Molecular analysis of a novel gene cluster encoding an insect toxin in plant-associated strains of Pseudomonas fluorescens

Pseudomonas fluorescens CHA0 and the related strain Pf-5 are well-characterized representatives of rhizosphere bacteria that have the capacity to protect crop plants from fungal root diseases, mainly by releasing a variety of exoproducts that are toxic to plant pathogenic fungi. Here, we report that the two plant-beneficial pseudomonads also exhibit potent insecticidal activity. Anti-insect activity is linked to a novel genomic locus encoding a large protein toxin termed Fit (for P. fluorescensinsecticidal toxin) that is related to the insect toxin Mcf (Makes caterpillars floppy) of the entomopathogen Photorhabdus luminescens, a mutualist of insect-invading nematodes. When injected into the haemocoel, even low doses of P. fluorescens CHA0 or Pf-5 killed larvae of the tobacco hornworm Manduca sexta and the greater wax moth Galleria mellonella. In contrast, mutants of CHA0 or Pf-5 with deletions in the Fit toxin gene were significantly less virulent to the larvae. When expressed from an inducible promoter in a non-toxic Escherichia coli host, the Fit toxin gene was sufficient to render the bacterium toxic to both insect hosts. Our findings establish the Fit gene products of P. fluorescens CHA0 and Pf-5 as potent insect toxins that define previously unappreciated anti-insect properties of these plant-colonizing bacteria

Cluster-based active learning for compact image classification

In this paper, we consider active sampling to label pixels grouped with hierarchical clustering. The objective of the method is to match the data relationships discovered by the clustering algorithm with the user's desired class semantics. The first is represented as a complete tree to be pruned and the second is iteratively provided by the user. The active learning algorithm proposed searches the pruning of the tree that best matches the labels of the sampled points. By choosing the part of the tree to sample from according to current pruning's uncertainty, sampling is focused on most uncertain clusters. This way, large clusters for which the class membership is already fixed are no longer queried and sampling is focused on division of clusters showing mixed labels. The model is tested on a VHR image in a multiclass classification setting. The method clearly outperforms random sampling in a transductive setting, but cannot generalize to unseen data, since it aims at optimizing the classification of a given cluster structure.

La actividad de los medios tradicionales en las redes Google Plus y Linkedin

L'era 2.0 ha arribat als nostres dies i amb això, les xarxes socials ja formen part de la vida diària de molts habitants del planeta. Cada dia, milions de persones es connecten i interactuen a través d'elles amb la finalitat d'entretenir-se i informar-se. Tot això ha fet que molts mitjans de comunicació tradicionals hagin hagut de renovar-se per oferir als usuaris un servei que anys enrere ni es plantejaven i que en alguns casos els ha agafat desprevinguts. Per això, el present Treball Final de Carrera analitza l'activitat dels mitjans El País, El Mundo, La Vanguardia i El Periódico de Catalunya a les xarxes socials Google+ i LinkedIn. La popularitat, la interactivitat i la influència seran factors determinants per veure quin és el mitjà que realitza un millor ús d'aquestes xarxes socials, minoritàries, que guanyen terreny en el dia a dia.

Estudi de la plataforma Google App Engine utilitzant Django

L'objectiu principal d'aquest treball es estudiar la plataforma Google App Engine en la seva versió en Phyton. Per a estudiar i provar la plataforma, s'ha desenvolupat una aplicació web de programari lliure que permet la publicació de blogs de viatges. Aquesta aplicació està desenvolupada sobre Django i s'integra amb altres serveis de Google com l'autenticació amb els seus comptes Google Maps o Picasa Web Albums.

In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae

Background: Current advances in genomics, proteomics and other areas of molecular biology make the identification and reconstruction of novel pathways an emerging area of great interest. One such class of pathways is involved in the biogenesis of Iron-Sulfur Clusters (ISC). Results: Our goal is the development of a new approach based on the use and combination of mathematical, theoretical and computational methods to identify the topology of a target network. In this approach, mathematical models play a central role for the evaluation of the alternative network structures that arise from literature data-mining, phylogenetic profiling, structural methods, and human curation. As a test case, we reconstruct the topology of the reaction and regulatory network for the mitochondrial ISC biogenesis pathway in S. cerevisiae. Predictions regarding how proteins act in ISC biogenesis are validated by comparison with published experimental results. For example, the predicted role of Arh1 and Yah1 and some of the interactions we predict for Grx5 both matches experimental evidence. A putative role for frataxin in directly regulating mitochondrial iron import is discarded from our analysis, which agrees with also published experimental results. Additionally, we propose a number of experiments for testing other predictions and further improve the identification of the network structure. Conclusion: We propose and apply an iterative in silico procedure for predictive reconstruction of the network topology of metabolic pathways. The procedure combines structural bioinformatics tools and mathematical modeling techniques that allow the reconstruction of biochemical networks. Using the Iron Sulfur cluster biogenesis in S. cerevisiae as a test case we indicate how this procedure can be used to analyze and validate the network model against experimental results. Critical evaluation of the obtained results through this procedure allows devising new wet lab experiments to confirm its predictions or provide alternative explanations for further improving the models.

