Electron driven reactions in complexes embedded in superfluid helium droplets

A thesis submitted to the University of Innsbruck for the doctor degree in Natural Sciences, Physics and New University of Lisbon for the doctor degree in Physics, Atomic and Molecular Physics

The role of ribonuclease R in bacterial adaptation to cold shock

RESUMO:Os microrganismos reagem à súbita descida de temperatura através de uma resposta adaptativa específica que assegura a sua sobrevivência em condições desfavoráveis. Esta adaptação inclui alterações na composição da membrana, na maquinaria de tradução e transcrição. A resposta ao choque térmico pelo frio induz uma repressão da transcrição. No entanto, a descida de temperatura induz a produção de um grupo de proteínas específicas que ajudam a ajustar/re-ajustar o metabolismo celular às novas condições ambientais. Em E. coli o processo de adaptação demora apenas quatro horas, no qual um grupo de proteínas específicas são induzidas. Depois desde período recomeça lentamente a produção de proteínas.A ribonuclease R, uma das proteínas induzidas durante o choque térmico pelo frio, é uma das principais ribonucleases em E. coli envolvidas na degradação do RNA. É uma exoribonuclease que degrada RNA de cadeia dupla, possui funções importantes na maturação e “turnover” do RNA, libertação de ribossomas e controlo de qualidade de proteínas e RNAs. O nível celular desta enzima aumenta até dez vezes após exposição ao frio e estabiliza em células na fase estacionária. A capacidade de degradar RNA de dupla cadeia é importante a baixas temperaturas quando as estruturas de RNA estão mais estáveis. No entanto, este mecanismo é desconhecido. Embora a resposta específica ao “cold shock” tenha sido descoberta há mais de duas décadas e o número de proteínas envolvidas sugerirem que esta adaptação é rápida e simples, continuamos longe de compreender este processo. No nosso trabalho pretendemos descobrir proteínas que interactuem com a RNase R em condições ambientais diferentes através do método “TAP-tag” e espectrometria de massa. A informação obtida pode ser utilizada para deduzir algumas das novas funções da RNase R durante a adaptação bacteriana ao frio e durante a fase estacionária. Mais importante ainda, RNase R poderá ser recrutada para um complexo de proteínas de elevado peso molecular durante o “cold-shock”.------------ABSTRACT:Microorganisms react to the rapid temperature downshift with a specific adaptative response that ensures their survival in unfavorable conditions. Adaptation includes changes in membrane composition, in translation and transcription machinery. Cold shock response leads to overall repression of translation. However, temperature downshift induces production of a set of specific proteins that help to tune cell metabolism and readjust it to the new environmental conditions. For Escherichia coli the adaptation process takes only about four hours with a relatively small set of specifically induced proteins involved. After this time, protein production resumes, although at a slower rate. One of the cold inducible proteins is RNase R, one of the main E. coli ribonucleases involved in RNA degradation. RNase R is an exoribonuclease that digest double stranded RNA, serves important functions in RNA maturation and turnover, release of stalled ribosomes by trans-translation, and RNA and protein quality control. The level of this enzyme increases about ten-fold after cold induction, and it is also stabilised in cells growing in stationary phase. The RNase R ability to digest structured RNA is important at low temperatures where RNA structures are stabilized but the exact role of this mechanism remains unclear. Although specific bacterial cold shock response was discovered over two decades ago and the number of proteins involved suggests that this adaptation is fast and simple, we are still far from understanding this process. In our work we aimed to discover the proteins interacting with RNase R in different environmental conditions using TAP tag method and mass spectrometry analysis. The information obtained can be used to deduce some of the new functions of RNase R during adaptation of bacteria to cold and in stationary growth phase. Most importantly RNase R can be recruited into a high molecular mass complex of protein in cold shock.

Cold Urticaria and Infectious Mononucleosis in Children

Physical urticaria includes a heterogeneous group of disorders characterized by the development of urticarial lesions and/or angioedema after exposure to certain physical stimuli. The authors present the case of a child with severe acquired cold urticaria secondary to infectious mononucleosis. Avoidance of exposure to cold was recommended; prophylactic treatment with ketotifen and cetirizine was begun and a self-administered epinephrine kit was prescribed. The results of ice cube test and symptoms significantly improved. Physical urticaria, which involves complex pathogenesis, clinical course and therapy, may be potentially life threatening. Evaluation and diagnosis are especially important in children. To our knowledge this is the first description of persistent severe cold-induced urticaria associated with infectious mononucleosis in a child.

