-tratamento (T3) observou-se uma estabilidade sagital de maxila (SNA) e mandíbula (SNB), das variáveis do padrão facial, da inclinação do incisivo superior, do ângulo nasolabial e do overjet . A mandíbula e a maxila continuaram a crescer no sentido antero-posterior, juntamente com as alturas faciais Houve também a extrusão de incisivos e molares. Já o plano oclusal e o ângulo goníaco diminuíram na fase pós-tratamento.(AU)

UMA ANÁLISE DA RELAÇÃO ENTRE VARIÁVEIS MACROECONÔMICAS E O COMPORTAMENTO DAS AÇÕES DE MAIOR LIQUIDEZ DO ÍNDICE IBOVESPA

As ações de maior liquidez do índice IBOVESPA, refletem o comportamento das ações de um modo geral, bem como a relação das variáveis macroeconômicas em seu comportamento e estão entre as mais negociadas no mercado de capitais brasileiro. Desta forma, pode-se entender que há reflexos de fatores que impactam as empresas de maior liquidez que definem o comportamento das variáveis macroeconômicas e que o inverso também é uma verdade, oscilações nos fatores macroeconômicos também afetam as ações de maior liquidez, como IPCA, PIB, SELIC e Taxa de Câmbio. O estudo propõe uma análise da relação existente entre variáveis macroeconômicas e o comportamento das ações de maior liquidez do índice IBOVESPA, corroborando com estudos que buscam entender a influência de fatores macroeconômicos sobre o preço de ações e contribuindo empiricamente com a formação de portfólios de investimento. O trabalho abrangeu o período de 2008 a 2014. Os resultados concluíram que a formação de carteiras, visando a proteção do capital investido, deve conter ativos com correlação negativa em relação às variáveis estudadas, o que torna possível a composição de uma carteira com risco reduzido.

Post-Bretton Woods evidence on PPP under different exchange rate regimes

This article investigates the behaviour of exchange rates across different regimes for a post-Bretton Woods period. The exchange rate regime classification is based on the classification of Frankel et al. (2004) who condensed the 10 categories of exchange rate regimes reported by the International Monetary Fund (IMF) into three categories. Panel unitroot tests and panel cointegration are used to examine the Purchasing Power Parity (PPP) hypothesis. The latter test is used to check for both the weak and strong forms of PPP. The panel unit-root tests show no evidence of PPP and suggest there is no difference in the behaviour of exchange rates across different regimes. However, failure to detect PPP across any of the regimes could be due to structural breaks. This assumption is reinforced by the results of cointegration tests, which suggest that there exists at least a weak form of PPP for the different regimes. The evidence for strong PPP decreases as the exchange rate regime moves away from a flexible exchange rate regime.

Predictors of adolescent sexual intentions and behavior: Attitudes, parenting, and neighborhood risk

The current study was a cross-sectional examination of data collected during an HIV risk reduction intervention in south Florida. The purpose of the study was to explore the relationships between neighborhood stress, parenting, attitudes, and adolescent sexual intentions and behavior. The Theory of Planned Behavior was used as a model to guide variable selection and propose an interaction pathway between predictors and outcomes. Potential predictor variables measured for adolescents ages 13–18 (n=196) included communication about sex, parent-family connectedness, parental presence, parent-adolescent activity participation, attitudes about sex and condom use, neighborhood disorder, and exposure to violence. Outcomes were behavioral intentions and sexual behavior for the previous eight months. Neighborhood data was supplemented with ZIP Code level data from regional sources and included median household income, percentage of minority and Hispanic residents, and number of foreclosures. Statistical tests included t-tests, Pearson's correlations, and hierarchical linear regressions. Results showed that males and older adolescents reported less positive behavioral intentions than females and adolescents younger than 16. Intentions were associated with condom attitudes, sexual attitudes, and parental presence; unprotected sexual behavior was associated with parental presence. The best fit model for intentions included gender, sexual attitudes, condom attitudes, parental presence, and neighborhood disorder. The unsafe sexual behavior model included whether the participant lived with both natural parents in the previous year, and the percent of Hispanic residents in the neighborhood. Study findings indicate that more research on adolescent sexual behavior is warranted, specifically examining the differentials between variables that affect intentions and those that affect behavior. A focus on gender and age differences during intervention development may allow for better targeting and more efficacious interventions. Adding peer and media influences to the framework of attitudes, parenting, and neighborhood may offer more insight into patterns of adolescent sexual behavior risk.

