Site-specific labeling of nucleotides for making RNA for high resolution NMR studies using an E. coli strain disabled in the oxidative pentose phosphate pathway

Escherichia coli (E. coli) is a versatile organism for making nucleotides labeled with stable isotopes ((13)C, (15)N, and/or (2)H) for structural and molecular dynamics characterizations. Growth of a mutant E. coli strain deficient in the pentose phosphate pathway enzyme glucose-6-phosphate dehydrogenase (K10-1516) on 2-(13)C-glycerol and (15)N-ammonium sulfate in Studier minimal medium enables labeling at sites useful for NMR spectroscopy. However, (13)C-sodium formate combined with (13)C-2-glycerol in the growth media adds labels to new positions. In the absence of labeled formate, both C5 and C6 positions of the pyrimidine rings are labeled with minimal multiplet splitting due to (1)J(C5C6) scalar coupling. However, the C2/C8 sites within purine rings and the C1'/C3'/C5' positions within the ribose rings have reduced labeling. Addition of (13)C-labeled formate leads to increased labeling at the base C2/C8 and the ribose C1'/C3'/C5' positions; these new specific labels result in two- to three-fold increase in the number of resolved resonances. This use of formate and (15)N-ammonium sulfate promises to extend further the utility of these alternate site specific labels to make labeled RNA for downstream biophysical applications such as structural, dynamics and functional studies of interesting biologically relevant RNAs.

[Immobilized ammonia-oxidizing bacteria Comamonas aquatic LNL3 and its partial nitrification characterization]

A new kind of ammonia-oxidizing bacteria (AOB)-Comamonas aquatic LNL3 was screened out and immobilized by Poly (HEA)-Poly (HEMA) copolymer carrier using irradiation techniques. Four kinds of impact factors on short-cut nitrification, including temperature, pH, DO and free ammonia (FA) concentration had been investigated. The result showed that AOB-Comamonas aquatic LNL3 had short-cut nitrification capability and the optimal temperature, pH, DO and FA concentration were 30 degrees C, 8.5, 4.03 mg/L and 9 mg/L respectively. Corresponding to above results, ammonia nitrogen removal rate and short-cut nitrification efficiency were 93.52%, 94.73%; 79.74%, 94.67%; 91.17%, 94.66% and 90%, 94.4% respectively.

Biodegradation of nicotine by a newly isolated Agrobacterium sp. strain S33

AIMS

To isolate and characterize bacteria capable of degrading nicotine from the rhizospheric soil of a tobacco plant and to use them to degrade the nicotine in tobacco solid waste.

METHODS AND RESULTS

A bacterium, strain S33, was newly isolated from the rhizospheric soil of a tobacco plant, and identified as Agrobacterium sp. based on morphology, physiological tests, Biolog MicroLog3 4.20 system and 16S rRNA gene sequence. Using nicotine as the sole source of carbon and nitrogen in the medium, it grew optimally with 1.0 g l(-1) of nicotine at 30 degrees C and pH 7.0, and nicotine was completely degraded within 6 h. The resting cells prepared from the glucose-ammonium medium or LB medium could not degrade nicotine within 10 h, while those prepared from the nicotine medium could completely degrade 3 g l(-1) of nicotine in 1.5 h at a maximal rate of 1.23 g nicotine h(-1) g(-1) dry cell. Using the medium containing nicotine, glucose and ammonium simultaneously to cultivate strain S33, the resting cells could degrade 98.87% of nicotine in tobacco solid waste with the concentration as 30 mg nicotine g(-1) dry weight tobacco solid waste within 7 h at a maximal rate of 0.46 g nicotine h(-1) g(-1) dry cell.

CONCLUSIONS

This is the first report that Agrobacterium sp. has the ability to degrade nicotine. Agrobacterium sp. S33 could use nicotine as the sole source of carbon and nitrogen. The use of resting cells of the strain S33 prepared from the nicotine-glucose-ammonium medium was an effective method to degrade nicotine and detoxify tobacco solid waste.

