Katarina Veljovic

An upgraded version of the Eta model

Upgrades implemented over a number of years in an open source version of the Eta model, posted at the CPTEC web site http://etamodel.cptec.inpe.br/, are summarized and examples of benefits are shown. The version originates from the NCEP’s Workstation Eta code posted on the NCEP web site http://www.emc.ncep.noaa.gov/mmb/wrkstn_eta, which differs from the NCEP’s latest operational Eta by having the WRF-NMM nonhydrostatic option included. Most of the upgrades made resulted from attention paid to less than satisfactory performance noted in several Eta results, and identification of the reasons for the problem. Others came from simple expectation that including a feature that is physically justified but is missing in the code should help. The most notable of the upgrades are the introduction of the so-called sloping steps, or discretized shaved cells topography; piecewise-linear finite-volume vertical advection of dynamic variables; vapor and hydrometeor loading in the hydrostatic equation, and changes aimed at refining the convection schemes available in the Eta. Several other modifications have to do with the calculation of exchange coefficients, conservation in the vertical diffusion, and diagnostic calculation of 10-m winds. Several examples showing improved performance resulting from the dynamics changes are given. One includes a case of unrealistically low temperatures in several mountain basins generated by a centered vertical advection difference scheme’s unphysical advection from below ground, removed by its replacement with a finite-volume scheme. Another is that of increased katabatic winds in the Terra Nova Bay Antarctica region. Successful forecast of the severe downslope zonda wind case in the lee of the highest peaks of the Andes is also shown, and some of the recent successful verification results of the use of the upgraded model are pointed out. The code is used at numerous places, and along with setup information it is available for outside users at the CPTEC Eta web site given above.

Preliminary characterization of lactic acid bacteria isolated from Zlatar cheese

Aims:  Isolation, characterization and identification of lactic acid bacteria (LAB) from artisanal Zlatar cheese during the ripening process and selection of strains with good technological characteristics.

The characterisation of lactic acid bacteria during the fermentation of an artisan Serbian sausage (Petrovská Klobása)

Petrovská Klobása is an artisan Serbian sausage made only from meat and spices without any additives or starter cultures. In order to characterise lactic acid bacteria (LAB) microflora, a total number of 404 LAB strains were isolated from 15 samples collected during 90 days of the fermentation and 120 days of storage of one batch of Petrovská Klobása. The isolates were preliminarily identified by phenotypic tests and subjected to (GTG)₅-PCR fingerprinting. Representatives of each group were identified by 16S rDNA sequencing. The results showed that among the isolates, Lactobacillus sakei and Leuconostoc mesenteroides predominate with 36.4% and 37.1% of total LAB strains, respectively. Pediococcus pentosaceus was also isolated in high proportion (18.4%) whereas Enterococcus durans and Enterococcus caseliflavus made only 1% and 6% of the total isolates, correspondingly. The analysis of vacuum packed and modified atmosphere packed (MAP) samples showed higher presence of L. mesenteroides and L. sakei in the total microflora.

Cloning and expression of a novel lactococcal aggregation factor from Lactococcus lactis subsp. lactis BGKP1

BackgroundAggregation may play a main role in the adhesion of bacteria to the gastrointestinal epithelium and their colonization ability, as well as in probiotic effects through co-aggregation with intestinal pathogens and their subsequent removal. The aggregation phenomenon in lactococci is directly associated with the sex factor and lactose plasmid co-integration event or duplication of the cell wall spanning (CWS) domain of PrtP proteinase.ResultsLactococcus lactis subsp. lactis BGKP1 was isolated from artisanal semi-hard homemade cheese and selected due to its strong auto-aggregation phenotype. Subsequently, non-aggregating derivative (Agg-) of BGKP1, designated as BGKP1-20, was isolated, too. Comparative analysis of cell surface proteins of BGKP1 and derivative BGKP1-20 revealed a protein of approximately 200 kDa only in the parental strain BGKP1. The gene involved in aggregation (aggL) was mapped on plasmid pKP1 (16.2 kb), cloned and expressed in homologous and heterologous lactococci and enterococci. This novel lactococcal aggregation protein was shown to be sufficient for cell aggregation in all tested hosts. In addition to the aggL gene, six more ORFs involved in replication (repB and repX), restriction and modification (hsdS), transposition (tnp) and possible interaction with mucin (mbpL) were also located on plasmid pKP1.ConclusionAggL is a new protein belonging to the collagen-binding superfamily of proteins and is sufficient for cell aggregation in lactococci.

Characterization of lactic acid bacteria isolated from artisanal Travnik young cheeses, sweet creams and sweet kajmaks over four seasons.

