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Growth Media (growth + media)
Kinds of Growth Media Selected AbstractsDeveloping transgenic arabidopsis plants to be metal-specific bioindicatorsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 1 2003Beth A. Krizek Abstract Deoxyribonucleic acid (DNA) microarrays provide a means to assess genome-wide expression patterns after exposure of an organism to different xenobiotics. Potential uses for this technology include identification of unknown toxicants, assessment of toxicity of new compounds, and characterization of the cellular mechanisms of toxicant action. Here we describe another use of DNA microarrays in toxicant-specific gene discovery. Combining results from two DNA microarray experiments, we have identified genes from the model plant Arabidopsis thaliana that are induced in response to one but not other heavy metals. The promoters of these genes should be useful in developing metal-specific transgenic biomonitors. To test this idea, we have fused the promoter of one of the newly identified Ni-inducible genes (AHB1) to the ,-glucuronidase (GUS) reporter gene. Arabidopsis plants containing the AHB1::GUS transgene show reporter gene activity when they are grown on media containing Ni but not when grown on media containing Cd, Cu, Zn, or without added metals. Thus, this approach has resulted in the creation of a transgenic strain of Arabidopsis that can report on the presence and concentration of Ni in plant growth media. Such transgenic models can serve as cheap and efficient biomonitors of bioavailable heavy metal contamination in soils and sediments. [source] Isolation and identification of equol-producing bacterial strains from cultures of pig faecesFEMS MICROBIOLOGY LETTERS, Issue 1 2008Zhuo-Teng Yu Abstract Transformation of daidzein to equol was compared during fermentation of three growth media inoculated with faeces from Erhualian piglets, but equol was produced from only one medium, M1. Two equol-producing strains (D1 and D2) were subsequently isolated using medium M1. Both strains were identified as Eubacterium sp., on the basis of morphological and physiological characteristics, and 16S rRNA gene sequence analysis showed that strains D1 and D2 were most closely related to previously characterized daidzein-metabolizing bacteria isolated from human faecal and rumen samples, respectively. This suggests that the ability to metabolize daidzein can be found among bacteria present within the mammalian intestine. The results provided the first account of conversion of daidzein directly to equol by bacterial species from farm animals. These strains may be of importance to the improvement of animal performance, and the use of medium M1 could provide a simple way to isolate bacterial strains capable of transforming daidzein into equol. [source] Inactivation of pqq genes of Enterobacter intermedium 60-2G reduces antifungal activity and induction of systemic resistanceFEMS MICROBIOLOGY LETTERS, Issue 1 2008Song Hee Han Abstract Enterobacter intermedium 60-2G, a phosphate solubilizing bacterium, has the ability to induce systemic resistance in plants against soft rot pathogen Erwinia carotovora. Glucose dehydrogenase, an enzyme that utilizes pyrroloquinoline quinone (PQQ) as a cofactor, is required for the synthesis of gluconic acid by E. intermedium 60-2G. Here, we report that the pqqA and pqqB genes are required for phosphate solubilization and induced systemic resistance against a soft rot pathogen in tobacco. Mutations in either the pqqA or pqqB gene abolished the production of 2-ketogluconic acid and eliminated the ability of E. intermedium to solubilize hydroxyapatite. Addition of gluconic acid to the growth media restored the ability of the pqqA mutant to produce 2-ketogluconic acid. Interestingly, both pqqA and pqqB mutants of E. intermedium lost their ability to inhibit the growth of the rice pathogen Magnaporthe grisea KI-409. Additionally, induced systemic resistance against the soft rot pathogen was attenuated in the pqq mutants. These functions were restored by complementation with the wild-type pqq gene cluster. Our findings suggest that PQQ plays an important function in beneficial traits including phosphate solubilization, antifungal activity, and induced systemic resistance of E. intermedium, possibly by acting as a cofactor for several enzymes including glucose dehydrogenase. [source] Hemin nutritional stress inhibits bacterial invasion of radicular dentine by two endodontic anaerobesINTERNATIONAL ENDODONTIC JOURNAL, Issue 