SIGNIFICANCE AND IMPACT OF THE STUDY

Nicotine in tobacco wastes is both toxic and harmful to human health and the environment. This study showed that Agrobacterium sp. S33 may be suitable for the disposal of tobacco wastes and reducing the nicotine content in tobacco leaves.

Do polyamines alter the sensitivity of lichens to nitrogen stress?

The sensitivity of lichens measuring photosynthetic efficiency and polyamines as modulator of nitrogen stress tolerance was investigated. Two lichen species with a markedly different tolerance to nitrogen compounds, namely Evernia prunastri (L.) Ach. and Xanthoria parietina (L.) Th.Fr., were incubated with deionized water (control) and solutions of KNO(3), NH(4)NO(3) and (NH(4))(2)SO(4) and then exposed to different light conditions. The F(v)/F(m) parameter (maximum quantum efficiency of photosystem II) was used as stress indicator. The results showed that F(v)/F(m) values, in the produced experimental conditions, were independent from the light gradient. Photosynthetic efficiency of E. prunastri was impaired by high ammonium concentrations, while nitrate had no effect; X. parietina was hardly influenced by nitrogen compounds. External supply of polyamines reduced the sensitivity of E. prunastri, while polyamine inhibitors reduced the tolerance of X. parietina to NH(4)(+), suggesting that polyamines play an important role in modulating the sensitivity/tolerance to nitrogen stress.

Production, characterization and application of keratinase from Streptomyces gulbargensis

A Streptomyces gulbargensis newly isolated, thermotolerant feather-degrading bacterial strain was investigated for its ability to produce keratinase enzyme. Maximum keratinolytic activity was observed at 45 degrees C and pH 9.0 at 120 h of incubation. Activity was completely stable (100%) between 30 and 45 degrees C and pH 7.0-9.0, respectively. Addition of starch to the growth medium affects the activity by means of increase in keratinase secretion. After seven days of cultivation, 10-fold increase (14.3 U ml(-1)) in keratinase activity was observed in the presence of 3g starch (per liter) of the medium. The enzyme was monomeric and had a molecular mass of 46 kDa. The enzyme activity was significantly inhibited by CaCl(2) and partly inhibited by EDTA, whereas, Na(2)SO(3) enhance the enzyme activity by 2.9 times more. In addition, native chicken feather was completely degraded at 96 h of incubation. The results obtained showed that newly isolated strain S. gulbargensis could be a useful in biotechnology in terms of valorization of keratin-containing wastes or in the leather industry.

Optimization of chemically defined medium for recombinant Pichia pastoris for biomass production

A chemically defined medium was optimized for the maximum biomass production of recombinant Pichia pastoris in the fermentor cultures using glycerol as the sole carbon source. Optimization was done using the statistical methods for getting the optimal level of salts, trace metals and vitamins for the growth of recombinant P. pastoris. The response surface methodology was effective in optimizing nutritional requirements using the limited number of experiments. The optimum medium composition was found to be 20 g/L glycerol, 7.5 g/L (NH4)2SO4, 1 g/L MgSO4.7H2O, 8.5 g/L KH2PO4, 1.5 mL/L vitamin solution and 20 mL/L trace metal solution. Using the optimized medium 11.25 g DCW/L biomass was produced giving a yield coefficient of 0.55 g biomass/g of glycerol in a batch culture. Chemostat cultivation of recombinant P. pastoris was done in the optimized medium at different dilution rates to determine the kinetic parameters for growth on glycerol. Maximum specific growth rate of 0.23 h(-1) and Monod saturation constant of 0.178 g/L were determined by applying Monod model on the steady state data. Products of fermentation pathway, ethanol and acetate, were not detected by HPLC even at higher dilution rates. This supports the notion that P. pastoris cells grow on glycerol by a respiratory route and are therefore an efficient biomass and protein producers.