Significance of Biogenic Amines in Cold-Smoked Fish and Their Relation to Microbiological Characteristics of Products Available in Portuguese Retail Markets

Studies on microbial characterization of cold-smoked salmon and salmon trout during cold storage were performed on samples available in the Portuguese market. Samples were also classified microbiologically according to guidelines for ready-to-eat (RTE) products. Further investigations on sample variability and microbial abilities to produce tyramine and histamine were also performed. The coefficient of variation for viable counts of different groups of microorganisms of samples collected at retail market point was high in the first 2 wk of storage, mainly in the Enterobacteriaceae group and aerobic plate count (APC), suggesting that microbiological characteristics of samples were different in numbers, even within the same batch from the same producer. This variation seemed to be decreased when storage and temperature were controlled under lab conditions. The numbers of Enterobacteriaceae were influenced by storage temperature, as indicated by low microbial numbers in samples from controlled refrigeration. Lactic acid bacteria (LAB) and Enterobacteriaceae were predominant in commercial products, a significant percentage of which were tyramine and less histamine producers. These results might be influenced by (1) the technological processes in the early stages of production, (2) contamination during the smoking process, and (3) conditions and temperature fluctuations during cold storage at retail market point of sale.

Insights into the role of almond CBF transcription factors in the environmental control of cold acclimation and dormancy break

Dissertation presented to obtain the Ph.D degree in Biology

Social-media monitoring for cold-start recommendations

Generating personalized movie recommendations to users is a problem that most commonly relies on user-movie ratings. These ratings are generally used either to understand the user preferences or to recommend movies that users with similar rating patterns have rated highly. However, movie recommenders are often subject to the Cold-Start problem: new movies have not been rated by anyone, so, they will not be recommended to anyone; likewise, the preferences of new users who have not rated any movie cannot be learned. In parallel, Social-Media platforms, such as Twitter, collect great amounts of user feedback on movies, as these are very popular nowadays. This thesis proposes to explore feedback shared on Twitter to predict the popularity of new movies and show how it can be used to tackle the Cold-Start problem. It also proposes, at a finer grain, to explore the reputation of directors and actors on IMDb to tackle the Cold-Start problem. To assess these aspects, a Reputation-enhanced Recommendation Algorithm is implemented and evaluated on a crawled IMDb dataset with previous user ratings of old movies,together with Twitter data crawled from January 2014 to March 2014, to recommend 60 movies affected by the Cold-Start problem. Twitter revealed to be a strong reputation predictor, and the Reputation-enhanced Recommendation Algorithm improved over several baseline methods. Additionally, the algorithm also proved to be useful when recommending movies in an extreme Cold-Start scenario, where both new movies and users are affected by the Cold-Start problem.

Rifampicin fails to eradicate mature biofilm formed by methicillin-resistant Staphylococcus aureus

INTRODUCTION: Antimicrobial activity on biofilms depends on their molecular size, positive charges, permeability coefficient, and bactericidal activity. Vancomycin is the primary choice for methicillin-resistant Staphylococcus aureus (MRSA) infection treatment; rifampicin has interesting antibiofilm properties, but its effectivity remains poorly defined. METHODS: Rifampicin activity alone and in combination with vancomycin against biofilm-forming MRSA was investigated, using a twofold serial broth microtiter method, biofilm challenge, and bacterial count recovery. RESULTS: Minimal inhibitory concentration (MIC) and minimal bactericidal concentration for vancomycin and rifampicin ranged from 0.5 to 1mg/l and 0.008 to 4mg/l, and from 1 to 4mg/l and 0.06 to 32mg/l, respectively. Mature biofilms were submitted to rifampicin and vancomycin exposure, and minimum biofilm eradication concentration ranged from 64 to 32,000 folds and from 32 to 512 folds higher than those for planktonic cells, respectively. Vancomycin (15mg/l) in combination with rifampicin at 6 dilutions higher each isolate MIC did not reach in vitro biofilm eradication but showed biofilm inhibitory capacity (1.43 and 0.56log10 CFU/ml reduction for weak and strong biofilm producers, respectively; p<0.05). CONCLUSIONS: In our setting, rifampicin alone failed to effectively kill biofilm-forming MRSA, demonstrating stronger inability to eradicate mature biofilm compared with vancomycin.

