Is methanogenesis related solely to methanogenic archaea?

https://doi.org/10.15157/publication-0

E-õppe kasutamispraktikad Tartu Ülikoolis sotsiaalteaduskonna näitel

The purpose of current research is to study how the students from Faculty of Social Sciences of Tartu University participate in e-Learning, their attitude to it and if the proportion of e- Learning is sufficient or not. Five main research questions are posed: - How the students assess e-Learning? - Which are the main obstructing factors for students to use e-Learning? - Is the proportion of e-Learning sufficient in the opinion of the students? - How the students assess the results of e-Learning compared with the results of traditional learning? - Which are the main motivators to participate in e-Learning? From theoretical points of view, I used the authors who had researched the using practices of e-Learning, the opportunities to research e-Learning and the positive and negative factors which influence the participation in e-Learning. The selection was made from random choice of students from Tartu University Faculty of Social Sciences who answered the poll at the web environment e-formular.com. The selection is not very representative but that is pilot study only. The poll consisted of 12 questions, including both multiple-choice questions and questions with free answers. 111 students answered to poll, including both stationary students and adult learners. The poll was opened to answering for two weeks from the end of March till the beginning of April. All filled questionnaires were accepted. The answers to research questions: - The students assess e-Learning rather positive way of learning because e-Learning enables them to study in suitable time and at convenient place chosen by themselves. The students also like the fact that the learning materials, tests and tasks are all available from the one web environment at the same time. - The fact that there is no contact with lecturer and co-students is considered as the biggest obstruction to participate in e-Learning. Not having contact makes learning more difficult and there is no discussion between students to understand the learning material better. The students are quite used with traditional learning and auditorial lectures and such attitude does not inspire to participate in e-Learning - Regarding the sufficiency of e-Learning proportion, there is no very firm stand according to answers. The opinions that proportion is "sufficient", "not sufficient" and "there is difficult to assess the sufficiency of proportion" were divided almost equally. - The learning results are basically the same than in traditional learning. The answers showed that the place and the way of learning did not play important role in learning results. There is possible to achieve positive results in web learning the same way as in traditional learning. - The most significant motivating factor is convenience and the opportunity to choose the place for learning. The fact that learning materials and tasks are collected into one web environment is also important - necessary material can be found more easily and learning is more convenient. Saving the time is also important factor because all necessary knowledgments are available from one web environment instead of sitting in lecture lasting for several hours. According to the results of current research, e-Learning is well welcomed among the students of Faculty of Sciences and the questionnaries showed expected results.http://tartu.ester.ee/record=b2450806~S1*es

Ettevõtete vaheline koostöö Jõgeva maakonna ettevõtete näitel

http://www.ester.ee/record=b4481935*es

Sügava ja raske puudega laste ja noorte mitteformaalsete hooldajate marginaliseerumine

http://tartu.ester.ee/record=b2651694~S1*es

Identification of ColR binding consensus and prediction of regulon of ColRS two-component system

<p>Abstract</p> <p>Background</p> <p>Conserved two-component system ColRS of <it>Pseudomonas </it>genus has been implicated in several unrelated phenotypes. For instance, deficiency of <it>P. putida </it>ColRS system results in lowered phenol tolerance, hindrance of transposition of Tn<it>4652 </it>and lysis of a subpopulation of glucose-grown bacteria. In order to discover molecular mechanisms behind these phenotypes, we focused here on identification of downstream components of ColRS signal transduction pathway.</p> <p>Results</p> <p>First, highly similar ColR binding sites were mapped upstream of outer membrane protein-encoding <it>oprQ </it>and a putative methyltransferase-encoding PP0903. These two ColR binding sequences were used as an input in computational genome-wide screening for new potential ColR recognition boxes upstream of different genes in <it>P. putida</it>. Biological relevance of a set of <it>in silico </it>predicted ColR-binding sites was analysed <it>in vivo </it>by studying the effect of ColR on transcription from promoters carrying these sites. This analysis disclosed seven novel genes of which six were positively and one negatively regulated by ColR. Interestingly, all promoters tested responded more significantly to the over-expression than to the absence of ColR suggesting that either ColR is limiting or ColS-activating signal is low under the conditions applied. The binding sites of ColR in the promoters analysed were validated by gel mobility shift and/or DNase I footprinting assays. ColR binding consensus was defined according to seven ColR binding motifs mapped by DNase I protection assay and this consensus was used to predict minimal regulon of ColRS system.</p> <p>Conclusion</p> <p>Combined usage of experimental and computational approach enabled us to define the binding consensus for response regulator ColR and to discover several new ColR-regulated genes. For instance, genes of outer membrane lipid A 3-O-deacylase PagL and cytoplasmic membrane diacylglycerol kinase DgkA are the members of ColR regulon. Furthermore, over 40 genes were predicted to be putatively controlled by ColRS two-component system in <it>P. putida</it>. It is notable that many of ColR-regulated genes encode membrane-related products thus confirming the previously proposed role of ColRS system in regulation of membrane functionality.</p