Effect of substrate particle size and additional nitrogen source on production of lignocellulolytic enzymes by Pleurotus ostreatus strains

Two strains of Pleurotus ostreatus (IE-8 and CP-50) were grown on defined medium added with wheat straw extract (WSE). Mycelia from these cultures were used as an inoculum for solid fermentation using sugar cane bagasse (C:N=142). This substrate was used separately either as a mixture of heterogeneous particle sizes (average size 2.9 mm) or as batches with two different particle sizes (0.92 mm and 1.68 mm). Protein enrichment and production of lignocellulolytic enzymes on each particle size was compared. The effect of ammonium sulphate (AS) addition was also analyzed (modified C:N=20), this compound favored higher levels of protein content. Strain CP-50 showed the highest increase of protein content (48% on particle size of 1.68 mm) when compared to media with no additional N source. However, strain IE-8 produced the highest levels of all enzymes: xylanases (5.79 IU/g dry wt on heterogeneous particles) and cellulases (0.18 IU/g dry wt on smallest particles), both without the addition of AS. The highest laccase activity (0.040 IU/g dry wt) was obtained on particles of 1.68 mm in the presence of AS. Since effect of particle size and addition AS was different for each strain, these criteria should be considered for diverse biotechnological applications.

Enhanced PHB production and scale up studies using cheese whey in fed batch culture of Methylobacterium sp. ZP24

Methylobacterium sp. ZP24 produced polyhydroxybutyrate (PHB) from disaccharides like lactose and sucrose. As Methylobacterium sp. ZP24 showed growth associated PHB production, an intermittent feeding strategy having lactose and ammonium sulfate at varying concentration was used towards reaching higher yield of the polymer. About 1.5-fold increase in PHB production was obtained by this intermittent feeding strategy. Further increase in PHB production by 0.8-fold could be achieved by limiting the dissolved oxygen (DO) levels in the fermenter. The decreased DO is thought to increase flux of acetyl CO-A towards PHB accumulation over TCA cycle. Cheese whey, a dairy waste product and being a rich source of utilizable sugar and other nutrients, when used in the bioreactor as a main substrate replacing the lactose, led to further increase in the PHB production by 2.5-fold. A total of 4.58-fold increase in the PHB production was obtained using limiting DO conditions with processed cheese whey supplemented with ammonium sulfate in fed batch culture of Methylobacterium sp. ZP24. The present investigation therefore reflects on the possibility of developing a cheap biological route for production of green thermoplastics.

Integration of global signaling pathways, cAMP-PKA, MAPK and TOR in the regulation of FLO11

The budding yeast, Saccharomyces cerevisiae, responds to various environmental cues by invoking specific adaptive mechanisms for their survival. Under nitrogen limitation, S. cerevisiae undergoes a dimorphic filamentous transition called pseudohyphae, which helps the cell to forage for nutrients and reach an environment conducive for growth. This transition is governed by a complex network of signaling pathways, namely cAMP-PKA, MAPK and TOR, which controls the transcriptional activation of FLO11, a flocculin gene that encodes a cell wall protein. However, little is known about how these pathways co-ordinate to govern the conversion of nutritional availability into gene expression. Here, we have analyzed an integrative network comprised of cAMP-PKA, MAPK and TOR pathways with respect to the availability of nitrogen source using experimental and steady state modeling approach. Our experiments demonstrate that the steady state expression of FLO11 was bistable over a range of inducing ammonium sulphate concentration based on the preculturing condition. We also show that yeast switched from FLO11 expression to accumulation of trehalose, a STRE response controlled by a transcriptional activator Msn2/4, with decrease in the inducing concentration to complete starvation. Steady state analysis of the integrative network revealed the relationship between the environment, signaling cascades and the expression of FLO11. We demonstrate that the double negative feedback loop in TOR pathway can elicit a bistable response, to differentiate between vegetative growth, filamentous growth and STRE response. Negative feedback on TOR pathway function to restrict the expression of FLO11 under nitrogen starved condition and also with re-addition of nitrogen to starved cells. In general, we show that these global signaling pathways respond with specific sensitivity to regulate the expression of FLO11 under nitrogen limitation. The holistic steady state modeling approach of the integrative network revealed how the global signaling pathways could differentiate between multiple phenotypes.