Influence of glucose concentration on the structure and quantity of biofilms formed by Candida parapsilosis

Candida parapsilosis is nowadays an emerging opportunistic pathogen and its increasing incidence is part related to the capacity to produce biofilm. In addition, one of the most important C. parapsilosis pathogenic risk factors includes the organisms\textquoteright selective growth capabilities in hyper alimentation solutions. Thus, in this study, we investigated the role of glucose in C. parapsilosis biofilm modulation, by studying biofilm formation, matrix composition and structure. Moreover, the expression of biofilm-related genes (BCR1, FKS1 and OLE1) were analyzed in the presence of different glucose percentages. The results demonstrated the importance of glucose in the modulation of C. parapsilosis biofilm. The concentration of glucose had direct implications on the C. parapsilosis transition of yeast cells to pseudohyphae. Additionally, it was demonstrated that biofilm related genes BCR1, FKS1 and OLE1 are involved in biofilm modulation by glucose. The mechanism by which glucose enhances biofilm formation is not fully understood, however with this study we were able to demonstrate that C. parapsilosis respond to stress conditions caused by elevated levels of glucose by up-regulating genes related to biofilm formation (BCR1, FKS1 and OLE1).

Physiological stress responses in the warm-water fish matrinxã (Brycon amazonicus ) subjected to a sudden cold shock

The present work evaluated several aspects of the generalized stress response [endocrine (cortisol), metabolic (glucose), hematologic (hematocrit and hemoglobin) and cellular (HSP70)] in the Amazonian warm-water fish matrinxã (Brycon amazonicus ) subjected to an acute cold shock. This species farming has been done in South America, and growth and feed conversion rates have been interesting. However, in subtropical areas of Brazil, where the water temperature can rapidly change, high rates of matrinxã mortality have been associated with abrupt decrease in the water temperature. Thus, we subjected matrinxã to a sudden cold shock by transferring the fish directly to tanks in which the water temperature was 10ºC below the initial conditions (cold shock from 28ºC to 18ºC). After 1h the fish were returned to the original tanks (28ºC). The handling associated with tank transfer was also imposed on control groups (not exposed to cold shock). While exposure to cold shock did not alter the measured physiological conditions within 1h, fish returned to the ambient condition (water at 28º C) significantly increased plasma cortisol and glucose levels. Exposure to cold shock and return to the warm water did not affect HSP70 levels. The increased plasma cortisol and glucose levels after returning the fish to warm water suggest that matrinxã requires cortisol and glucose for adaptation to increased temperature.

Escherichia coli and Enterococcus faecalis are able to incorporate and enhance a pre-formed Gardnerella vaginalis biofilm

Gardnerella vaginalis is the most frequent microorganism found in bacterial vaginosis (BV), while Escherichia coli and Enterococcus faecalis are amongst the most frequent pathogens found in urinary tract infections (UTIs). This study aimed to evaluate possible interactions between UTIs pathogens and G. vaginalis using an in vitro dual-species biofilm model. Our results showed that dual-species biofilms reached significantly higher bacterial concentration than mono-species biofilms. Moreover, visualization of dual-populations species in the biofilms, using the epifluorescence microscopy, revealed that all of the urogenital pathogens co-existed with G. vaginalis. In conclusion, our work demonstrates that uropathogens can incorporate into mature BV biofilms.

Engineering a commercial cold-adapted xylanase for improved low pH stability

Dissertação de mestrado em Genética Molecular

Compositional analysis of biofilms formed by Staphylococcus aureus isolated from food sources

The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fmicb. 2016.00390

Application of data mining for assessment of material properties : creep behavior of high-temperature steels

Magdeburg, Univ., Fak. für Maschinenbau, Diss., 2009

Notes on a collection of cold-blooded vertebrates from Ontario / by S. E. Meek and H. W. Clark.

v.3:no.7(1902)

Notes on a collection of cold-blooded vertebrates from the Olympic Mountains, by S. E. Meek.

v.1:no.12(1899)