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Author Demongeot, J.; Goles, E.; Morvan, M.; Noual, M.; Sene, S. pdf  doi
openurl 
  Title Attraction Basins as Gauges of Robustness against Boundary Conditions in Biological Complex Systems Type
  Year 2010 Publication Plos One Abbreviated Journal PLoS One  
  Volume 5 Issue 8 Pages 18 pp  
  Keywords  
  Abstract One fundamental concept in the context of biological systems on which researches have flourished in the past decade is that of the apparent robustness of these systems, i.e., their ability to resist to perturbations or constraints induced by external or boundary elements such as electromagnetic fields acting on neural networks, micro-RNAs acting on genetic networks and even hormone flows acting both on neural and genetic networks. Recent studies have shown the importance of addressing the question of the environmental robustness of biological networks such as neural and genetic networks. In some cases, external regulatory elements can be given a relevant formal representation by assimilating them to or modeling them by boundary conditions. This article presents a generic mathematical approach to understand the influence of boundary elements on the dynamics of regulation networks, considering their attraction basins as gauges of their robustness. The application of this method on a real genetic regulation network will point out a mathematical explanation of a biological phenomenon which has only been observed experimentally until now, namely the necessity of the presence of gibberellin for the flower of the plant Arabidopsis thaliana to develop normally.  
  Address [Demongeot, Jacques] Univ Grenoble 1, TIMC IMAG, CNRS, UMR 5525, La Tronche, France, Email: Sylvain.Sene@ibisc.univ-evry.fr  
  Corporate Author Thesis  
  Publisher Public Library Science Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1932-6203 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000280605400002 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 92  
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Author Gaitan-Espitia, J.D.; Arias, M.B.; Lardies, M.A.; Nespolo, R.F. pdf  doi
openurl 
  Title Variation in Thermal Sensitivity and Thermal Tolerances in an Invasive Species across a Climatic Gradient: Lessons from the Land Snail Cornu aspersum Type
  Year 2013 Publication Plos One Abbreviated Journal PLoS One  
  Volume 8 Issue 8 Pages  
  Keywords  
  Abstract The ability of organisms to perform at different temperatures could be described by a continuous nonlinear reaction norm (i.e., thermal performance curve, TPC), in which the phenotypic trait value varies as a function of temperature. Almost any shift in the parameters of this performance curve could highlight the direct effect of temperature on organism fitness, providing a powerful framework for testing thermal adaptation hypotheses. Inter-and intraspecific differences in this performance curve are also reflected in thermal tolerances limits (e. g., critical and lethal limits), influencing the biogeographic patterns of species' distribution. Within this context, here we investigated the intraspecific variation in thermal sensitivities and thermal tolerances in three populations of the invasive snail Cornu aspersum across a geographical gradient, characterized by different climatic conditions. Thus, we examined population differentiation in the TPCs, thermal-coma recovery times, expression of heat-shock proteins and standard metabolic rate (i.e., energetic costs of physiological differentiation). We tested two competing hypotheses regarding thermal adaptation (the “hotter is better” and the generalist-specialist trade-offs). Our results show that the differences in thermal sensitivity among populations of C. aspersum follow a latitudinal pattern, which is likely the result of a combination of thermodynamic constraints (“hotter is better”) and thermal adaptations to their local environments (generalist-specialist trade-offs). This finding is also consistent with some thermal tolerance indices such as the Heat-Shock Protein Response and the recovery time from chill-coma. However, mixed responses in the evaluated traits suggest that thermal adaptation in this species is not complete, as we were not able to detect any differences in neither energetic costs of physiological differentiation among populations, nor in the heat-coma recovery.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1932-6203 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000324465000111 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 313  
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Author Goldstein-Daruech, N.; Cope, E.K.; Zhao, K.Q.; Vukovic, K.; Kofonow, J.M.; Doghramji, L.; Gonzalez, B.; Chiu, A.G.; Kennedy, D.W.; Palmer, J.N.; Leid, J.G.; Kreindler, J.L.; Cohen, N.A. pdf  doi