Feasibility of nitrification/denitrification in a sequencing batch biofilm reactor with liquid circulation applied to post-treatment

An investigation was performed on the biological removal of ammonium nitrogen from synthetic wastewater by the simultaneous nitrification/denitrification (SND) process, using a sequencing batch biofilm reactor (SBBR). System behavior was analyzed as to the effects of sludge type used as inoculum (autotrophic/heterotrophic), wastewater feed strategy (batch/fed-batch) and aeration strategy (continuous/intermittent). The presence of an autotrophic aerobic sludge showed to be essential for nitrification startup, despite publications stating the existence of heterotrophic organisms capable of nitrifying organic and inorganic nitrogen compounds at low dissolved oxygen concentrations. As to feed strategy, batch operation (synthetic wastewater containing 100 mg COD/L and 50 mg N-NH(4)(+)/L) followed by fed-batch (synthetic wastewater with 100 mg COD/L) during a whole cycle seemed to be the most adequate, mainly during the denitrification phase. Regarding aeration strategy, an intermittent mode, with dissolved oxygen concentration of 2.0mg/L in the aeration phase, showed the best results. Under these optimal conditions, 97% of influent ammonium nitrogen (80% of total nitrogen) was removed at a rate of 86.5 mg N-NH(4)(+)/Ld. In the treated effluent only 0.2 mg N-NO(2)(-)/L,4.6 mg N-NO(3)(-)/L and 1.0 mg N-NH(4)(+)/L remained, demonstrating the potential viability of this process in post-treatment of wastewaters containing ammonium nitrogen.

Optimization of polyhydroxybutyrate production from a wild type and two mutant strains of Rhodobacter sphaeroides using statistical method

Interaction studies using central composite design (CCD) gave the optimum concentrations of acetate at 4 g l(-1) and (NH4)2SO4 at 0.01 g l(-1) with an optimum temperature of 35 degrees C. Rhodobacter sphaeroides N20 gave the highest PHB (7.8 g l(-1)) and biomass (DCW) (8.2 g l(-1)) values compared to the wild type strain and the mutant strain U7. The CCD results predicted that the optimum medium for the mutant strain N20 consisted of 3.90 g l(-1) acetate, 0.01 g l(-1) (NH4)2SO4 at 33.5 degrees C (R2=0.985). Validation of this model by culturing the mutant strain in this optimum medium exhibited similar values of PHB (7.76 g l(-1)), biomass (8.32 g l(-1)) and the PHB content in the cell 93.2% of DCW. Similar amounts of PHB were also obtained in batch fermentations using a 5-l bioreactor. The effect of pH and aeration rate was also studied and the optimum values were found to be pH 7.0 with an aeration rate of 1.0 vvm. Under these optimal conditions, strain N20 produced the highest amount of PHB production (8.76 g l(-1)), PHB content (95.4% of DCW) as well as the product yield (Yp/x) (0.72). These results are the highest values ever obtained from photosynthetic bacteria reported so far.

Fatty acid and carotenoid production by Sporobolomyces ruberrimus when using technical glycerol and ammonium sulfate