2 2007R. M. Love Abstract Aim, To determine if anaerobic bacteria routinely found in infected dentine and root canals require the presence of heme in the environment in order for them to invade dentinal tubules. Methodology, Noncarious, unrestored human teeth with single root canals were prepared for invasion experiments and soaked in either TSB-M supplemented with hemin (5 ,g mL,1) (n = 12 roots), TSB-M media (n = 12 roots) or TSB-M media followed by hemin soak (n = 12 roots) for 2 days, then inoculated with either Prevotella intermedia ATCC 25611 or Peptostreptococcus micros ATCC 33270 and incubated anaerobically for 14 days. Roots were prepared for light microscopy, stained with Brown and Brenn or antisera raised to the bacteria, and invasion within tubules assessed using a tubule invasion index (TI). Data were analysed using Student's t -test and Mann,Whitney U -test. Results,Prevotella intermedia (TI = 0.7 ± 0.04) and P. micros (TI = 0.96 ± 0.08) showed low invasion when grown in the presence of hemin with cells generally restricted to the superficial 20 ,m of the tubules, whilst neither bacteria invaded tubules (TI = 0) when hemin was absent from the growth media (P < 0.01). Conclusions, Hemin was required in the growth medium for P. intermedia and P. micros to invade dentinal tubules. [source] Multienzyme Profiling of Thermophilic Microorganisms with a Substrate Cocktail AssayADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 7-8 2005Renaud Sicard Abstract Labeled substrates for 16 different catalytic activities were combined into a cocktail reagent for multienzyme functional profiling, called PHENOZYMTM. The assay involves a single reaction followed by determination of substrate consumption by HPLC-analysis. The method allows a rapid identification of multiple enzyme activities, and is compatible with a diversity of growth media and reaction conditions (pH, temperature). The PHENOZYMTM cocktail was used to analyze the activity of 16 enzyme activities in a series of microbial strains, including thermophilic microorganisms. The functional profiles were used for a functional classification of the different microbial strains tested by hierarchical cluster analysis. The resulting "phylo-enzymatic" tree revealed associations consistent with the known phylogenetic classification of the strains. The influence of the culture medium on the enzyme activity profiles was also apparent. [source] Sequential secretion of collagenolytic, elastolytic, and keratinolytic proteases in peptide-limited cultures of two Bacillus cereus strains isolated from woolJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2009A.C. Ad, güzel Abstract Aims:, To characterize the secretion of proteolytic activities against keratin, collagen and elastin in liquid cultures of Bacillus cereus IZ-06b and IZ-06r isolated from wool. Methods and Results:, Growth of B. cereus IZ-06b and IZ-06r were characterized in batch culture. Both strains needed an organic nitrogen source, were able to grow on wool or peptone as sole carbon and nitrogen sources, and metabolized glucose, maltose and other simple sugars. Proteolytic activities were investigated in batch cultures grown in peptide-restricted, carbon-sufficient medium. Secretion of proteases was induced by peptide limitation while different proteolytic activities appeared sequentially in the growth medium. When the most available components of the peptone were depleted, collagenolytic and elastolytic proteases were produced. These were later replaced by the production of keratinolytic protease. Conclusions:,B. cereus can adjust its proteolytic affinity profile in response to the supply of organic nitrogen and sequentially secrete proteases with activities targeted against increasingly inaccessible proteinous substrates as the nutritional availability in the environment deteriorates. Significance and Impact of the Study:, Peptide-limited, carbon-sufficient growth media containing no proteinous substrates are well suited for protease production in B. cereus while growth conditions can be adjusted to optimize the proteolytic affinity profiles. [source] Interactions of Salmonella enterica with lettuce leavesJOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2009Y. Kroupitski Abstract Aims:, To investigate the interactions of Salmonella enterica with abiotic and plant surfaces and their effect on the tolerance of the pathogen to various stressors. Methods and Results:,Salmonella strains were tested for their ability to form biofilm in various growth media using a polystyrene