The Politics of Gender Socialization

This manuscript is comprised of three papers that examine the far-reaching and often invisible political outcomes of gender role socialization in the United States. These papers focus primarily on two areas: political confidence amongst girls and women, and the effects of gender on survey measurement and data quality.

Chapter one focuses on political confidence, and the likelihood that women will run for political office. Women continue to be underrepresented at all levels of political leadership, and their lack of political ambition, relative to men, has been identified as a primary cause. In this paper, I explore the relationship between an individual's masculinity and femininity and her development of political ambition. Using original survey data from the 2012 Cooperative Congressional Election Study (CCES), I first empirically demonstrate that gender (masculinity/femininity) and sex (male/female) are unique elements of identity and, moreover, are both independently related to political ambition. I then explore the relevance of gender for the study of candidate emergence, testing whether and how masculinity and femininity might be related to political ambition are supported empirically. While the results suggest that masculinity is positively associated with the development of political ambition, the relationship between femininity and candidate emergence seems to be more complicated and not what prevailing stereotypes might lead us to expect. Moreover, while the relationship between masculinity and political ambition is the same for men and women, the relationship between femininity and political ambition is very different for women than it is for men. This study suggests that gender role socialization is highly related with both men's and women's desire to seek positions of political leadership.

Chapter two continues this exploration of gendered differences in the development of political ambition, this time exploring how social attractiveness and gendered perceptions of political leadership impact the desire to hold political office.Women are persistently underrepresented as candidates for public office and remain underrepresented at all levels of government in the United States. Previous literature suggests that the gendered ambition gap, gender socialization, insufficient recruitment, media scrutiny, family responsibilities, modern campaign strategies, and political opportunity structures all contribute to the gender imbalance in pools of officeholders and candidates. To explain women's reticence to run, scholars have offered explanations addressing structural, institutional, and individual-level factors that deter women from becoming candidates, especially for high positions in the U.S. government. This paper examines a previously unexplored factor: how dating and socialized norms of sexual attraction affect political ambition. This study investigates whether young, single, and heterosexual women's desire for male attention and fear of being perceived as unattractive or "too ambitious" present obstacles to running for office. The results of these experiments suggest that social expectations about gender, attraction and sexuality, and political office-holding may contribute to women's reticence to pursue political leadership. Chapter two is a co-authored work and represents the joint efforts of Laura Lazarus Frankel, Shauna Shames, and Nadia Farjood.

Chapter 3 bridges survey methodology and gender socialization, focusing on how interviewer sex affects survey measurement and data quality. Specifically, this paper examines whether and how matching interviewer and respondent sex affects panel attrition--respondents dropping out of the study after participating in the first wave. While the majority of research on interviewer effects suggests that matching interviewer and respondent characteristics (homophily) yields higher quality data, little work has examined whether this pattern holds true in the area of panel attrition. Using paradata from the General Social Survey (GSS), I explore this question. My analysis reveals that, despite its broader positive effects on data quality, matching interviewer and respondent sex increases likelihood to attrit. Interestingly, this phenomenon only emerges amongst male respondents. However, while assigning female interviewers to male respondents decreases their propensity to attrit, it also increases the likelihood of biased responses on gender related items. These conflicting outcomes represent a tradeoff for scholars and survey researchers, requiring careful consideration of mode, content, and study goals when designing surveys and/or analyzing survey data. The implications of these patterns and areas for further research are discussed.

Together, these papers illustrate two ways that gender norms are related to political outcomes: they contribute to patterns of candidate emergence and affect the measurement of political attitudes and behaviors.

Association Between Results of a Gene Expression Signature Assay and Recurrence-Free Interval in Patients With Stage II Colon Cancer in Cancer and Leukemia Group B 9581 (Alliance)

PURPOSE: Conventional staging methods are inadequate to identify patients with stage II colon cancer (CC) who are at high risk of recurrence after surgery with curative intent. ColDx is a gene expression, microarray-based assay shown to be independently prognostic for recurrence-free interval (RFI) and overall survival in CC. The objective of this study was to further validate ColDx using formalin-fixed, paraffin-embedded specimens collected as part of the Alliance phase III trial, C9581.