The production of carotenoids, lipid content, and fatty acid composition were all studied in a strain of Sporobolomyces ruberrimus when using different concentrations of technical glycerol as the carbon source and ammonium sulfate as the nitrogen source. The total lipids represented an average of 13% of the dry weight, and the maximum lipids were obtained when using 65.5 g/l technical glycerol (133.63 mg/ g). The optimal conditions for fatty acid production were at 27 degrees C using 20 g of ammonium sulfate and a pH range from 6 to 7, which produced a fatty acid yield of 32.5+/-1 mg/g, including 1.27+/- 0.15 mg of linolenic acid (LNA), 7.50+/-0.45 mg of linoleic acid (LLA), 5.50+/-0.35 mg of palmitic acid (PA), 0.60+/-0.03 mg of palmitoleic acid (PAL), 1.28+/-0.11 mg of stearic acid (SA), 9.09+/-0.22 mg of oleic acid, 2.50+/-0.10 mg of erucic acid (EA), and 4.25+/-0.20 mg of lignoceric acid (LCA), where the palmitic, oleic, and linoleic acids combined formed about 37% of the total fatty acids. The concentration of total carotenoids was 2.80 mg/g when using 20 g of ammonium sulfate, and consisted of torularhodin (2.70 mg/g) and beta-carotene (0.10 mg/ g), at 23 degrees C and pH 6. However, the highest amount with the maximum specific growth rate was obtained (micromax=0.096 h(-1)) with an ammonium sulfate concentration of 30 g/l.

Dynamics of 15N natural abundance in wood-decomposing fungi and their ecophysiological implications

Nine species of basidiomycota and one species of ascomycota were grown in an ammonium sulphate media and on beech wood; and the general (15)N dynamic patterns of the hyphae were examined. The fungal body initially became depleted in (15)N in both the types of incubation. However, the underlying mechanisms were quite different, that is, significant fungal (15)N drop on the beech wood is associated with the fungal N reallocation and the uptake of atmospheric ammonia and/or NO(x), in addition to isotope fractionation during assimilation. Although the (15)N values of the wood-decomposing basidiocarps were generally close to the (15)N values of the wood, it does not always indicate that the wood derived N was the sole N source for the fungi throughout the growth periods as shown in our wood-decomposing experiment.

Purification and characterization of extracellular beta-glucosidase from Sinorhizobium kostiense AFK-13 and its algal lytic effect on Anabaena flos-aquae

A beta-glucosidase from the algal lytic bacterium Sinorhizobium kostiense AFK-13, grown in complex media containing cellobiose, was purified to homogeneity by successive ammonium sulfate precipitation, and anion-exchange and gel-filtration chromatographies. The enzyme was shown to be a monomeric protein with an apparent molecular mass of 52 kDa and isoelectric point of approximately 5.4. It was optimally active at pH 6.0 and 40'C and possessed a specific activity of 260.4 U/mg of protein against 4-nitrophenyl-beta-D-glucopyranoside (pNPG). A temperature-stability analysis demonstrated that the enzyme was unstable at 50 degrees C and above. The enzyme did not require divalent cations for activity, and its activity was significantly suppressed by Hg+2 and Ag+, whereas sodium dodecyl sulfate (SDS) and Triton X-100 moderately inhibited the enzyme to under 70% of its initial activity. In an algal lytic activity analysis, the growth of cyanobacteria, such as Anabaena flos-aquae, A. cylindrica, A. macrospora, Oscillatoria sancta, and Microcystis aeruginosa, was strongly inhibited by a treatment of 20 ppm/disc or 30 ppm/disc concentration of the enzyme.

Biosynthesis of polyhydroxybutyrate (PHB) and extracellular polymeric substances (EPS) by Ralstonia eutropha ATCC 17699 in batch cultures

The production of polyhydroxybutyrate (PHB) and extracellular polymeric substances (EPS) by Ralstonia eutropha ATCC 17699 at various glucose and (NH4)2SO4 concentrations in batch cultures were investigated. The biosynthesis of EPS by R. eutropha closely coupled with cell growth, while PHB was synthesized only under nitrogen-deficient and cell-growth-limited conditions. Experimental results show that the specific PHB production rate had an exponential correlation with both specific cell growth rate and EPS production rate. Furthermore, PHB was observed as the main storage of carbon and energy source by R. eutropha under nitrogen-limited conditions. In addition, experiments were conducted based on central composite design to optimize the batch culture for a high PHB yield. The PHB yield on glucose reached a maximum value of 0.34 g/g at glucose concentrations of 38.2 g/l and (NH4)2SO4 of 3.2 g/l.