plate model. Strong biofilm producers were found to attach better to intact Romaine lettuce leaf tissue compared to weak producers. Confocal microscopy and viable count studies revealed preferential attachment of Salmonella to cut-regions of the leaf after 2 h at 25°C, but not for 18 h at 4°C. Storage of intact lettuce pieces contaminated with Salmonella for 9 days at 4°C resulted only in small changes in population size. Exposure of lettuce-associated Salmonella cells to acidic conditions (pH 3·0) revealed increased tolerance of the attached vs planktonic bacteria. Conclusions:, Biofilm formation on polystyrene may provide a suitable model to predict the initial interaction of Salmonella with cut Romaine lettuce leaves. Association of the pathogen with lettuce leaves facilitates its persistence during storage and enhances its acid tolerance. Significance and Impact of the Study:, Understanding the interactions between foodborne pathogens and lettuce might be useful in developing new approaches to prevent fresh produce-associated outbreaks. [source] Effect of various growth media upon survival during storage of freeze-dried Enterococcus faecalis and Enterococcus duransJOURNAL OF APPLIED MICROBIOLOGY, Issue 6 2003A.S. Carvalho Abstract Aims: The effects of three different growth media (MRS, M17 and Lee's) on survival during freeze-drying and subsequent storage of six strains of Enterococcus faecalis and two strains of E. durans were investigated. Methods and Results: Distinct Enterococcus spp. strains were grown on M17, MRS and Lee's broth, freeze-dried and stored at 20°C in air under darkness. At regular intervals throughout storage, freeze-dried samples were rehydrated and then plated on M17 agar. Conclusions: A higher survival rate during storage of dried E. durans was obtained when growth occurred in MRS. The same effect was not observed, however, for the majority of E. faecalis strains, which clearly survived better in the dried state when this organism had been grown in M17 or Lee's medium. Significance and Impact of Study: The survival of the dried Enterococcus spp. tested during storage was shown to be strain-specific and dependent on the growth medium. [source] Different combinations of salts affect the growth and bacteriocin production by Lactobacillus salivarius CRL 1328JOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 1 2010María Silvina Juárez Tomás Abstract BACKGROUND: The culture medium for optimal growth of vaginal Lactobacillus salivarius CRL 1328 is different from that for optimal bacteriocin production. To simultaneously obtain high amount of biomass and bacteriocin of this microorganism, the effects of different basal culture media and salts on both responses were evaluated. The study was performed by using a complete factorial experimental design 26, with central points. Sixty-four different growth media, which resulted from the combinations of two basal culture media and two concentrations of five salts (ammonium citrate, sodium acetate, MgSO4, MnSO4, and K2HPO4) were assayed. RESULTS: Only the addition of MnSO4 to each culture medium significantly stimulated the growth of L. salivarius. The presence of sodium acetate or MgSO4 stimulated the bacteriocin production, while MnSO4 and K2HPO4 exerted an inhibitory effect. However, the simultaneous addition of MnSO4 and sodium acetate to both basal culture media allowed high bacteriocin levels to be reached, attenuating the inhibitory effect of Mn2+. CONCLUSIONS: The application of a complete experimental design contributed to simultaneous optimization of the biomass and bacteriocin production of L. salivarius CRL 1328. The results obtained are potentially applicable to the technological production of probiotic bacteria and antagonistic substance to be included in a probiotic pharmaceutical product. Copyright © 2009 Society of Chemical Industry [source] ISOLATION AND CHARACTERIZATION OF BACTERIOCIN-PRODUCING MICROORGANISMS FROM AGOS-OSJOURNAL OF FOOD SAFETY, Issue 3 2000JULIE D. TAN ABSTRACT Agos-os, a fermented meat and sweetpotato mixture, was produced and analyzed for its microbial characteristics. pH decreased during fermentation. Mold and anaerobic bacterial counts increased while yeasts and aerobic bacterial counts decreased during the third and seventh day of fermentation. Six isolates with the widest zones of inhibition on the indicator lawn were selected for bacteriocin production. These isolates had exactly the same morphological, physiological and biochemical characteristics. The ribosomal RNA sequence was 99.5% identical