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Search Results: 1 - 10 of 435 matches for " Gorazd Avgu tin "
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Inability of Prevotella bryantii to Form a Functional Shine-Dalgarno Interaction Reflects Unique Evolution of Ribosome Binding Sites in Bacteroidetes
Toma? Accetto, Gorazd Avgutin
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0022914
Abstract: The Shine-Dalgarno (SD) sequence is a key element directing the translation to initiate at the authentic start codons and also enabling translation initiation to proceed in 5′ untranslated mRNA regions (5′-UTRs) containing moderately strong secondary structures. Bioinformatic analysis of almost forty genomes from the major bacterial phylum Bacteroidetes revealed, however, a general absence of SD sequence, drop in GC content and consequently reduced tendency to form secondary structures in 5′-UTRs. The experiments using the Prevotella bryantii TC1-1 expression system were in agreement with these findings: neither addition nor omission of SD sequence in the unstructured 5′-UTR affected the level of the reporter protein, non-specific nuclease NucB. Further, NucB level in P. bryantii TC1-1, contrary to hMGFP level in Escherichia coli, was five times lower when SD sequence formed part of the secondary structure with a folding energy -5,2 kcal/mol. Also, the extended SD sequences did not affect protein levels as in E. coli. It seems therefore that a functional SD interaction does not take place during the translation initiation in P. bryanttii TC1-1 and possibly other members of phylum Bacteroidetes although the anti SD sequence is present in 16S rRNA genes of their genomes. We thus propose that in the absence of the SD sequence interaction, the selection of genuine start codons in Bacteroidetes is accomplished by binding of ribosomal protein S1 to unstructured 5′-UTR as opposed to coding region which is inaccessible due to mRNA secondary structure. Additionally, we found that sequence logos of region preceding the start codons may be used as taxonomical markers. Depending on whether complete sequence logo or only part of it, such as information content and base proportion at specific positions, is used, bacterial genera or families and in some cases even bacterial phyla can be distinguished.
Prebavna mikrobiota kot dejavnik pri razvoju debelosti
Vesna Jerman, Gorazd Avgu tin
Acta agriculturae Slovenica , 2010, DOI: 10.2478/v10014-010-0007-z
Abstract: The increased prevalence of obesity in modern society is associated with incidence of obesity related diseases and represents a financial burden on public health. Important discovery in the field of microbial ecology of the gut was the possible involvement of the gut microbiota in obesity development. Using new molecular techniques and gnotobiotic animal models has revealed the relation between the regulation of body mass and energy balance of the host with the microbial community of the gut. Gut microbiota affects nutrient intake, facilitate the extraction of energy from food and promote storage of the calories in host adipose tissue through processes of fermentation, absorption and through the effect on the expression of host genes (e.g. Fiaf) and the activity of host enzymes (e.g. AMPK). In obese mice and humans the gut microbiota is clearly able to obtain energy from food more effectively as in the lean subjects. There are significant differences in the composition of microbial communities in relation to fat vs. lean phenotype. In the gut of obese animals and humans the increased proportion of the Firmicutes at the expense on Bacteroidetes was consistently detected. Both are the dominant bacterial groups in mammalian gastrointestinal tract, accounting together for 90% of all bacteria. It has been shown that gut microbiota is involved also in patophysiology of obesity through factors such as microbial LPS. Existing results show that high fat diet can affect the composition of microbial community in the gut and that these changes can further affect the incidence of metabolic disease. This evidence potentially opens a new field of manipulation of the gut microbiota as a new strategy to treat obesity and related diseases.
Animal production systems as a selective environment for antibiotic resistance genes
Jerneja Ambro i Avgu tin
Acta agriculturae Slovenica , 2012, DOI: 10.2478/v10014-012-0008-1
Abstract: In the last decade antibiotic usage in animal production systems has received a considerable public attention. The use, overuse and misuse of antibiotics provided an excellent environment for the selection and dissemination of antibiotic resistant bacteria and resistance genes across a wide diversity of bacteria, mainly through horizontal gene transfer. Resistance genes move between animal and human bacteria mainly through the food chain. Thus resistance generated in animal production environments could result in the loss of effectiveness of antibiotics used for the treatment of human diseases. The increasing threat of emerging bacterial pathogens resistant to a variety of antibiotics and the economic and human burden have moved the legislators in EU to ban antibiotic usage in animal food production as growth promoters in 2006 and recently proposed further non-binding recommendations to ban antibiotics for prophylactic use too. The costs for such actions will presumably be much lower in comparison to the costs of leaving the issue as it is. However, in non EU countries such measures have not been adopted yet. The mechanisms and examples of antibiotic resistance development and dissemination are described, focusing on antibiotics used both in human and veterinary medicine and animal food production.