Mixture design as a first step for optimization of fermentation medium for cutinase production from Colletotrichum lindemuthianum

Cutinase enzymes from fungi have found diverse applications in industry. However, most of the available literature on cutinase production is related to the cultivation of genetically engineered bacteria or yeast cells. In the present study, we use mixture design experiments to evaluate the influence of six nutrient elements on production of cutinase from the fungus Colletotrichum lindemuthianum. The nutritional elements were starch, glucose, ammonium sulfate, yeast extract, magnesium sulfate, and potassium phosphate. In the experimental design, we imposed the constraints that exactly one factor must be omitted in each set of experiments and no factor can account for more than one third of the mixture. Thirty different sets of experiments were designed. Results obtained showed that while starch is found to have negative influence on the production of the enzyme, yeast extract and potassium phosphate have a strong positive influence. Magnesium sulfate, ammonium sulfate, and glucose have low positive influence on the enzyme production. Contour plots have also been created to obtain information concerning the interaction effects of the media components on enzyme production.

Effect of the addition of nitrogen sources to cassava fiber and carbon-to-nitrogen ratios on Agaricus brasiliensis growth

The same substratum formulation to grow Agaricus bisporus has been used to grow Agaricus brasiliensis since its culture started in Brazil. Despite being different species, many of the same rules have been used for composting or axenic cultivation when it comes to nitrogen content and source in the substrate. The aim of this study was to verify the mycelial growth of A. brasiliensis in different ammonium sulfate and (or) urea concentrations added to cassava fiber and different carbon-to-nitrogen (C:N) ratios to increase the efficiency of axenic cultivation. Two nitrogen sources (urea and (or) ammonium sulfate) added to cassava fiber were tested for the in vitro mycelial growth in different C:N ratios (ranging from 2.5:l to 50:l) in the dark at 28 °C. The radial mycelial growth was measured after 8 days of growth and recorded photographically at the end of the experiment. Nitrogen from urea enhanced fungal growth better than ammonium sulfate or any mixture of nitrogen. The best C:N ratios for fungal growth were from 10:l to 50:l; C:N ratios below 10:l inhibited fungal growth.Key words: Agaricus brasiliensis, Agaricus blazei, Agaricus subrufescens, nitrogen, C:N ratio.

Accumulation of ammonium in Norway spruce (Picea abies) seedlings measured by in vivo 14N-NMR

(14)N-NMR and (31)P-NMR have been used to monitor the in vivo pH in roots, stems, and needles from seedlings of Norway spruce, a typical ammonium-tolerant plant. The vacuolar and cytoplasmic pH measured by (31)P-NMR was found to be c. pH 4.8 and 7.0, respectively, with no significant difference between plants growing with ammonium or nitrate as the N-source. The (1)H-coupled (14) NH 4+ resonance is pH-sensitive: at alkaline pH it is a narrow singlet line and below pH 4 it is an increasing multiplet line with five signals. The pH values in ammonium-containing compartments measured by (14)N-NMR ranged from 3.7 to 3.9, notably lower than the estimated pH values of the P(i) pools. This suggests that, in seedlings of Norway spruce, ammonium is stored in vacuoles with low pH possibly to protect the seedlings against the toxic effects of ammonium ( NH 4+) or ammonia (NH3). It was also found that concentrations of malate were 3-6 times higher in stems than in roots and needles, with nitrate-grown plants containing more malate than plants grown with ammonium.