The aim of this study was to investigate the composition of lactic acid bacteria (LAB) in autochthonous young cheeses, sweet creams and sweet kajmaks produced in the Vlašić mountain region of central Bosnia and Herzegovina near the town of Travnik over a four season period. These three products were made from cows milk by a traditional method without the addition of a starter culture. Preliminary characterization with phenotype-based assays and identification using rep-PCR with a (GTG)5 primer and 16S rDNA sequence analysis were undertaken for 460 LAB isolates obtained from all the examined samples. Fifteen species were identified as follows: Lactococcus lactis, Lactococcus raffinolactis, Lactococcus garviae, Lactobacillus casei, Lactobacillus plantarum, Lactobacillus helveticus, Enterococcus faecium, Enterococcus durans, Enterococcus faecalis, Enterococcus italicus, Leuconostoc mesenteroides, Leuconostoc pseudomesenteroides, Leuconostoc lactis, Streptococcus thermophilus and Streptococcus mitis. A wide genotypic and phenotypic heterogeneity of the species was observed, particularly within the Lc. lactis strains. In all of the tested dairy products across four seasons, a significantly positive correlation (r = 0.690) between the presence of lactococci and enterococci and a negative correlation (r = 0.722) between the presence of lactococci and leuconostocs were recorded. Forty-five percent of the lactobacilli and 54.4% of the lactococci exhibited proteolytic activity, whereas 18.7% of the total LAB isolates exhibited antimicrobial activity.

EPS-SJ Exopolisaccharide Produced by the Strain Lactobacillus paracasei subsp. paracasei BGSJ2-8 Is Involved in Adhesion to Epithelial Intestinal Cells and Decrease on E. coli Association to Caco-2 Cells

The aim of this study was to determine the role of an exopolysaccharide produced by natural dairy isolate Lactobacillus paracasei subsp. paracasei BGSJ2-8, in the adhesion to intestinal epithelial cells and a decrease in Escherichia coli’s association with Caco-2 cells. Annotation of the BGSJ2-8 genome showed the presence of a gene cluster, epsSJ, which encodes the biosynthesis of the strain-specific exopolysaccharide EPS-SJ, detected as two fractions (P1 and P2) by size exclusion chromatography (SEC) coupled with multi-angle laser light scattering (MALLS) detection. SEC-MALLS analysis revealed that an EPS-SJ- mutant (EPS7, obtained by insertion mutagenesis of the glps_2198 gene encoding primary glycosyltransferase) does not produce the P2 fraction of EPS-SJ. Transmission electron microscopy showed that EPS7 mutant has a thinner cell wall compared to the EPS-SJ+ strain BGSJ2-83 (a plasmid free-derivative of BGSJ2-8). Interestingly, strain BGSJ2-83 showed higher adhesion to Caco-2 epithelial intestinal cell line than the EPS7 mutant. Accordingly, BGSJ2-83 effectively reduced E. coli ATCC25922’s association with Caco-2 cells, while EPS7 did not show statistically significant differences. In addition, the effect of EPS-SJ on the proliferation of lymphocytes in gastrointestinal associated lymphoid tissue (GALT) was tested and the results showed that the reduction of GALT lymphocyte proliferation was higher by BGSJ2-83 than by the mutant. To the best of our knowledge this is the first report indicating that the presence of EPS (EPS-SJ) on the surface of lactobacilli can improve communication between bacteria and intestinal epithelium, implying its possible role in gut colonization.

Limited area NWP and regional climate modeling: a test of the relaxation vs Eta lateral boundary conditions

With very few exceptions, just about all limited area models (LAMs) used in operational NWP and regional climate modeling use the Davies (Q J R Meteorol Soc 102:405–418, 1976) relaxation lateral boundary conditions (LBCs), even though they make no effort to respect the basic mathematics of the problem. While in the early stages of the primitive equation LAM development in the seventies numerous schemes have been proposed and tested, LAM communities have eventually for the most part settled on the relaxation LBCs with few questions asked. An exception is the Eta model used extensively at NCEP and several other centers, in which the Mesinger (Contrib Atmos Phys 50:200–210, 1977) LBCs are used, designed and based on knowledge available before the introduction of the relaxation scheme. They prescribe variables along the outermost row of grid points only; all of them at the inflow points and one less at the outflow points where the tangential velocity components are extrapolated from inside of the model domain. Additional schemes are in place to suppress separation of gravity-wave solutions on C-subgrids of the model’s E-grid. A recent paper of Veljovic et al. (Meteor Zeitschrift 19:237–246, 2010) included three 32-day forecasts done with both the Eta and the relaxation LBCs and the comparison of some of their verification results. Here we extend this experiment by three additional forecasts to arrive at an ensemble of six members run with both schemes, and present a more complete discussion of results. We in addition show results of one of these forecasts in which the linear change of relaxation coefficients was replaced by the change following the recommendation of Lehmann (Meteorol Atmos Phys 52:1–14, 1993). We feel that the results of our two verification schemes strongly suggest the advantage of the Eta over the conventional relaxation scheme, thereby raising doubts as to the justification for its use.