openurl 
  Title Tobacco Smoke Mediated Induction of Sinonasal Microbial Biofilms Type
  Year 2011 Publication Plos One Abbreviated Journal PLoS One  
  Volume 6 Issue 1 Pages 7 pp  
  Keywords  
  Abstract Cigarette smokers and those exposed to second hand smoke are more susceptible to life threatening infection than nonsmokers. While much is known about the devastating effect tobacco exposure has on the human body, less is known about the effect of tobacco smoke on the commensal and commonly found pathogenic bacteria of the human respiratory tract, or human respiratory tract microbiome. Chronic rhinosinusitis (CRS) is a common medical complaint, affecting 16% of the US population with an estimated aggregated cost of $6 billion annually. Epidemiologic studies demonstrate a correlation between tobacco smoke exposure and rhinosinusitis. Although a common cause of CRS has not been defined, bacterial presence within the nasal and paranasal sinuses is assumed to be contributory. Here we demonstrate that repetitive tobacco smoke exposure induces biofilm formation in a diverse set of bacteria isolated from the sinonasal cavities of patients with CRS. Additionally, bacteria isolated from patients with tobacco smoke exposure demonstrate robust in vitro biofilm formation when challenged with tobacco smoke compared to those isolated from smoke naive patients. Lastly, bacteria from smoke exposed patients can revert to a non-biofilm phenotype when grown in the absence of tobacco smoke. These observations support the hypothesis that tobacco exposure induces sinonasal biofilm formation, thereby contributing to the conversion of a transient and medically treatable infection to a persistent and therapeutically recalcitrant condition.  
  Address [Goldstein-Daruech, Natalia; Zhao, Ke-Qing; Kofonow, Jennifer M.; Doghramji, Laurel; Chiu, Alexander G.; Kennedy, David W.; Palmer, James N.; Cohen, Noam A.] Univ Penn, Dept Otorhinolaryngol Head & Neck Surg, Philadelphia, PA 19104 USA, Email: cohenn@uphs.upenn.edu  
  Corporate Author Thesis  
  Publisher Public Library Science Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1932-6203 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000286511900008 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 117  
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Author Lykidis, A.; Perez-Pantoja, D.; Ledger, T.; Mavromatis, K.; Anderson, I.J.; Ivanova, N.N.; Hooper, S.D.; Lapidus, A.; Lucas, S.; Gonzalez, B.; Kyrpides, N.C. pdf  doi
openurl 
  Title The Complete Multipartite Genome Sequence of Cupriavidus necator JMP134, a Versatile Pollutant Degrader Type
  Year 2010 Publication Plos One Abbreviated Journal PLoS One  
  Volume 5 Issue 3 Pages 13 pp  
  Keywords  
  Abstract Background: Cupriavidus necator JMP134 is a Gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source. Methodology/ Principal Findings: Its genome consists of four replicons (two chromosomes and two plasmids) containing a total of 6631 protein coding genes. Comparative analysis identified 1910 core genes common to the four genomes compared (C. necator JMP134, C. necator H16, C. metallidurans CH34, R. solanacearum GMI1000). Although secondary chromosomes found in the Cupriavidus, Ralstonia, and Burkholderia lineages are all derived from plasmids, analyses of the plasmid partition proteins located on those chromosomes indicate that different plasmids gave rise to the secondary chromosomes in each lineage. The C. necator JMP134 genome contains 300 genes putatively involved in the catabolism of aromatic compounds and encodes most of the central ring-cleavage pathways. This strain also shows additional metabolic capabilities towards alicyclic compounds and the potential for catabolism of almost all proteinogenic amino acids. This remarkable catabolic potential seems to be sustained by a high degree of genetic redundancy, most probably enabling this catabolically versatile bacterium with different levels of metabolic responses and alternative regulation necessary to cope with a challenging environment. From the comparison of Cupriavidus genomes, it is possible to state that a broad metabolic capability is a general trait for Cupriavidus genus, however certain specialization towards a nutritional niche (xenobiotics degradation, chemolithoautotrophy or symbiotic nitrogen fixation) seems to be shaped mostly by the acquisition of “specialized” plasmids. Conclusions/Significance: The availability of the complete genome sequence for C. necator JMP134 provides the groundwork for further elucidation of the mechanisms and regulation of chloroaromatic compound biodegradation.  