Global Gene Expression Profiling of Bacillus subtilis in Response to Ammonium and Tryptophan Starvation as Revealed by Transcriptome and Proteome Analysis

The global gene expression profile of Bacillus subtilis in response to ammonium and tryptophan starvation was analyzed using transcriptomics and proteomics which gained novel insights into these starvation responses. The results demonstrate that both starvation conditions induce specific, overlapping and general starvation responses. The TnrA regulon, the glutamine synthetase (glnA) as well as the sigma(L)-dependent bkd and roc operons were most strongly and specifically induced after ammonium starvation. These are involved in the uptake and utilization of ammonium and alternative nitrogen sources such as amino acids, gamma-aminobutyrate, nitrate/nitrite, uric acid/urea and oligopeptides. In addition, several carbon catabolite-controlled genes (e.g. acsA, citB), the alpha-acetolactate synthase/-decarboxylase alsSD operon and several aminotransferase genes were specifically induced after ammonium starvation. The induction of sigma(F)- and sigma(E)-dependent sporulation proteins at later time points in ammonium-starved cells was accompanied by an increased sporulation frequency. The specific response to tryptophan starvation includes the TRAP-regulated tryptophan biosynthesis genes, some RelA-dependent genes (e.g. adeC, ald) as well as spo0E. Furthermore, we recognized overlapping responses between ammonium and tryptophan starvation (e.g. dat, maeN) as well as the common induction of the CodY and sigma(H) general starvation regulons and the RelA-dependent stringent response. Many genes encoding proteins of so far unknown functions could be assigned to specifically or commonly induced genes.

Location of the cell-binding domain of CP65, a 65kDa cysteine proteinase involved in Trichomonas vaginalis cytotoxicity

The cysteine proteinase (CP) of 65kDa, CP65, binds to the surface of HeLa cells and is involved in Trichomonas vaginalis cellular damage. To identify and locate the CP65 cellular-binding domain, we enriched the CP65 protein band by ammonium sulfate fractionation and ion-exchange chromatography and the N-terminal sequence was obtained. A 618bp gene fragment was obtained by PCR using genomic DNA as template and primers derived from the N-terminal sequence of CP65 and the Asn papain-catalytic conserved region. This gene fragment encodes for 206 amino acid (aa) residues corresponding to the N-terminal region of a mature CP with 67-76% identity to the reported trichomonad cathepsin-L-like CPs. This gene fragment was expressed in a bacterial system for antibody production and functional analysis. Antibodies against the native trichomonad CP65 recognized the recombinant protein, referred to as rCP65, confirming its relationship with the CP65 gene. The rCP65 protein was bound to the surface of HeLa cells and competed with the native CP65 for binding. Antibodies to the rCP65 (alpha-rCP65) reacted with the trichomonad CP65 located on the parasite surface, and inhibited trichomonal cytotoxicity in a concentration-dependent manner. These data strongly suggest that this gene fragment encodes for the putative cell-binding domain (CBD) of CP65 located at its N-terminal region.

Bone mineral response to ammonium sulphate offered as a lick supplement in beef calves

Sixteen Bonsmara calves (4 males, 12 females) between 10 and 18 months of age were blocked according to age and sex and randomly assigned to 2 groups. They were offered licks containing bone meal and salt (50:50 ratio) (control) and bone meal and ammonium sulphate (NH4SO4) at 1.25, 2.5, 5, 10, 15, and 18 % (treatment) to evaluate the effects of dietary anions on bone phosphate (P) concentration. Bone P concentration was significantly (P0.05) higher in the NH4SO4 group compared with the control group, indicating that NH4SO4 was able to increase the P content of bone at each of the 6 concentrations used in the lick relative to the control animals, thereby improving the P status of the animals. Ammonium sulphate at 15% and 18% in the lick also significantly (P 0.05) increased bone P compared with the lower concentrations of NH4SO4. Bone calcium (Ca) fluctuated as a result of the acidogenic lick. There was absorption of Ca when P was being resorbed and resorption of Ca when P was being absorbed into and out of bone. Bone Ca:P ratio ranged from 3.2 to 6.4 among the control group and 1.6 to 4.3 among the treatment group. Animals receiving the acidogenic lick had a higher percentage ash compared to the control group for most of the experimental period. Bone magnesium (Mg) fluctuated in response to the acidogenic lick, and it was difficult to show a relationship between bone Mg and Ca or P. The overall mean cortical bone thickness was significantly (P 0.05) greater in treatment (1.60 mm) compared with control (1.43 mm) calves and this was also true at sampling periods 2, 4, 5 and 6. Bone thickness followed bone P and not bone Ca. Results from this research indicate that the addition of ammonium sulphate to a lick had a beneficial effect in improving the P status by increasing bone P and improving the mineral status of bone by increasing the thickness of cortical bone and percentage ash.