Genotypic diversity and virulent factors of Staphylococcus epidermidis isolated from human breast milk.

Staphylococcus epidermidis strains were isolated from the expressed human breast milk (EHM) of 14 healthy donor mothers. Genetic diversity was evaluated using RAPD-PCR REP-PCR and pulse-field gel electrophoresis (PFGE). PFGE allowed the best discrimination of the isolates, since it provided for the greatest diversity of the analyzed genomes. Among the S. epidermidis strains, resistance to gentamicin, tetracycline, erythromycin, clindamycin or vancomycin was detected, whilst four isolates were multiresistant. The results from our study demonstrate that staphylococci from EHM could be reservoirs of resistance genes, since we showed that tetK could be transferred from EHM staphylococci to Gram-negative Escherichia coli. Most of the staphylococcal strains displayed excellent proteolytic and lipolytic activities. Additionally, the presence of ica genes, which was related to their ability to form a biofilm on tissue culture plates, and the presence of virulence factors including autolysin/adhesin AtLE, point to their pathogenic potential.

In vitro and in vivo antagonistic activity of new probiotic culture against Clostridium difficile and Clostridium perfringens

BackgroundGenus Clostridium accompanies more than 200 known species and at least 30 among them are associated with human and animal diseases. At the moment, the treatment of clostridial infections is based on use of antibiotics. However, due to the European ban on the use of antibiotics in livestock production, novel therapeutic strategies for treatment of these hardly curable infections have been evaluated. Hence, in this study the antimicrobial effect of newly designed probiotic culture consisted of natural isolates Lactobacillus helveticus BGRA43, Lactobacillus fermentum BGHI14 and Streptococcus thermophilus BGVLJ1-44 against Clostridium difficile and Clostridium perfringens was analyzed.ResultsThe probiotic culture showed strong in vitro antimicrobial effect on C. difficile (human clinical isolate). In addition, individual strains and the probiotic combination exhibited immunomodulatory activity. The probiotic combination significantly increased the proliferation of GALT lymphocytes. At the other hand, none of the bacterial treatments (individual strains and the combination) induced the production of proinflammatory cytokines IL-6 and IL-1β by intestinal epithelial cells, Caco-2. Interestingly, Caco-2 cells exposed to the probiotic combination produced significantly elevated amount of TGFβ pointing to potential protecting effect of the probiotic. In addition, the results of field trial on spontaneously infected goats revealed reduction of C. perfringens in goats (below the detection threshold) after the probiotic treatment.ConclusionsThe results of this study indicated that the novel probiotic deserves to be further investigated as a promising antimicrobial agent against C. difficile and C. perfringens.

Environmental waters and blaNDM-1 in Belgrade, Serbia: Endemicity questioned

New Delhi metallo-beta-lactamase-1 (NDM-1) will soon become the most commonly isolated and distributed metallo-beta-lactamase worldwide due to its rapid international dissemination and its ability to be expressed by numerous Gram-negative pathogens. NDM-positive bacteria pose a significant public health threat in the Indian subcontinent and the Balkans, which have been designated as endemic regions. Our study was focused on urban rivers, a lake and springheads as a potential source of NDM-1-producing strains in Serbia, but also as a source of other metallo-beta-lactamases and extended-spectrum beta-lactamase (ESBL) producing bacteria. A total of 69 beta-lactam resistant isolates, belonging to 12 bacterial genera, were collected from 8 out of 10 different locations in Belgrade, of which the most were from a popular recreational site, Ada Ciganlija Lake. Phenotypic tests revealed 7 (10.14%) ESBL-producing isolates and 39 (56.52%) isolates resistant to imipenem, of which 32 were positive for metallo-beta-lactamase (MBL) production. PCR and sequencing revealed the presence of genetic determinants for SHV (3 isolates), DHA-1 (1 isolate) and CMY-2 (1 isolate) beta-lactamases. However, we did not detect any NDM-1-producing strains (previously described cases of NDM-1 from Serbia were limited to Belgrade), so we propose that Serbian NDM-1 is in fact a transplant and a nosocomial, rather than an environmental, issue and that Serbia is not an endemic region for NDM-1.