Influence of growth conditions on the nisin production of bioengineered <Emphasis Type="Italic">Lactococcus lactis</Emphasis> strains

Nisin production of three bioengineered strains, (LAC338, LAC339 and LAC340) with immunity (nisFEG) and/or regulation (nisRK) genes of nisin biosynthesis on plasmids in the Lactococcus lactis LL27 nisin producer, was evaluated under pH-controlled and pH-uncontrolled batch fermentations. Optimization studies showed that fructose and yeast extract yielded the highest nisin activity. The strains LAC338, LAC339, and LAC340 produced 24, 45, and 44% more nisin, respectively, than wild-type L. lactis LL27 after 12-h incubation. However, sharp decreases in the yield of nisin were observed at the late phase of fermentation with LAC339 and LL27 in contrast to LAC340 and LAC338 strains for which the high level of nisin could be maintained longer. Obviously, increasing the copy number of the regulation genes together with immunity genes in the nisin producers retarded the loss of nisin in the late phase of the fermentation.     

The role of <Emphasis Type="Italic">stj</Emphasis> fimbrial operon in the intestinal persistence of <Emphasis Type="Italic">Salmonella</Emphasis> Typhimurium in mice

Salmonella Typhimurium contains 13 operons coding for fimbriae with unique binding specificities to host epithelial surfaces. stj operon is only detected in S. Typhimurium genome suggesting that Stj fimbria may effect serovarspecific virulence characteristics. In this study, the role of stj fimbrial operon in the long-term persistence of S. Typhimurium was identified by competitive infection experiment in genetically resistant mouse (CBA) model system. Knock-out mutation of stjA (major subunit of the Stj fimbria) gene reduced recovery of S. Typhimurium from fecal samples and its colonization to spleen, cecum and mesenteric lymph nodes over a 34-day time period (p < 0.05). This data indicate that stj fimbrial operon has a role in long-term intestinal persistence of S. Typhimurium in CBA mice.     

New information for Ilex phylogenetics based on the plastid psbA‐trnH intergenic spacer (Aquifoliaceae)

The aim of the present work was to clarify the origin and phylogenetic position of the species belonging to the genus Ilex (Aquifoliaceae), especially the South American species. Phylogenetic relationships of the genus Ilex were investigated using the plastid psbA‐trnH intergenic spacer and parsimony and Bayesian analyses. The psbA‐trnH intergenic spacer was shown to evolve slowly within Ilex, but a major gap present in this region was useful in the phylogenetic study of the genus. To obtain more potentially parsimonious characters, atpB‐rbcL intergenic spacer data were combined with those for psbA‐trnH. Many gaps present in the psbA‐trnH region were useful in the phylogenetic study of the genus Ilex. The topology of the trees showed that, in general, the clades are strongly related to geographical areas, a fact especially evident in certain different Asian lineages. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 159 , 182–193.     

Metabolic network discovery through reverse engineering of metabolome data

Reverse engineering of high-throughput omics data to infer underlying biological networks is one of the challenges in systems biology. However, applications in the field of metabolomics are rather limited. We have focused on a systematic analysis of metabolic network inference from in silico metabolome data based on statistical similarity measures. Three different data types based on biological/environmental variability around steady state were analyzed to compare the relative information content of the data types for inferring the network. Comparing the inference power of different similarity scores indicated the clear superiority of conditioning or pruning based scores as they have the ability to eliminate indirect interactions. We also show that a mathematical measure based on the Fisher information matrix gives clues on the information quality of different data types to better represent the underlying metabolic network topology. Results on several datasets of increasing complexity consistently show that metabolic variations observed at steady state, the simplest experimental analysis, are already informative to reveal the connectivity of the underlying metabolic network with a low false-positive rate when proper similarity-score approaches are employed. For experimental situations this implies that a single organism under slightly varying conditions may already generate more than enough information to rightly infer networks. Detailed examination of the strengths of interactions of the underlying metabolic networks demonstrates that the edges that cannot be captured by similarity scores mainly belong to metabolites connected with weak interaction strength.     

Extracellular polysaccharide production byRhizobium ciceri from Turkey

The ability of theRhizobium ciceri, to produce extracellular polysaccharides (EPS) was investigated. Tested carbon and nitrogen sources influced EPS synthesis whenR. ciceri Rc5 was grown in a chemically defined medium. Mannitol was the most efficient carbon source among the six sources tested (sucrose, glucose, arabinose, fructose, xylose and rhamnose) and sodium nitrate was the most efficient nitrogen source among the two tested (ammonium sulphate and glycine). High amounts of EPS (1182.0 and 1015 μg ml−1, respectively) were produced by the Rc5 strain in mannitol and sodium nitrate respectively, which was accompanied by a great increase in the production compared to the control.     

Anaerobic Biodegradation of Poly-3-Hydroxybutyrate (PHB) by Sulfate Reducing Bacterium Desulfotomaculum sp.