Coscheduling techniques and monitoring tools for non-dedicated cluster computing

Our efforts are directed towards the understanding of the coscheduling mechanism in a NOW system when a parallel job is executed jointly with local workloads, balancing parallel performance against the local interactive response. Explicit and implicit coscheduling techniques in a PVM-Linux NOW (or cluster) have been implemented. Furthermore, dynamic coscheduling remains an open question when parallel jobs are executed in a non-dedicated Cluster. A basis model for dynamic coscheduling in Cluster systems is presented in this paper. Also, one dynamic coscheduling algorithm for this model is proposed. The applicability of this algorithm has been proved and its performance analyzed by simulation. Finally, a new tool (named Monito) for monitoring the different queues of messages in such an environments is presented. The main aim of implementing this facility is to provide a mean of capturing the bottlenecks and overheads of the communication system in a PVM-Linux cluster.

Zim17/Tim15 links mitochondrial iron–sulfur cluster biosynthesis to nuclear genome stability

Genomic instability is related to a wide-range of human diseases. Here, we show that mitochondrial iron–sulfur cluster biosynthesis is important for the maintenance of nuclear genome stability in Saccharomyces cerevisiae. Cells lacking the mitochondrial chaperone Zim17 (Tim15/Hep1), a component of the iron–sulfur biosynthesis machinery, have limited respiration activity, mimic the metabolic response to iron starvation and suffer a dramatic increase in nuclear genome recombination. Increased oxidative damage or deficient DNA repair do not account for the observed genomic hyperrecombination. Impaired cell-cycle progression and genetic interactions of ZIM17 with components of the RFC-like complex involved in mitotic checkpoints indicate that replicative stress causes hyperrecombination in zim17Δ mutants. Furthermore, nuclear accumulation of pre-ribosomal particles in zim17Δ mutants reinforces the importance of iron–sulfur clusters in normal ribosome biosynthesis. We propose that compromised ribosome biosynthesis and cell-cycle progression are interconnected, together contributing to replicative stress and nuclear genome instability in zim17Δ mutants.

Acute schistosomiasis: a risk underestimated by travelers and a diagnosis frequently missed by general practitioners-a cluster analysis of 42 travelers.

BACKGROUND: In 2011, a patient was admitted to our hospital with acute schistosomiasis after having returned from Madagascar and having bathed at the Lily waterfalls. On the basis of this patient's indication, infection was suspected in 41 other subjects. This study investigated (1) the knowledge of the travelers about the risks of schistosomiasis and their related behavior to evaluate the appropriateness of prevention messages and (2) the diagnostic workup of symptomatic travelers by general practitioners to evaluate medical care of travelers with a history of freshwater exposure in tropical areas. METHODS: A questionnaire was sent to the 42 travelers with potential exposure to schistosomiasis. It focused on pre-travel knowledge of the disease, bathing conditions, clinical presentation, first suspected diagnosis, and treatment. RESULTS: Of the 42 questionnaires, 40 (95%) were returned, among which 37 travelers (92%) reported an exposure to freshwater, and 18 (45%) were aware of the risk of schistosomiasis. Among these latter subjects, 16 (89%) still reported an exposure to freshwater. Serology was positive in 28 (78%) of 36 exposed subjects at least 3 months after exposure. Of the 28 infected travelers, 23 (82%) exhibited symptoms and 16 (70%) consulted their general practitioner before the information about the outbreak had spread, but none of these patients had a serology for schistosomiasis done during the first consultation. CONCLUSIONS: The usual prevention message of avoiding freshwater contact when traveling in tropical regions had no impact on the behavior of these travelers, who still went swimming at the Lily waterfalls. This prevention message should, therefore, be either modified or abandoned. The clinical presentation of acute schistosomiasis is often misleading. General practitioners should at least request an eosinophil count, when confronted with a returning traveler with fever. If eosinophilia is detected, it should prompt the search for a parasitic disease.