with Enterococcus faecalis VRE 1492. The identification was confirmed through DNA homology test by the EMBL Genbank, Canada. This bacterium produced the L-isomer lactic acid. The amount of bacteriocin produced by the bacterium was optimized by growing the bacterium at different growth media, initial pH and fermentation time. Maximum production of bacteriocin was achieved in MRS (De Man Rugosa and Sharpe) medium (with glucose) at pH 7.50. The crude bacteriocin inhibited the growth of gram-positive bacteria such as Lactobacillus sake 15521 and Listeria innocua. The gram-negative bacteria such as Escherichia coli DH 5-alpha (with plasmid, PUC), Salmonella typhii and Staphylococcus aureus were weakly inhibited. Other microorganisms such as Lactobacillus curvatus D31685, Lactobacillus confusius M23036, Lactococcus lactis MG1363, Leuconostoc paramesenteroides S67831, Pediococcus pentosaceus M58834, Saccharomyces cerevisiae SS553 (wild type) and Escherichia coli JM109 (no plasmid) were not inhibited. [source] Factors Affecting the Hydroxycinnamate Decarboxylase/Vinylphenol Reductase Activity of Dekkera/Brettanomyces: Application for Dekkera/Brettanomyces Control in Red Wine MakingJOURNAL OF FOOD SCIENCE, Issue 1 2009S. Benito ABSTRACT:, The growth of Dekkera/Brettanomyces yeasts during the ageing of red wines,which can seriously reduce the quality of the final product,is difficult to control. The present study examines the hydroxycinnamate decarboxylase/vinylphenol reductase activity of different strains of Dekkera bruxellensis and Dekkera anomala under a range of growth-limiting conditions with the aim of finding solutions to this problem. The yeasts were cultured in in-house growth media containing different quantities of growth inhibitors such as ethanol, SO2, ascorbic acid, benzoic acid and nicostatin, different sugar contents, and at different pHs and temperatures. The reduction of p -coumaric acid and the formation of 4-ethylphenol were periodically monitored by HPLC-PDA. The results of this study allow the optimization of differential media for detecting/culturing these yeasts, and suggest possible ways of controlling these organisms in wineries. [source] Human oral keratinocyte E-cadherin degradation by Candida albicans and Candida glabrataJOURNAL OF ORAL PATHOLOGY & MEDICINE, Issue 3 2010Pirjo Pärnänen J Oral Pathol Med (2010) 39: 275,278 Background:, E-cadherin (E-Cad) is a 120-kDa adhesive protein found in adherens junctions of the digestive tract epithelium. We tested the ability of two Candida strains to degrade human E-Cad in the Candida virulence factor perspective. Materials and methods:, We set out to study oral mucosal E-Cad degradation by clinical and reference strains of Candida albicans and Candida glabrata. We also included hyphal and secreted aspartic proteinase (Sap) mutants of C. albicans to test the effect of yeast/hyphal transition on the ability to degrade E-Cad. The tests were performed at pH 4 and pH 6 to determine the effect of local tissue acidity on the activation of Saps. The C. albicans strains used were: CCUG 32723; clinical strain SC5314 which is known to be strongly invasive; hyphal mutants of SC5314: HLC52 (efg1/efg1), HLC54 (cph1/cph1 efg1/efg1) and JKC19 (cph1/cph1); clinical strain B1134; Sap 1,3 and Sap 4,6 mutants of SC5314. The C. glabrata strains used were ATCC 90030, and the clinical strains 5WT and G212. Results:, The sonicated yeast cells of C. albicans JKC19 and SC5314, both in hyphal form, degraded E-Cad at pH 4. The 10× concentrated growth media of the strains HLC-52, HLC-54, 32723 and B1134; all in yeast form, caused degradation at pH 4, HLC-52 and HLC-54 also at pH 6. The C. glabrata strains did not degrade E-Cad. Conclusions:, pH is a strain dependent triggering factor in activating yeast or hyphal form related Candida Saps in degrading epithelial cell associated E-Cads. [source] Culture of Staphylococcus xylosus in fish processing by-product-based media for lipase productionLETTERS IN APPLIED MICROBIOLOGY, Issue 6 2008F. Ben Rebah Abstract Aims:, The objective of this study was to demonstrate that fish-processing by-products could be used as sole raw material to sustain the growth of Staphylococcus xylosus for lipase production. Methods and Results:, Bacterial growth was tested on supernatants generated by boiling (100°C for 20 min) of tuna, sardine, cuttlefish and shrimp by-products from fish processing industries. Among all samples tested, only supernatants generated from shrimp and cuttlefish by-products sustained the growth of