The impact of ColRS two-component system and TtgABC efflux pump on phenol tolerance of Pseudomonas putida becomes evident only in growing bacteria

<p>Abstract</p> <p>Background</p> <p>We have recently found that <it>Pseudomonas putida </it>deficient in ColRS two-component system is sensitive to phenol and displays a serious defect on solid glucose medium where subpopulation of bacteria lyses. The latter phenotype is significantly enhanced by the presence of phenol in growth medium. Here, we focused on identification of factors affecting phenol tolerance of the <it>colR</it>-deficient <it>P. putida</it>.</p> <p>Results</p> <p>By using transposon mutagenesis approach we identified a set of phenol-tolerant derivatives of <it>colR</it>-deficient strain. Surprisingly, half of independent phenol tolerant clones possessed miniTn5 insertion in the <it>ttgABC </it>operon. However, though inactivation of TtgABC efflux pump significantly enhanced phenol tolerance, it did not affect phenol-enhanced autolysis of the <it>colR </it>mutant on glucose medium indicating that phenol- and glucose-caused stresses experienced by the <it>colR</it>-deficient <it>P. putida </it>are not coupled. Inactivation of TtgABC pump significantly increased the phenol tolerance of the wild-type <it>P. putida </it>as well. Comparison of phenol tolerance of growing <it>versus </it>starving bacteria revealed that both ColRS and TtgABC systems affect phenol tolerance only under growth conditions and not under starvation. Flow cytometry analysis showed that phenol strongly inhibited cell division and to some extent also caused cell membrane permeabilization to propidium iodide. Single cell analysis of populations of the <it>ttgC- </it>and <it>colRttgC-</it>deficient strains revealed that their membrane permeabilization by phenol resembles that of the wild-type and the <it>colR </it>mutant, respectively. However, cell division of <it>P. putida </it>with inactivated TtgABC pump seemed to be less sensitive to phenol than that of the parental strain. At the same time, cell division appeared to be more inhibited in the <it>colR</it>-mutant strain than in the wild-type <it>P. putida</it>.</p> <p>Conclusions</p> <p>ColRS signal system and TtgABC efflux pump are involved in the phenol tolerance of <it>P. putida</it>. However, as they affect phenol tolerance of growing bacteria only, this indicates that they participate in the regulation of processes which are active during the growth and/or cell division. Single cell analysis data indicated that the cell division step of cell cycle is particularly sensitive to the toxic effect of phenol and its inhibition can be considered as an adaptive response under conditions of phenol stress.</p

Quorum sensing in Pseudomonas savastanoi pv. savastanoi and Erwinia toletana: role in virulence and interspecies interactions in the olive knot

The olive-knot disease (Olea europea L.) is caused by the bacterium Pseudomonas savastanoi pv. savastanoi (PSV). PSV in the olive-knot undergoes interspecies interactions with the harmless endophyte Erwina toletana (ET); PSV and ET co-localize and form a stable community resulting in a more aggressive disease. PSV and ET produce the same type of the N-acylhomoserine lactone (AHL) quorum sensing (QS) signal and they share AHLs in planta. In this work we have further studied the AHL QS systems of PSV and ET in order to determine possible molecular mechanism(s) involved in this bacterial inter-species interaction/cooperation. The AHL QS regulons of PSV and ET were determined allowing the identification of several QS-regulated genes. Surprisingly, the PSV QS regulon consisted of only a few loci whereas in ET many putative metabolic genes were regulated by QS among which several involved in carbohydrate metabolism. One of these loci was the aldolase-encoding gene garL, which resulted to be essential for both co-localization of PSV and ET cells inside olive knots as well as knot development. This study further highlighted that pathogens can cooperate with commensal members of the plant microbiome. SIGNIFICANCE OF THIS STUDY: This is a report on studies of the quorum sensing (QS) systems of olive knot pathogen Pseudomonas savastanoi pv. savastanoi and olive-knot cooperator Erwinia toletana. These two bacterial species form a stable community in the olive knot, share QS signals and cooperate resulting in a more aggressive disease. In this work we further studied the QS systems by determining their regulons as well studying QS-regulated genes which might play a role in this cooperation. This represents a unique in vivo interspecies bacterial virulence model and highlights the importance of bacterial interspecies interaction in disease