Evolution and cellular function of monothiol glutaredoxins: involvement in iron-sulphur cluster assembly

A number of bacterial species, mostly proteobacteria, possess monothiol glutaredoxins homologous to the Saccharomyces cerevisiae mitochondrial protein Grx5, which is involved in iron–sulphur cluster synthesis. Phylogenetic profiling is used to predict that bacterial monothiol glutaredoxins also participate in the iron–sulphur cluster (ISC) assembly machinery, because their phylogenetic profiles are similar to the profiles of the bacterial homologues of yeast ISC proteins. High evolutionary cooccurrence is observed between the Grx5 homologues and the homologues of the Yah1 ferredoxin, the scaffold proteins Isa1 and Isa2, the frataxin protein Yfh1 and the Nfu1 protein. This suggests that a specific functional interaction exists between these ISC machinery proteins. Physical interaction analyses using low-definition protein docking predict the formation of strong and specific complexes between Grx5 and several components of the yeast ISC machinery. Two-hybrid analysis has confirmed the in vivo interaction between Grx5 and Isa1. Sequence comparison techniques and cladistics indicate that the other two monothiol glutaredoxins of S. cerevisiae, Grx3 and Grx4, have evolved from the fusion of a thioredoxin gene with a monothiol glutaredoxin gene early in the eukaryotic lineage, leading to differential functional specialization. While bacteria do not contain these chimaeric glutaredoxins, in many eukaryotic species Grx5 and Grx3/4-type monothiol glutaredoxins coexist in the cell.

Subtypes of adolescents with substance use disorders and psychiatric comorbidity using cluster and discriminant analysis of MMPI-A profiles

The main aim of this study was to replicate and extend previous results on subtypes of adolescents with substance use disorders (SUD), according to their Minnesota Multiphasic Personality Inventory for adolescents (MMPI-A) profiles. Sixty patients with SUD and psychiatric comorbidity (41.7% male, mean age = 15.9 years old) completed the MMPI-A, the Teen Addiction Severity Index (T-ASI), the Child Behaviour Checklist (CBCL), and were interviewed in order to determine DSMIV diagnoses and level of substance use. Mean MMPI-A personality profile showed moderate peaks in Psychopathic Deviate, Depression and Hysteria scales. Hierarchical cluster analysis revealed four profiles (acting-out, 35% of the sample; disorganized-conflictive, 15%; normative-impulsive, 15%; and deceptive-concealed, 35%). External correlates were found between cluster 1, CBCL externalizing symptoms at a clinical level and conduct disorders, and between cluster 2 and mixed CBCL internalized/externalized symptoms at a clinical level. Discriminant analysis showed that Depression, Psychopathic Deviate and Psychasthenia MMPI-A scales correctly classified 90% of the patients into the clusters obtained.

Competitive Analysis of the Northwest Russian Transport Logistics Cluster – Finnish Perspective

Tutkimus tarkastelee Luoteis-Venäjän liikennelogistiikkaklusteria. Tarkoitus on selvittää klusterin nykyinen rakenne ja kilpailukyky sekä klusterin tarjoamat liiketoimintamahdollisuudet suomalaisille logistiikkayrityksille. Työssä käsitellään neljää perusliikennemuotoa: rautatie-, maantie-, meri- ja sisävesi-, sekä ilmaliikennettä. Tutkimuksen aineisto on kerätty tutkimusta varten laadituista kyselyistä, haastatteluista sekä aiemmin julkaistusta materiaalista. Venäjä on suunnitellut kehittävänsä voimakkaasti liikenneinfrastruktuuria, mm. julkaisemalla protektionistisen liikennestrategiasuunnitelman. Ongelmana ovat olleet toteutukset, jotka ovat jääneet yleensä puutteellisiksi. Tällä hetkellä todellista kilpailukykyä löytyy ainoastaan rautatieliikenteestä, muut kolme liikennemuotoa omaavat potentiaalisen kilpailukyvyn. Venäjällä on mahdollisuus hyötyä laajasta pinta-alastaan Aasian ja Euroopan liikenteen yhdistäjänä. Yksi konkreettisimmista esimerkeistä on Trans Siperian rautatie, joka kaipaisi vielä lisäkehitystä. Suomi on toiminut Venäjän liikenteessä arvotavaran kauttakulkumaana, vuonna 2003 noin 30–40 % Venäjän tuonnin arvosta kulki Suomen kautta. Venäjälle tullaan tuomaan arvotavaraa vielä useita vuosia, mutta reittien osalta kilpailu on tiukentunut. Suomalaisten yritysten liiketoimintamahdollisuuksiin esitetään kaksi mallia: kauttakulkuliikenteen lisäarvologistiset (VAL) operaatiot Suomessa tai etabloituminen Venäjän logistisiin ketjuihin. Suomalaisten olisi syytä parantaa yhteistyötään yritysten ja yliopistojen ym. koulutuslaitosten välillä. Myös yhteistyökumppaneiden hakeminen esimerkiksi Ruotsista voisi tuoda merkittäviä etuja. Suomalaista osaamista voitaisiin hyödyntää parhaiten etabloitumalla Venäjän markkinoille, esimerkiksi keskittymällä Venäjän logististen ketjujen johtamiseen. Myös VAL palveluiden johtamiseen Venäjällä olisi erittäin hyvä tilaisuus, koska Venäjän oma tietotaito logistiikassa ei ole vielä kehittynyt kansainväliselle tasolle, mutta kustannustaso on alhaisempi kuin Suomessa.