S. xylosus. Shrimp-based medium gave the highest growth (A600 = 22) after 22 h of culture and exhibited the maximum lipase activity (28 U ml,1). This effect may be explained by better availability of nutrients, especially, in shrimp by-products. Standard medium (SM) amendments to sardine and tuna by-product-based media stimulated the growth of S. xylosus and the highest A600 values were obtained with 75% SM. Lipase activity, however, remained below 4 U ml,1 for both sardine and tuna by-product-based media. Conclusions:, Fish by-products could be used for the production of highly valuable enzymes. Significance and Impact of the Study:, The use of fish by-products in producing S. xylosus- growth media can reduce environmental problems associated with waste disposal and, simultaneously, lower the cost of biomass and enzyme production. [source] Adequate phenylalanine synthesis mediated by G protein is critical for protection from UV radiation damage in young etiolated Arabidopsis thaliana seedlingsPLANT CELL & ENVIRONMENT, Issue 12 2008KATHERINE M. WARPEHA ABSTRACT Etiolated Arabidopsis thaliana seedlings, lacking a functional prephenate dehydratase1 gene (PD1), also lack the ability to synthesize phenylalanine (Phe) and, as a consequence, phenylpropanoid pigments. We find that low doses of ultraviolet (UV)-C (254 nm) are lethal and low doses of UV-B cause severe damage to etiolated pd1 mutants, but not to wild-type (wt) seedlings. Furthermore, exposure to UV-C is lethal to etiolated gcr1 (encoding a putative G protein-coupled receptor in Arabidopsis) mutants and gpa1 (encoding the sole G protein , subunit in Arabidopsis) mutants. Addition of Phe to growth media restores wt levels of UV resistance to pd1 mutants. The data indicate that the Arabidopsis G protein-signalling pathway is critical to providing protection from UV, and does so via the activation of PD1, resulting in the synthesis of Phe. Cotyledons of etiolated pd1 mutants have proplastids (compared with etioplasts in wt), less cuticular wax and fewer long-chain fatty acids. Phe-derived pigments do not collect in the epidermal cells of pd1 mutants when seedlings are treated with UV, particularly at the cotyledon tip. Addition of Phe to the growth media restores a wt phenotype to pd1 mutants. [source] Group A streptococcus cell-associated pathogenic proteins as revealed by growth in hyaluronic acid-enriched mediaPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 9 2007Meng Zhang Dr. Abstract Group A streptococcus (GAS), also know as Streptococcus pyogenes, is a human pathogen and can cause several fatal invasive diseases such as necrotising fasciitis, the so-called flesh-eating disease, and toxic shock syndrome. The destruction of connective tissue and the hyaluronic acid (HA) therein, is a key element of GAS pathogenesis. We therefore propagated GAS in HA-enriched growth media in an attempt to create a simple biological system that could reflect some elements of GAS pathogenesis. Our results show that several recognised virulence factors were up-regulated in HA-enriched media, including the M1 protein, a collagen-like surface protein and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase, which has been shown to play important roles in streptococcal pathogenesis. Interestingly, two hypothetical proteins of unknown function were also up-regulated and detailed bioinformatics analysis showed that at least one of these hypothetical proteins is likely to be involved in pathogenesis. It was therefore concluded that this simple biological system provided a valuable tool for the identification of potential GAS virulence factors. [source] Translational and transcriptional analysis of Sulfolobus solfataricus P2 to provide insights into alcohol and ketone utilisationPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 3 2007Poh Kuan Chong Abstract The potential of Sulfolobus solfataricus P2 for alcohol or ketone bioconversion was explored in this study. S. solfataricus was grown in different concentrations (0.1,0.8% w/v) of alcohols or ketones (ethanol, iso-propanol, n -propanol, acetone, phenol and hexanol) in the presence of 0.4% w/v glucose. Consequently, the addition of these alcohols or ketones into the growth media had an inhibitory effect on biomass production, whereby lag times increased and specific growth rates decreased when compared to a glucose control. Complete glucose utilisation was observed in all cultures, although slower rates of glucose consumption were observed in experimental cultures (average of 14.9,mg/L/h compared to 18.9,mg/L/h