Evolutionary rewiring of bacterial regulatory networks

Bacteria have evolved complex regulatory networks that enable integration of multiple intracellular and extracellular signals to coordinate responses to environmental changes. However, our knowledge of how regulatory systems function and evolve is still relatively limited. There is often extensive homology between components of different networks, due to past cycles of gene duplication, divergence, and horizontal gene transfer, raising the possibility of cross-talk or redundancy. Consequently, evolutionary resilience is built into gene networks – homology between regulators can potentially allow rapid rescue of lost regulatory function across distant regions of the genome. In our recent study [Taylor, et al. Science (2015), 347(6225)] we find that mutations that facilitate cross-talk between pathways can contribute to gene network evolution, but that such mutations come with severe pleiotropic costs. Arising from this work are a number of questions surrounding how this phenomenon occurs

Coping with environmental eukaryotes; identification of pseudomonas syringae genes during the interaction with alternative hosts or predators

Understanding the molecular mechanisms underpinning the ecological success of plant pathogens is critical to develop strategies for controlling diseases and protecting crops. Recent observations have shown that plant pathogenic bacteria, particularly Pseudomonas, exist in a range of natural environments away from their natural plant host e.g., water courses, soil, non-host plants. This exposes them to a variety of eukaryotic predators such as nematodes, insects and amoebae present in the environment. Nematodes and amoeba in particular are bacterial predators while insect herbivores may act as indirect predators, ingesting bacteria on plant tissue. We therefore postulated that bacteria are probably under selective pressure to avoid or survive predation and have therefore developed appropriate coping mechanisms. We tested the hypothesis that plant pathogenic Pseudomonas syringae are able to cope with predation pressure and found that three pathovars show weak, but significant resistance or toxicity. To identify the gene systems that contribute to resistance or toxicity we applied a heterologous screening technique, called Rapid Virulence Annotation (RVA), for anti-predation and toxicity mechanisms. Three cosmid libraries for P. syringae pv. aesculi, pv. tomato and pv. phaseolicola, of approximately 2000 cosmids each, were screened in the susceptible/non-toxic bacterium Escherichia coli against nematode, amoebae and an insect. A number of potential conserved and unique genes were identified which included genes encoding haemolysins, biofilm formation, motility and adhesion. These data provide the first multi-pathovar comparative insight to how plant pathogens cope with different predation pressures and infection of an insect gut and provide a foundation for further study into the function of selected genes and their role in ecological success

Parenting behavior and the risk of becoming a victim and a bully/victim : a meta-analysis study

Objective: Being bullied has adverse effects on children's health. Children's family experiences and parenting behavior before entering school help shape their capacity to adapt and cope at school and have an impact on children's peer relationship, hence it is important to identify how parenting styles and parent–child relationship are related to victimization in order to develop intervention programs to prevent or mitigate victimization in childhood and adolescence. Methods: We conducted a systematic review of the published literature on parenting behavior and peer victimization using MEDLINE, PsychINFO, Eric and EMBASE from 1970 through the end of December 2012. We included prospective cohort studies and cross-sectional studies that investigated the association between parenting behavior and peer victimization. Results: Both victims and those who both bully and are victims (bully/victims) were more likely to be exposed to negative parenting behavior including abuse and neglect and maladaptive parenting. The effects were generally small to moderate for victims (Hedge's g range: 0.10–0.31) but moderate for bully/victims (0.13–0.68). Positive parenting behavior including good communication of parents with the child, warm and affectionate relationship, parental involvement and support, and parental supervision were protective against peer victimization. The protective effects were generally small to moderate for both victims (Hedge's g: range: −0.12 to −0.22) and bully/victims (−0.17 to −0.42). Conclusions: Negative parenting behavior is related to a moderate increase of risk for becoming a bully/victim and small to moderate effects on victim status at school. Intervention programs against bullying should extend their focus beyond schools to include families and start before children enter school

Phenazine-1-carboxylic acid production by Pseudomonas fluorescens LBUM636 alters Phytophthora infestans' growth and late blight development

Phytophthora infestans causes late blight of potato, one of the most devastating diseases affecting potato production. Alternative approaches for controlling late blight are being increasingly sought due to increasing environmental concerns over the use of chemical pesticides and the increasing resistance of P. infestans to fungicides. Our research group has isolated a new strain of Pseudomonas fluorescens (LBUM636) of biocontrol interest producing the antibiotic phenazine-1-carboxylic acid (PCA). Wild-type LBUM636 was shown to significantly inhibit the growth of P. infestans in in vitro confrontational assays while its isogenic mutant (phzC-; not producing PCA) only slightly altered the pathogen’s growth. Wild-type LBUM636, but not the phzC- mutant, also completely repressed disease symptom development on tubers. A pot experiment revealed that wild-type LBUM636 can significantly reduce P. infestans populations in the rhizosphere and in the roots of potato plants, as well as reduce in planta disease symptoms due to PCA production. The expression of eight common plant defense-related genes (ChtA, PR-1b, PR-2, PR-5, LOX, PIN2, PAL-2, and ERF3) was quantified in tubers, roots and leaves by RT-qPCR and revealed that the biocontrol observed was not associated with the induction of a plant defense response by LBUM636. Instead, a direct interaction between P. infestans and LBUM636 is required and PCA production appears to be a key factor for LBUM636’s biocontrol ability

Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223

Abstract Background Phytophthora infestans is responsible for late blight, one of the most important potato diseases. Phenazine-1-carboxylic acid (PCA)-producing Pseudomonas fluorescens strain LBUM223 isolated in our laboratory shows biocontrol potential against various plant pathogens. To characterize the effect of LBUM223 on the transcriptome of P. infestans, we conducted an in vitro time-course study. Confrontational assay was performed using P. infestans inoculated alone (control) or with LBUM223, its phzC- isogenic mutant (not producing PCA), or exogenically applied PCA. Destructive sampling was performed at 6, 9 and 12 days and the transcriptome of P. infestans was analysed using RNA-Seq. The expression of a subset of differentially expressed genes was validated by RT-qPCR. Results Both LBUM223 and exogenically applied PCA significantly repressed P. infestans’ growth at all times. Compared to the control treatment, transcriptomic analyses showed that the percentages of all P. infestans’ genes significantly altered by LBUM223 and exogenically applied PCA increased as time progressed, from 50 to 61% and from to 32 to 46%, respectively. When applying an absolute cut-off value of 3 fold change or more for all three harvesting times, 207 genes were found significantly differentially expressed by PCA, either produced by LBUM223 or exogenically applied. Gene ontology analysis revealed that both treatments altered the expression of key functional genes involved in major functions like phosphorylation mechanisms, transmembrane transport and oxidoreduction activities. Interestingly, even though no host plant tissue was present in the in vitro system, PCA also led to the overexpression of several genes encoding effectors. The mutant only slightly repressed P. infestans’ growth and barely altered its transcriptome. Conclusions Our study suggests that PCA is involved in P. infestans’ growth repression and led to important transcriptomic changes by both up- and down-regulating gene expression in P. infestans over time. Different metabolic functions were altered and many effectors were found to be upregulated, suggesting their implication in biocontrol

Long-term induction of defense gene expression in potato by pseudomonas sp. LBUM223 and streptomyces scabies

Streptomyces scabies is a causal agent of common scab of potato, which generates necrotic tuber lesions. We have previously demonstrated that inoculation of potato plants with phenazine-1-carboxylic acid (PCA)- producing Pseudomonas sp. LBUM223 could significantly reduce common scab symptoms. In the present study, we investigated whether LBUM223 or an isogenic phzC- mutant not producing PCA could elicit an induced systemic resistance response in potato. The expression of eight defense-related genes (salicylic acid [SA]-related ChtA, PR-1b, PR-2, and PR-5; and jasmonic acid and ethylene-related LOX, PIN2, PAL-2, and ERF3) was quantified using newly developed TaqMan reverse-transcription quantitative polymerase chain reaction assays in 5- and 10-week-old potted potato plants. Although only wild-type LBUM223 was capable of significantly reducing common scab symptoms, the presence of both LBUM223 and its PCA-deficient mutant were equally able to upregulate the expression of LOX and PR-5. The presence of S. scabies overexpressed all SA-related genes. This indicates that (i) upregulation of potato defense-related genes by LBUM223 is unlikely to contribute to common scab's control and (ii) LBUM223's capacity to produce PCA is not involved in this upregulation. These results suggest that a direct interaction occurring between S. scabies and PCA-producing LBUM223 is more likely involved in controlling common scab development

Involvement in bullying and suicide-related behavior at 11 years : a prospective birth cohort study

Objective To study the prospective link between involvement in bullying (bully, victim, bully/victim), and subsequent suicide ideation and suicidal/self-injurious behavior, in preadolescent children in the United Kingdom. Method A total of 6,043 children in the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort were assessed to ascertain involvement in bullying between 4 and 10 years and suicide related behavior at 11.7 years. Results Peer victimization (victim, bully/victim) was significantly associated with suicide ideation and suicidal/self-injurious behavior after adjusting for confounders. Bully/victims were at heightened risk for suicide ideation (odds ratio [OR]; 95% confidence interval [CI]): child report at 8 years (OR = 2.84; CI = 1.81–4.45); child report at 10 years (OR = 3.20; CI = 2.07–4.95); mother report (OR = 2.71; CI = 1.81–4.05); teacher report (OR = 2.79; CI = 1.62–4.81), as were chronic victims: child report (OR = 3.26; CI = 2.24–4.75); mother report (OR = 2.49; CI = 1.64–3.79); teacher report (OR = 5.99; CI = 2.79–12.88). Similarly, bully/victims were at heightened risk for suicidal/self-injurious behavior: child report at 8 years (OR = 2.67; CI = 1.66–4.29); child report at 10 years (OR = 3.34; CI = 2.17–5.15); mother report (OR = 2.09; CI = CI = 1.36–3.20); teacher report (OR = 2.44, CI = 1.39–4.30); as were chronic victims: child report (OR = 4.10; CI = 2.76–6.08); mother report (OR = 1.91; 1.22–2.99); teacher report (OR = 3.26; CI = 1.38–7.68). Pure bullies had increased risk of suicide ideation according to child report at age 8 years (OR = 3.60; CI = 1.46–8.84), suicidal/self-injurious behavior according to child report at age 8 years (OR = 3.02; CI = 1.14–8.02), and teacher report (OR = 1.84; CI = 1.09–3.10). Conclusions Children involved in bullying, in any role, and especially bully/victims and chronic victims, are at increased risk for suicide ideation and suicidal/self-injurious behavior in preadolescence

Additional file 3: of Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223

List of selected genes validated by qPCR. The expression of 27 targeted genes and 2 references genes was studied using the SYBR green technology, while the expression of 7 targeted genes was studied using the TaqMan probe technology. (XLSX 12 kb