PATIENTS AND METHODS: C9581 evaluated edrecolomab versus observation in patients with stage II CC and reported no survival benefit. Under an initial case-cohort sampling design, a randomly selected subcohort (RS) comprised 514 patients from 901 eligible patients with available tissue. Forty-nine additional patients with recurrence events were included in the analysis. Final analysis comprised 393 patients: 360 RS (58 events) and 33 non-RS events. Risk status was determined for each patient by ColDx. The Self-Prentice method was used to test the association between the resulting ColDx risk score and RFI adjusting for standard prognostic variables.

RESULTS: Fifty-five percent of patients (216 of 393) were classified as high risk. After adjustment for prognostic variables that included mismatch repair (MMR) deficiency, ColDx high-risk patients exhibited significantly worse RFI (multivariable hazard ratio, 2.13; 95% CI, 1.3 to 3.5; P < .01). Age and MMR status were marginally significant. RFI at 5 years for patients classified as high risk was 82% (95% CI, 79% to 85%), compared with 91% (95% CI, 89% to 93%) for patients classified as low risk.

CONCLUSION: ColDx is associated with RFI in the C9581 subsample in the presence of other prognostic factors, including MMR deficiency. ColDx could be incorporated with the traditional clinical markers of risk to refine patient prognosis.

Use of Galleria mellonella as a model organism to study Legionella pneumophila infection.

Legionella pneumophila, the causative agent of a severe pneumonia named Legionnaires' disease, is an important human pathogen that infects and replicates within alveolar macrophages. Its virulence depends on the Dot/Icm type IV secretion system (T4SS), which is essential to establish a replication permissive vacuole known as the Legionella containing vacuole (LCV). L. pneumophila infection can be modeled in mice however most mouse strains are not permissive, leading to the search for novel infection models. We have recently shown that the larvae of the wax moth Galleria mellonella are suitable for investigation of L. pneumophila infection. G. mellonella is increasingly used as an infection model for human pathogens and a good correlation exists between virulence of several bacterial species in the insect and in mammalian models. A key component of the larvae's immune defenses are hemocytes, professional phagocytes, which take up and destroy invaders. L. pneumophila is able to infect, form a LCV and replicate within these cells. Here we demonstrate protocols for analyzing L. pneumophila virulence in the G. mellonella model, including how to grow infectious L. pneumophila, pretreat the larvae with inhibitors, infect the larvae and how to extract infected cells for quantification and immunofluorescence microscopy. We also describe how to quantify bacterial replication and fitness in competition assays. These approaches allow for the rapid screening of mutants to determine factors important in L. pneumophila virulence, describing a new tool to aid our understanding of this complex pathogen.

EspZ of enteropathogenic and enterohemorrhagic Escherichia coli regulates type III secretion system protein translocation

UNLABELLED: Translocation of effector proteins via a type III secretion system (T3SS) is a widespread infection strategy among Gram-negative bacterial pathogens. Each pathogen translocates a particular set of effectors that subvert cell signaling in a way that suits its particular infection cycle. However, as effector unbalance might lead to cytotoxicity, the pathogens must employ mechanisms that regulate the intracellular effector concentration. We present evidence that the effector EspZ controls T3SS effector translocation from enteropathogenic (EPEC) and enterohemorrhagic (EHEC) Escherichia coli. Consistently, an EPEC espZ mutant is highly cytotoxic. Following ectopic expression, we found that EspZ inhibited the formation of actin pedestals as it blocked the translocation of Tir, as well as other effectors, including Map and EspF. Moreover, during infection EspZ inhibited effector translocation following superinfection. Importantly, while EspZ of EHEC O157:H7 had a universal "translocation stop" activity, EspZ of EPEC inhibited effector translocation from typical EPEC strains but not from EHEC O157:H7 or its progenitor, atypical EPEC O55:H7. We found that the N and C termini of EspZ, which contains two transmembrane domains, face the cytosolic leaflet of the plasma membrane at the site of bacterial attachment, while the extracellular loop of EspZ is responsible for its strain-specific activity. These results show that EPEC and EHEC acquired a sophisticated mechanism to regulate the effector translocation.