in the control). On the other hand, incomplete solvent utilisation was observed, with the highest solvent consumption being approximately 51% of the initial concentration in acetone cultures. Translational responses of S. solfataricus towards these alcohols or ketones were then investigated using the isobaric tags for relative and absolute quantitation (iTRAQ) technique. The majority (>80%) of proteins identified and quantified showed no discernable changes in regulation compared to the control. These results, along with those obtained from transcriptional analysis of key genes involved within this catabolic process using quantitative RT-PCR and metabolite analysis, demonstrate successful alcohol or ketone conversion in S. solfataricus. [source] Volatile organoselenium monitoring in production and gastric digestion processes of selenized yeast by solid-phase microextraction-multicapillary gas chromatography coupled microwave-induced plasma atomic emission spectrometry,APPLIED ORGANOMETALLIC CHEMISTRY, Issue 12 2004J. Sanz Landaluze Abstract Evolution of volatile organoselenium compounds in the production and gastric digestion of selenized yeast has been monitored. The industrial production of these kinds of material, employed as food supplements, has been simulated in a process of yeast enrichment with inorganic selenium selenium (IV) in different growth media, with variation of the pH value. The in vitro gastric digestion process was carried out with pepsin in an acid and salt mixture. Determination of volatile species of selenium was achieved coupling solid-phase microextraction (SPME) for preconcentration and sample,matrix separation and microwave-induced plasma atomic emission spectrometry, in combination with multicapillary (MC) gas chromatography for separation and detection of the selenium species. The MC column was operated at low temperatures (,30 °C). The method was optimized, using a chemometric approach, with respect to the detection of organoselenium species such as dimethylselenide, diethylselenide and dimethyldiselenide. SPME sampling was carried out in the headspace above the corresponding solutions. Separation is fast, with a chromatogram being obtained in less than 5 min, and the detection limits were at the low parts per billion level for all species investigated. The results of the yeast enrichment process demonstrate inorganic selenium transformation into volatile organic species. The presence of inorganic selenium gave rise to at least five different volatile species after metabolization by yeast, with dimethylselenide and dimethyldiselenide being the predominant species. Commercial pasteurized yeast, containing mainly selenomethionine for use as a food supplement, and tablets were found to be still active under conditions of the simulation of the digestion process, even though producing relatively low amounts of organoselenium compounds. Copyright © 2004 John Wiley & Sons, Ltd. [source] Speciation of essential and toxic elements in edible mushrooms: size-exclusion chromatography separation with on-line UV,inductively coupled plasma mass spectrometry detectionAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 4 2004Rodolfo G. Wuilloud Abstract Size-exclusion liquid chromatography was coupled to UV and inductively coupled plasma mass spectrometry (ICP-MS) for detection to perform elemental speciation studies on different edible mushrooms. Molecular weight (MW) distribution patterns of several elements among different fractions present in various edible mushrooms are presented. The association of the elements with the high and low MW fractions was observed using sequential detection by UV and ICP-MS. Separation was performed using a Superdex 75 column. Variability of the fractionation patterns with three different extraction media (0.05 mol l,1 NaOH; 0.05 mol l,1 HCl; hot water at 60°C) was evaluated for mushroom species. A comparative elemental speciation study was performed in order to determine the differences in the fractionation patterns of silver, arsenic, cadmium, mercury, lead, and tin in Boletus edulis, Agaricus bisporus, and Lentinus edodes. Differences in the fractionation patterns of the elements were found to depend on the mushroom species and the extraction medium. Most of the elements were associated with high mw fractions. It was not possible to assess the trace metal contributions from the mushroom growth media. Copyright © 2004 John Wiley & Sons, Ltd. [source] Expression of merA, trxA, amoA, and hao in continuously cultured Nitrosomonas europaea cells