  Address [Lykidis, Athanasios; Mavromatis, Kostantinos; Anderson, Iain J.; Ivanova, Natalia N.; Hooper, Sean D.; Lapidus, Alla; Lucas, Susan; Kyrpides, Nikos C.] US DOE, Joint Genome Inst, Walnut Creek, CA USA, Email: alykidis@lbl.gov  
  Corporate Author Thesis  
  Publisher Public Library Science Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1932-6203 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000275894300005 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 86  
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Author Poupin, M.J.; Timmermann, T.; Vega, A.; Zuniga, A.; Gonzalez, B. pdf  doi
openurl 
  Title Effects of the Plant Growth-Promoting Bacterium Burkholderia phytofirmans PsJN throughout the Life Cycle of Arabidopsis thaliana Type
  Year 2013 Publication Plos One Abbreviated Journal PLoS One  
  Volume 8 Issue 7 Pages 15 pp  
  Keywords  
  Abstract Plant growth-promoting rhizobacteria (PGPR) induce positive effects in plants, such as increased growth or reduced stress susceptibility. The mechanisms behind PGPR/plant interaction are poorly understood, as most studies have described short-term responses on plants and only a few studies have analyzed plant molecular responses under PGPR colonization. Here, we studied the effects of the PGPR bacterial model Burkholderia phytofirmans PsJN on the whole life cycle of Arabidopsis thaliana plants. We reported that at different plant developmental points, strain PsJN can be found in the rhizosphere and also colonizing their internal tissues. In early ontogeny, strain PsJN increased several growth parameters and accelerated growth rate of the plants. Also, an Arabidopsis transcriptome analysis revealed that 408 genes showed differential expression in PsJN-inoculated plants; some of these genes are involved in stress response and hormone pathways. Specifically, genes implicated in auxin and gibberellin pathways were induced. Quantitative transcriptional analyses of selected genes in different developmental stages revealed that the beginning of these changes could be evidenced early in development, especially among the down-regulated genes. The inoculation with heat-killed bacteria provoked a more severe transcriptional response in plants, but was not able to induce plant growth-promotion. Later in ontogeny, the growth rates of inoculated plants decreased with respect to the non-inoculated group and, interestingly, the inoculation accelerated the flowering time and the appearance of senescence signs in plants; these modifications correlate with the early up-regulation of flowering control genes. Then, we show that a single inoculation with a PGPR could affect the whole life cycle of a plant, accelerating its growth rate and shortening its vegetative period, both effects relevant for most crops. Thus, these findings provide novel and interesting aspects of these relevant biological interactions.  
  Address [Josefina Poupin, Maria; Timmermann, Tania; Zuniga, Ana; Gonzalez, Bernardo] Univ Adolfo Ibanez, Fac Ingn & Ciencias, Lab Bioingn, Santiago, Chile, Email: mpoupin@uai.cl  
  Corporate Author Thesis  
  Publisher Public Library Science Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1932-6203 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000323110600043 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 306  
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Author Rengifo, F.; Ruz, G.A.; Mascareno, A. pdf  doi
openurl 
  Title Managing the 1920s' Chilean educational crisis: A historical view combined with machine learning Type
  Year 2018 Publication Plos One Abbreviated Journal PLoS One  
  Volume 13 Issue 5 Pages 23 pp  
  Keywords  
  Abstract In the first decades of the 20 th century, political actors diagnosed the incubation of a crisis in the Chilean schooling process. Low rates of enrollment, literacy, and attendance, inefficiency in the use of resources, poverty, and a reduced number of schools were the main factors explaining the crisis. As a response, the Law on Compulsory Primary Education, considering mandatory for children between 6 and 14 years old to attend any school for at least four years, was passed in 1920. Using data from Censuses of the Republic of Chile from 1920 and 1930, reports of the Ministry of Justice, the Ministry of Education, and the Statistical Yearbooks between 1895 and 1930, we apply machine learning techniques (clustering and decision trees) to assess the impact of this law on the Chilean schooling process between 1920 and 1930. We conclude that the law had a positive impact on the schooling indicators in this period. Even though it did not overcome the differences between urban and rural zones, it brought about a general improvement of the schooling process and a more efficient use of resources and infrastructure in both big urban centers and small-urban and rural zones, thereby managing the so-called crisis of the Republic.  