The census of bookbindings
Blanka Avgutin-Florjanovi?
Knji?nica : Revija za Podro?je Bibliotekarstva in Informacijske Znanosti , 2003,
Abstract: The beginnings of the library of the Franciscan monastery of Kostanjevica in Nova Gorica date back to the middle of the 17th century, but in its collection one can also find incunabula and prints from the 16th century. The paper presents a survey form for older books,which is regulary used in the conservation-restoration treatment, and a suggested method of describing older bookbindings for librarians. An analyisis and damage description, as well as information on the protection and recommended storage of older books are also included. The documentation pertaining to each item is added.
Biological Activities of Ethanolic Extracts from Deep-Sea Antarctic Marine Sponges
Tom Turk,Jerneja Ambro?i? Avgutin,Ur?ka Batista,Ga?per Strugar,Rok Kosmina,Sandra ?ivovi?,Dorte Janussen,Silke Kauferstein,Dietrich Mebs,Kristina Sep?i?
Marine Drugs , 2013, DOI: 10.3390/md11041126
Abstract: We report on the screening of ethanolic extracts from 33 deep-sea Antarctic marine sponges for different biological activities. We monitored hemolysis, inhibition of acetylcholinesterase, cytotoxicity towards normal and transformed cells and growth inhibition of laboratory, commensal and clinically and ecologically relevant bacteria. The most prominent activities were associated with the extracts from sponges belonging to the genus Latrunculia, which show all of these activities. While most of these activities are associated to already known secondary metabolites, the extremely strong acetylcholinesterase inhibitory potential appears to be related to a compound unknown to date. Extracts from Tetilla leptoderma, Bathydorus cf. spinosus, Xestospongia sp., Rossella sp., Rossella cf. racovitzae and Halichondria osculum were hemolytic, with the last two also showing moderate cytotoxic potential. The antibacterial tests showed significantly greater activities of the extracts of these Antarctic sponges towards ecologically relevant bacteria from sea water and from Arctic ice. This indicates their ecological relevance for inhibition of bacterial microfouling.
A Longitudinal Analysis of the Stability of Household Money Demand  [PDF]
Jan Tin
Modern Economy (ME) , 2011, DOI: 10.4236/me.2011.23046
Abstract: Past aggregate time-series studies, conducted under the assumption of a representative economic agent, frequently show that the demand for narrowly defined M1, especially non-interest-yielding demand deposit, is unstable during periods of financial innovations. Whether this is longitudinally the case among life-cycle savers is unclear. This study utilizes longitudinal data to take another look and find that volatility in the demand for non-interest-earning checking accounts in the mid and late 1990s is attributable solely to the portion held for the transactions motive. When the conventional Baumol-Tobin model is extended to include human capital and family formation variables representing the life-cycle motive, equilibrium money demand is a stable function of both economic and demographic variables.
Hemodynamic changes during weaning: can we assess and predict cardiac-related weaning failure by transthoracic echocardiography?
Gorazd Voga
Critical Care , 2010, DOI: 10.1186/cc9085
Abstract: In the previous issue of Critical Care, Caille and colleagues [1] evaluated the ability of transthoracic echocardiography (TTE) to predict cardiac-related weaning failure and to assess the hemodynamic changes before and 30 minutes after the start of a spontaneous breathing trial (SBT). The authors measured maximal velocities of mitral E and A waves, deceleration time of E wave (DTE), maximal velocity of E' wave measured by tissue Doppler at lateral mitral annulus, and left ventricular (LV) stroke volume.Weaning failed in 23 of 117 patients, and failure was of cardiac origin in the majority (20 of 23) of them. In patients with weaning failure, a significantly lower heart rate and E/E' ratio and a higher left ventricular ejection fraction (LVEF) were observed before SBT. During SBT, significant increases in cardiac output, systolic arterial pressure, and E/A relation and a nonsignificant increase in E/E' were observed, with significant shortening of DTE. Weaning failure was observed in 17% of patients with LVEF of greater than 50%, 13% of patients with LVEF of 35% to 50%, and 31% of patients with LVEF of less than 35%. Before SBT, DTE was significantly shorter and E/E' was significantly higher in patients with LVEF of less than 35%. During SBT, E/A increased and DTE decreased significantly in patients with LVEF of less than 50%.If these results are translated into simple clinical language, patients with weaning failure were tachycardic and had depressed systolic function and diastolic dysfunction (short DTE) with elevated LV filling pressure (high E/E' ratio) before SBT. During SBT, a further increase in LV filling pressure (increased E/A and E/E' ratio) and deterioration of diastolic function were observed.TTE was therefore able to identify patients who were at risk of cardiac-related weaning failure by measuring relatively simple and reproducible variables (LVEF, E/E', and DTE) before SBT. Moreover, hemodynamic changes (increase of pulmonary artery occlusion pressur
Pulmonary artery occlusion pressure estimation by transesophageal echocardiography: is simpler better?