IMPORTANCE: Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) are important diarrheal pathogens responsible for significant morbidity and mortality in developing countries and the developed world, respectively. The virulence strategy of EPEC and EHEC revolves around a conserved type III secretion system (T3SS), which translocates bacterial proteins known as effectors directly into host cells. Previous studies have shown that when cells are infected in two waves with EPEC, the first wave inhibits effector translocation by the second wave in a T3SS-dependent manner, although the factor involved was not known. Importantly, we identified EspZ as the effector responsible for blocking protein translocation following a secondary EPEC infection. Interestingly, we found that while EspZ of EHEC can block protein translocation from both EPEC and EHEC strains, EPEC EspZ cannot block translocation from EHEC. These studies show that EPEC and EHEC employ a novel infection strategy to regulate T3SS translocation.

Legionella pneumophila secretes a mitochondrial carrier protein during infection

The Mitochondrial Carrier Family (MCF) is a signature group of integral membrane proteins that transport metabolites across the mitochondrial inner membrane in eukaryotes. MCF proteins are characterized by six transmembrane segments that assemble to form a highly-selective channel for metabolite transport. We discovered a novel MCF member, termed Legionellanucleotide carrier Protein (LncP), encoded in the genome of Legionella pneumophila, the causative agent of Legionnaire's disease. LncP was secreted via the bacterial Dot/Icm type IV secretion system into macrophages and assembled in the mitochondrial inner membrane. In a yeast cellular system, LncP induced a dominant-negative phenotype that was rescued by deleting an endogenous ATP carrier. Substrate transport studies on purified LncP reconstituted in liposomes revealed that it catalyzes unidirectional transport and exchange of ATP transport across membranes, thereby supporting a role for LncP as an ATP transporter. A hidden Markov model revealed further MCF proteins in the intracellular pathogens, Legionella longbeachae and Neorickettsia sennetsu, thereby challenging the notion that MCF proteins exist exclusively in eukaryotic organisms.

The enteropathogenic Escherichia coli effector NleH inhibits apoptosis induced by Clostridium difficile toxin B

Clostridium difficile is a leading cause of nosocomial infections, causing a spectrum of diseases ranging from diarrhoea to pseudomembranous colitis triggered by a range of virulence factors including C. difficile toxins A (TcdA) and B (TcdB). TcdA and TcdB are monoglucosyltransferases that irreversibly glycosylate small Rho GTPases, inhibiting their ability to interact with their effectors, guanine nucleotide exchange factors, and membrane partners, leading to disruption of downstream signalling pathways and cell death. In addition, TcdB targets the mitochondria, inducing the intrinsic apoptotic pathway resulting in TcdB-mediated apoptosis. Modulation of apoptosis is a common strategy used by infectious agents. Recently, we have shown that the enteropathogenic Escherichia coli (EPEC) type III secretion system effector NleH has a broad-range anti-apoptotic activity. In this study we examined the effects of NleH on cells challenged with TcdB. During infection with wild-type EPEC, NleH inhibited TcdB-induced apoptosis at both low and high toxin concentrations. Transfected nleH1 alone was sufficient to block TcdB-induced cell rounding, nuclear condensation, mitochondrial swelling and lysis, and activation of caspase-3. These results show that NleH acts via a global anti-apoptotic pathway.

NleH effectors interact with Bax inhibitor-1 to block apoptosis during enteropathogenic Escherichia coli infection

The human pathogens enteropathogenic (EPEC) and enterohemorrhagic Escherichia coli and the related mouse pathogen Citrobacter rodentium subvert a variety of host cell signaling pathways via their plethora of type III secreted effectors, including triggering of an early apoptotic response. EPEC-infected cells do not develop late apoptotic symptoms, however. In this study we demonstrate that the NleH family effectors, homologs of the Shigella effector kinase OspG, blocks apoptosis. During EPEC infection, NleH effectors inhibit elevation of cytosolic Ca(2+) concentrations, nuclear condensation, caspase-3 activation, and membrane blebbing and promote cell survival. NleH1 alone is sufficient to prevent procaspase-3 cleavage induced by the proapoptotic compounds staurosporine, brefeldin A, and tunicamycin. Using C. rodentium, we found that NleH inhibits procaspase-3 cleavage at the bacterial attachment sites in vivo. A yeast two-hybrid screen identified the endoplasmic reticulum six-transmembrane protein Bax inhibitor-1 (BI-1) as an NleH-interacting partner. We mapped the NleH-binding site to the N-terminal 40 amino acids of BI-1. Knockdown of BI-1 resulted in the loss of NleH's antiapoptotic activity. These results indicate that NleH effectors are inhibitors of apoptosis that may act through BI-1 to carry out their cytoprotective function.