  Address [Rengifo, Francisca; Mascareno, Aldo] Univ Adolfo Ibanez, Sch Govt, Santiago, Chile, Email: gonzalo.ruz@uai.cl  
  Corporate Author Thesis  
  Publisher Public Library Science Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1932-6203 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000433634800033 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 878  
Permanent link to this record
 

 
Author Timmermann, T.; Poupin, M.J.; Vega, A.; Urrutia, C.; Ruz, G.A.; Gonzalez, B. doi  openurl
  Title Gene networks underlying the early regulation of Paraburkholderia phytofirmans PsJN induced systemic resistance in Arabidopsis Type
  Year 2019 Publication Plos One Abbreviated Journal PLoS One  
  Volume 14 Issue 8 Pages 24 pp  
  Keywords  
  Abstract Plant defense responses to biotic stresses are complex biological processes, all governed by sophisticated molecular regulations. Induced systemic resistance (ISR) is one of these defense mechanisms where beneficial bacteria or fungi prime plants to resist pathogens or pest attacks. In ISR, the defense arsenal in plants remains dormant and it is only triggered by an infection, allowing a better allocation of plant resources. Our group recently described that the well-known beneficial bacterium Paraburkholderia phytofirmans PsJN is able to induce Arabidopsis thaliana resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 through ISR, and that ethylene, jasmonate and salicylic acid are involved in this protection. Nevertheless, the molecular networks governing this beneficial interaction remain unknown. To tackle this issue, we analyzed the temporal changes in the transcriptome of PsJN-inoculated plants before and after being infected with Pst DC3000. These data were used to perform a gene network analysis to identify highly connected transcription factors. Before the pathogen challenge, the strain PsJN regulated 405 genes (corresponding to 1.8% of the analyzed genome). PsJN-inoculated plants presented a faster and stronger transcriptional response at 1-hour post infection (hpi) compared with the non-inoculated plants, which presented the highest transcriptional changes at 24 hpi. A principal component analysis showed that PsJN-induced plant responses to the pathogen could be differentiated from those induced by the pathogen itself. Forty-eight transcription factors were regulated by PsJN at 1 hpi, and a system biology analysis revealed a network with four clusters. Within these clusters LHY, WRKY28, MYB31 and RRTF1 are highly connected transcription factors, which could act as hub regulators in this interaction. Concordantly with our previous results, these clusters are related to jasmonate, ethylene, salicylic, acid and ROS pathways. These results indicate that a rapid and specific response of PsJN-inoculated plants to the virulent DC3000 strain could be the pivotal element in the protection mechanism.  
  Address [Timmermann, Tania; Josefina Poupin, Maria; Urrutia, Cristobal; Ruz, Gonzalo A.; Gonzalez, Bernardo] Univ Adolfo Ibanez, Lab Bioingn, Fac Ingn & Ciencias, Santiago, Chile, Email: bernardo.gonzalez@uai.cl  
  Corporate Author Thesis  
  Publisher Public Library Science Place of Publication Editor  
  Language English Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1932-6203 ISBN Medium  
  Area Expedition Conference  
  Notes WOS:000485036900060 Approved  
  Call Number UAI @ eduardo.moreno @ Serial 1054  
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