Gorazd Voga
Critical Care , 2008, DOI: 10.1186/cc6831
Abstract: Vignon and colleagues [1] prospectively assessed the ability of transesophageal echocardiography (TEE) to predict PAOP higher than 18 mmHg in mechanically ventilated patients with an inserted pulmonary artery catheter. In a first group, they analyzed simple Doppler variables derived from transmitral flow (TMF) and pulmonary venous flow (PVF) and performed the usual measurements and calculations (maximal velocity and velocity time integral of E (the maximal velocity of early diastolic TMF) and A (the maximal velocity of late diastolic TMF) wave, E/A ratio, E wave deceleration time (EDT), maximal velocity and velocity time integral of S (the maximal systolic PVF velocity) and D (the maximal diastolic PVF velocity) wave, S/D ratio, atrial filling fraction and systolic fraction of pulmonary venous flow (SFPVF)). TMF recording was inadequate for analysis in 10% of patients. The correlations between Doppler variables and pulmonary artery occlusion pressure (PAOP) were better in patients with depressed left ventricular (LV) systolic function than in those with normal LV systolic function. PAOP could be predicted by E/A >1.4, EDT >100 ms, atrial filling fraction >31% and SFPVF >44%, with similar sensitivity and specificity and acceptable positive and negative predictive values. In a second group these cutoff values were prospectively evaluated for prediction of PAOP higher than 18 mmHg. Additionally, they measured maximal early diastolic velocity of lateral mitral annulus by tissue Doppler (Ea) and color M-mode Doppler flow propagation velocity (Vp). An E/Ea ratio <8 and an E/Vp ratio <1.7 were predictive for PAOP >18 mmHg, but the use of these additional variables did not improve the correct estimation of PAOP.Elevated PAOP reflects an increase of LV end-diastolic pressure due to LV diastolic and/or systolic dysfunction/failure. PAOP less than 18 mmHg, if measured, supports criteria for the definition of acute respiratory distress syndrome and acute lung injury.Clinical an
Sense-making methodology as a foundation for user studies
Gorazd Vodeb
Knji?nica : Revija za Podro?je Bibliotekarstva in Informacijske Znanosti , 2004,
Abstract: The article presents Brenda Dervin’s sense-making methodology approach to user studies. The concepts of subject, gap, verbing, information etc. are outlined. They form a foundation for the theory’s process approach to information behavior research. The sense-making triangle, as a basic model, facilitates the conceptualisation of information or communication behaviour in individual contexts. The article also presents the theory’s view on information systems design, role of power and methodological implications for studying information seeking and use.
Information behaviour of graduate students: a qualitative user study
Gorazd Vodeb
Knji?nica : Revija za Podro?je Bibliotekarstva in Informacijske Znanosti , 2004,
Abstract: The article presents a qualitative user study exploring information behaviour of graduate students. The study is conceptually based on Brenda Dervin’s Sense-Making Methodology. The information behaviour is conceptualised as a process. The author conducted 13 interviews using the time-line micro moment interview technique. Data were transcribed and then condensed using the ATLAS/ti program for qualitative analysis. The basic approach to the analysis was to compare the moments of sense making instances within the situation of the same actor and also a comparison of moments across situations of different actors. The characteristics of actors’ situations was described. The most intensive information activity of graduate students was found during the completion of their studies. The proposed model consisted of three successive types of gaps: topic selection gap, topic ignorance gap and literature collecting gap. The article also presents findings about the process of writing and information habits.
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