exposed to cadmium sulfate additionsBIOTECHNOLOGY & BIOENGINEERING, Issue 5 2009Tyler S. Radniecki Abstract The effects of CdSO4 additions on the gene expressions of a mercury reductase, merA, an oxidative stress protein, trxA, the ammonia-monooxygenase enzyme (AMO), amoA, and the hydroxylamine oxidoreductase enzyme (HAO), hao, were examined in continuously cultured N. europaea cells. The reactor was fed 50,mM NH4+ and was operated for 78 days with a 6.9 days hydraulic retention time. Over this period, six successive batch additions of CdSO4 were made with increasing maximum concentrations ranging from 1 to 60,µM Cd2+. The expression of merA was highly correlated with the level of Cd2+ within the reactor (Rs,=,0.90) with significant up-regulation measured at non-inhibitory Cd2+ concentrations. Cd2+ appears to target AMO specifically at lower concentrations and caused oxidative stress at higher concentrations, as indicated by the SOURs (specific oxygen uptake rates) and the up-regulation of trxA. Since Cd2+ inhibition is irreversible and amoA was up-regulated in response to Cd2+ inhibition, it is hypothesized that de novo synthesis of the AMO enzyme occurred and was responsible for the observed recovery in activity. Continuously cultured N. europaea cells were more resistant to Cd2+ inhibition than previously examined batch cultured cells due to the presence of Mg2+ and Ca2+ in the growth media, suggesting that Cd2+ enters the cell through Mg2+ and Ca2+ import channels. The up-regulation of merA during exposure to non-inhibitory Cd2+ levels indicates that merA is an excellent early warning signal for Cd2+ inhibition. Biotechnol. Bioeng. 2009; 104: 1004,1011. © 2009 Wiley Periodicals, Inc. [source] Computational identification of altered metabolism using gene expression and metabolic pathwaysBIOTECHNOLOGY & BIOENGINEERING, Issue 4 2009Hojung Nam Abstract Understanding altered metabolism is an important issue because altered metabolism is often revealed as a cause or an effect in pathogenesis. It has also been shown to be an important factor in the manipulation of an organism's metabolism in metabolic engineering. Unfortunately, it is not yet possible to measure the concentration levels of all metabolites in the genome-wide scale of a metabolic network; consequently, a method that infers the alteration of metabolism is beneficial. The present study proposes a computational method that identifies genome-wide altered metabolism by analyzing functional units of KEGG pathways. As control of a metabolic pathway is accomplished by altering the activity of at least one rate-determining step enzyme, not all gene expressions of enzymes in the pathway demonstrate significant changes even if the pathway is altered. Therefore, we measure the alteration levels of a metabolic pathway by selectively observing expression levels of significantly changed genes in a pathway. The proposed method was applied to two strains of Saccharomyces cerevisiae gene expression profiles measured in very high-gravity (VHG) fermentation. The method identified altered metabolic pathways whose properties are related to ethanol and osmotic stress responses which had been known to be observed in VHG fermentation because of the high sugar concentration in growth media and high ethanol concentration in fermentation products. With the identified altered pathways, the proposed method achieved best accuracy and sensitivity rates for the Red Star (RS) strain compared to other three related studies (gene-set enrichment analysis (GSEA), significance analysis of microarray to gene set (SAM-GS), reporter metabolite), and for the CEN.PK 113-7D (CEN) strain, the proposed method and the GSEA method showed comparably similar performances. Biotechnol. Bioeng. 2009;103: 835,843. © 2009 Wiley Periodicals, Inc. [source] Expression of merA, amoA and hao in continuously cultured Nitrosomonas europaea cells exposed to zinc chloride additionsBIOTECHNOLOGY & BIOENGINEERING, Issue 2 2009Tyler S. Radniecki Abstract The effects of ZnCl2 additions on a mercuric reductase, merA, ammonia monooxygenase, amoA, and hydroxylamine (NH2OH) oxidoreductase, hao, gene expression were examined in continuously cultured Nitrosomonas europaea cells. The reactor was operated for 85 days with a 6.9 d hydraulic retention time and with four successive additions of ZnCl2 achieving maximum concentrations from 3 to 90 µM Zn2+. Continuously cultured N. europaea cells were more resistant to Zn2+ inhibition than previously examined batch cultured cells due to the presence of Mg2+ in the