Poly-3-hydroxybutyrate (PHB) film pieces were degraded by sulfate reducing Desulfotomaculum sp. incubated under anaerobic laboratory conditions. Degradation started with adherence of the microbial cells and followed by formation of black colonies on the film surface. Scanning electron microscopic (SEM) observations revealed the presence of bacteria and formation of small holes on the film. After 60 days of incubation at 30°C, 10 % weight loss in polymer and 13 % sulfate reduction in the medium was observed. According to gel permeation chromatography (GPC) analysis, the molecular weight of the PHB decreased after 30 days and did not decrease further at a more extended incubation period. Loss of weight of PHB does not seem to be correlated with molecular weight decrease.     

Metabolic and evolutionary engineering research in Turkey and beyond

This review discusses metabolic engineering research with an emphasis on evolutionary (whole cell and protein) engineering, which is an inverse metabolic engineering approach. For each section on metabolic, inverse metabolic and evolutionary engineering research, a general review of the major global studies in the literature is made and research examples from Turkey are given and discussed. It is expected that with the rapid development in systems biology and the novel powerful analytical technologies to identify the genetic basis of cellular phenotypes, metabolic and evolutionary engineering research will become widespread and increasingly important in Turkey, following global scientific trends.     

Uric acid stimulates proliferative pathways in vascular smooth muscle cells through the activation of p38 MAPK,p44/42 MAPK and PDGFRβ

Hyperuricemia and angiotensin II (Ang II) may have a pathogenetic role in the development of hypertension and atherosclerosis as well as cardiovascular disease (CVD) and its prognosis. The purpose of this study was to investigate whether uric acid can induce proliferative pathways of vascular smooth muscle cell (VSMC) that are thought to be responsible for the development of CVD. The phosphorylation of p38 mitogen-activated protein kinase (p38 MAPK), p44/42 mitogen-activated protein kinase (p44/42 MAPK) and platelet-derived growth factor receptor β (PDGFRβ) was measured by Elisa and Western blot techniques to determine the activation of proliferative pathways in primary cultured VSMCs from rat aorta. Results demonstrated that uric acid can stimulate p38 MAPK, p44/42 MAPK and PDGFRβ phosphorylation in a time- and concentration-dependent manner. Furthermore, treatment of VSMCs with the angiotensin II type I receptor (AT1R) inhibitor losartan suppressed p38 MAPK and p44/42 MAPK induction by uric acid. The stimulatory effect of uric acid on p38 MAPK was higher compared to that of Ang II. The results of this study show for the first time that uric acid-induced PDGFRβ phosphorylation plays a crucial role in the development of CVDs and that elevated uric acid levels could be a potential therapeutical target in CVD patients.     

A GIS-based risk reduction approach for the hazardous materials routing problem in Gaziantep

The transportation of hazardous materials assumes a fundamental importance, especially in urban areas, in order to identify possible alternative routes and to choose the route with minimum risk. Therefore, considering minimization risk rather than minimization distance to prevent a potential danger being transformed into a real event is necessary. In this article , a geographic information system (GIS)–based solution approach is developed to quantify the factors on each link in the network that contribute to a possible route. Based on the origin and destination of each shipment, the risks associated with the routes that minimize (1) the transport distance, (2) the population exposure, (3) the probability of an incident, and (4) the emergency response are evaluated. Proposed risk models are applied to fuel-oil transportation problem between resource point and 78 gasoline stations through the road network of Gaziantep city center. Results show that the proposed framework can contribute to the thought processes of policy-makers and carriers when they evaluate possible routes in order to minimize damage for transporting fuel oil.     

Micropropagation of the pistachio and its rootstocks by temporary immersion system

Although several studies have been reported on the micropropagation of the pistachio and its rootstocks, to date none of them had been efficient on the mass production of these plants in bioreactor systems. Thus, the micropropagation of juvenile pistachio shoot tips and nodal buds was investigated in a temporary immersion bioreactor system (RITA^®) and on a conventional semi-solid medium. Among the tested immersion conditions, immersion for 24 min every 16 h reduced vitrification and improved proliferation in the pistachio. Interactions were evident in immersion time and frequency in nodal segments. Nodal buds were better than shoot tips as the highest multiple shoot formation was recorded in MS medium containing 4 mg L^?1 BA and 0.1 mg L^?1 GA₃ in RITA^®. Although shoot tip necrosis (STN) was observed in shoots proliferated on semi-solid MS medium, such a symptom did not occur in shoots sprouted in the RITA^®. Additionally, these optimized conditions were applied to nodal buds of mature male pistachio ‘Atl?’ and Pistacia rootstocks (P. khinjuk Stocks and P. atlantica Desf.), and the micropropagation in the bioreactor system, in comparison to the semi-solid medium, was also improved. Furthermore, in vitro rooting of pistachio plantlets, despite the lower range (27.5 %), was also achieved in RITA^®. However, rooting was better on semi-solid medium for all tested species (ranged between 50 and 70 %). The results of this study showed that RITA^® could be used for the mass propagation of pistachio and its rootstocks, as well as for other woody plant species.