A simplified method for purification of recombinant soluble DnaA proteins

An improved, simplified method for the purification of recombinant, tagged DnaA proteins is described. The presented protocol allowed us to purify soluble DnaA proteins from two different bacterial species: Helicobacter pylori and Streptomyces coelicolor, but it can most likely also be used for the isolation of DnaA proteins from other bacteria, as it was adapted for Mycobacterium tuberculosis DnaA. The isolation procedure consists of protein precipitation with ammonium sulphate followed by affinity chromatography. The composition of the buffers used at each purification step is crucial for the successful isolation of the recombinant DnaA proteins. The universality of the method in terms of its application to differently tagged proteins (His-tagged or GST-tagged) as well as different properties of purified proteins (e.g., highly aggregating truncated forms) makes the protocol highly useful for all studies requiring purified and active DnaA proteins.

Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization

The objective of this study was to explore the long-term effects of different organic and inorganic fertilizers on activity and composition of the denitrifying and total bacterial communities in arable soil. Soil from the following six treatments was analyzed in an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO3)2, (NH4)2SO4, and unfertilized and unfertilized bare fallow. All plots but the fallow were planted with corn. The activity was measured in terms of potential denitrification rate and basal soil respiration. The nosZ and narG genes were used as functional markers of the denitrifying community, and the composition was analyzed using denaturing gradient gel electrophoresis of nosZ and restriction fragment length polymorphism of narG, together with cloning and sequencing. A fingerprint of the total bacterial community was assessed by ribosomal intergenic spacer region analysis (RISA). The potential denitrification rates were higher in plots treated with organic fertilizer than in those with only mineral fertilizer. The basal soil respiration rates were positively correlated to soil carbon content, and the highest rates were found in the plots with the addition of sewage sludge. Fingerprints of the nosZ and narG genes, as well as the RISA, showed significant differences in the corresponding communities in the plots treated with (NH4)2SO4 and sewage sludge, which exhibited the lowest pH. In contrast, similar patterns were observed among the other four treatments, unfertilized plots with and without crops and the plots treated with Ca(NO3)2 or with manure. This study shows that the addition of different fertilizers affects both the activity and the composition of the denitrifying communities in arable soil on a long-term basis. However, the treatments in which the denitrifying and bacterial community composition differed the most did not correspond to treatments with the most different activities, showing that potential activity was uncoupled to community composition.

Negative second virial coefficients as predictors of protein crystal growth: evidence from sedimentation equilibrium studies that refutes the designation of those light scattering parameters as osmotic virial coefficients

The effects of ammonium sulphate concentration on the osmotic second virial coefficient (BAA/MA) for equine serum albumin (pH 5.6, 20 degrees C) have been examined by sedimentation equilibrium. After an initial steep decrease with increasing ammonium sulphate concentration, BAA/MA assumes an essentially concentration-independent magnitude of 8-9 ml/g. Such behaviour conforms with the statistical-mechanical prediction that a sufficient increase in ionic strength should effectively eliminate the contributions of charge interactions to BAA/MA but have no effect on the covolume contribution (8.4 ml/g for serum albumin). A similar situation is shown to apply to published sedimentation equilibrium data for lysozyme (pH 4.5). Although termed osmotic second virial coefficients and designated as such (B22), the negative values obtained in published light scattering studies of both systems have been described incorrectly because of the concomitant inclusion of the protein-salt contribution to thermodynamic nonideality of the protein. Those negative values are still valid predictors of conditions conducive to crystal growth inasmuch as they do reflect situations in which there is net attraction between protein molecules. However, the source of attraction responsible for the negative virial coefficient stems from the protein-salt rather than the protein-protein contribution, which is necessarily positive.