growth media, suggesting that Zn2+ enters the cell through Mg2+ import channels. The maximum merA up-regulation was 45-fold and expression increased with increases in Zn2+ concentration and decreased as Zn2+ concentrations decreased. Although Zn2+ irreversibly inactivated ammonia oxidation in N. europaea, the addition of either 600 µM CuSO4 or 2250 µM MgSO4 protected N. europaea from ZnCl2 inhibition, indicating a competition between Zn2+ and Cu2+/Mg2+ for uptake and/or AMO active sites. Since ZnCl2 inhibition is irreversible and amoA was up-regulated at 30 and 90 µM additions, it is hypothesized that de novo synthesis of the AMO enzyme is needed to overcome inhibition. The up-regulation of merA during exposure to non-inhibitory Zn2+ levels indicates that merA is an excellent early warning signal for Zn2+ inhibition. Biotechnol. Bioeng. 2009;102: 546,553. © 2008 Wiley Periodicals, Inc. [source] Microarray Studies in Bacillus subtilisBIOTECHNOLOGY JOURNAL, Issue 7 2009nar Kocaba Abstract This review focuses on the construction of a global, comprehensive understanding of Bacillus subtilis through microarray studies. The microarray studies in B. subtilis were analysed based on the theme of the work, by mentioning the growth media, bioreactor operation conditions, RNA isolation method, number of data points analysed in exponential or stationary phases, compared genotypes, induction and repression ratios, investigated gene(s) and their positive and/or negative influences. Based on the theme and scope of the studies, the articles were reviewed under seven thematic sections, i.e., effects of gene deletion(s) or overexpression, effects of overexression of heterologous genes, comparison of global gene expression between aerobic and anaerobic respiration, effects of temperature change, effects of transported molecules, effects of limitations and stress conditions, and other microarray studies in B. subtilis. [source] Identification of gene disruptions for increased poly-3-hydroxybutyrate accumulation in Synechocystis PCC 6803BIOTECHNOLOGY PROGRESS, Issue 5 2009Keith E. J. Tyo Abstract Inverse metabolic engineering (IME) is a combinatorial approach for identifying genotypes associated with a particular phenotype of interest. In this study, gene disruptions that increase the biosynthesis of poly-3-hydroxybutyrate (PHB) in the photosynthetic bacterium Synechocystis PCC6803 were identified. A Synechocystis mutant library was constructed by homologous recombination between the Synechocystis genome and a mutagenized genomic plasmid library generated through transposon insertion. Using a fluorescence-activated cell sorting-based high throughput screen, high PHB accumulating mutants from the library grown in different nutrient conditions were isolated and characterized. While several mutants isolated from the screen had increased PHB accumulation, transposon insertions in only two ORFs could be linked to increased PHB production. Disruptions of sll0461, coding for gamma-glutamyl phosphate reductase (proA), and sll0565, a hypothetical protein, resulted in increased accumulation in standard growth media and acetate supplemented media. These genetic perturbations have increased PHB accumulation in Synechocystis and serve as markers for engineering increased polymer production in higher photosynthetic organisms. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Alternative Drying Processes for the Industrial Preservation of Lactic Acid Starter CulturesBIOTECHNOLOGY PROGRESS, Issue 2 2007Chalat Santivarangkna The preservation of lactic acid starter cultures by alternative drying processes has attracted increasing attention due to the high costs and energy consumption of freezing and freeze drying. This review thus aims to provide a survey regarding the state of knowledge of starter culture production at high levels of viability. The results from numerous studies on various drying processes and lactic acid bacteria are summarized. The alternative drying processes considered, such as spray drying, fluidized bed drying, and vacuum drying, are mainly of industrial interest. The features, advantages, and disadvantages of these drying processes are described. In conclusion, the important factors that need to be considered, standardized, or optimized to achieve high levels of viability include intrinsic tolerance of cultures, growth media and conditions, stress induction, cell harvesting conditions, protective agents, rehydration conditions, enumeration of cells, and storage conditions. [source] | ||||||||||||||||||||||||||||