Degradation of chromosomal proteins during dissociation and reconstitution of chromatin

Histones and nonhistone chromosomal proteins are degraded when chromatin is exposed to 2 M NaCl-5 M urea (pH 6–8) which has been most often used for disscciation and reconstitution of chromatin. Histones and nonhistone proteins are also degraded in 5 M urea (pH 6–8).     

Effects of low urea concentrations on protein-water interactions

Solvent properties of aqueous media (dipolarity/polarizability, hydrogen bond donor acidity, and hydrogen bond acceptor basicity) were measured in the coexisting phases of Dextran–PEG aqueous two-phase systems (ATPSs) containing .5 and 2.0 M urea. The differences between the electrostatic and hydrophobic properties of the phases in the ATPSs were quantified by analysis of partitioning of the homologous series of sodium salts of dinitrophenylated amino acids with aliphatic alkyl side chains. Furthermore, partitioning of eleven different proteins in the ATPSs was studied. The analysis of protein partition behavior in a set of ATPSs with protective osmolytes (sorbitol, sucrose, trehalose, and TMAO) at the concentration of .5 M, in osmolyte-free ATPS, and in ATPSs with .5 or 2.0 M urea in terms of the solvent properties of the phases was performed. The results show unambiguously that even at the urea concentration of .5 M, this denaturant affects partitioning of all proteins (except concanavalin A) through direct urea–protein interactions and via its effect on the solvent properties of the media. The direct urea–protein interactions seem to prevail over the urea effects on the solvent properties of water at the concentration of .5 M urea and appear to be completely dominant at 2.0 M urea concentration.     

Elucidation of stable intermediates in urea-induced unfolding pathway of human carbonic anhydrase IX

Human carbonic anhydrase IX (CAIX) has evolved as a promising biomarker for cancer prognosis, due to its overexpression in various cancers and restricted expression in normal tissue. However, limited information is available on its biophysical behavior. The unfolding of CAIX in aqueous urea solution was studied using all-atom molecular dynamics simulation approach. The results of this study revealed a stable intermediate state along the unfolding pathway of CAIX. At intermediate concentrations of urea (2.0–4.0 M), the protein displays a native-like structure with a large population of its secondary structure and hydrophobic contacts remaining intact in addition to small confined overall motions. Beyond 4.0 M urea, the unfolding is more gradual and at 8.0 M urea the structure is largely collapsed due to the solvent effect. The hydrophobic contact analysis suggests that the contact in terminal α-helices is separated initially which propagates in the loss of contacts from centrally located β-sheets. The reduction of 60–65% tertiary contacts in 7.0–8.0 M urea suggested the presence of residual structure in unfolded state and is confirmed with structural snap shot. Free energy landscape analysis suggested that unfolding of CAIX exists through the different intermediate states.     

Enhancement of nitrogen release properties of urea–kaolinite fertilizer with chitosan binder

The use of controlled release fertilizer (CRF) has become a new trend to minimize environmental pollution. In this study, urea–kaolinite containing 20 wt% urea after one hour dry grinding was mixed with different concentrations of chitosan as a binder to prepare nitrogen-based CRF. Fourier transform infrared spectroscopy confirmed the hydrogen bonding between urea and kaolinite. Covalent interaction between urea–kaolinite and chitosan make the granules stronger. The nitrogen release was measured in 5 days interval using a diacetylmonoxime calorimetric method at a wavelength of 527 nm. The results illustrated that by increasing the chitosan concentration from 3 to 7.5%, nitrogen release decreased from 41.23 to 25.25% after one day and from 77.31 to 59.27% after 30 days incubation in water. Compressive stress at break tests confirmed that granules with chitosan 6% had the highest resistance and were chosen for ammonia volatilization tests. Ammonia volatilization was carried out using the forced-draft technique for a period of 10 weeks. The results showed that the total amount of ammonia loss for conventional urea fertilizer and urea–kaolinite–chitosan granules was 68.63 and 56.75%, respectively. This controlled release product could be applied in agricultural crop production purpose due to its controlled solubility in the soil, high nutrient use efficiency and potential economic benefits.     

The ornithine cycle enzyme arginase from Agaricus bisporus and its role in urea accumulation in fruit bodies

An extensive survey of higher fungi revealed that members of the family Agaricaceae, including Agaricus bisporus, accumulate substantial amounts of urea in their fruit bodies. An important role of the ornithine cycle enzymes in urea accumulation has been proposed. In this work, we present the cloning and sequencing of the arginase gene and its promoter region from A. bisporus. A PCR-probe based on fungal arginase was used to identify the A. bisporus arginase gene from a cDNA library. The arginase cDNA encodes a 311-aa protein which is most likely expressed in the cytosol. Expression of the cDNA in Escherichia coli was established as a His-tagged fusion protein. The arginase gene was used as a molecular marker to study expression and regulation during sporophore formation and postharvest development. The expression of the arginase gene was significantly up-regulated from developmental stage 3 onwards for all the tissues studied. A maximum of expression was reached at stage 6 for both stipe and cap tissue. In postharvest stages 5, 6 and 7 the level of expression observed was similar to normal growth stages 5, 6 and 7. A good correlation was found between arginase expression and urea content of stipe, velum, gills, cap and peel tissue. For all tissues the urea content decreased over the first four stages of development. From stage 4 onwards urea accumulated again except for stipe tissue where no significant changes were observed. The same trend was also observed for postharvest development, but the observed increase of urea in postharvest tissues was much higher.     

Antibodies to 5 M urea soluble chromosomal proteins from HeLa cells

The tissue specificity of a chromosomal protein fraction, extractable from chromatin with 5 M urea at low ionic strength, has been examined in HeLa, A549 and HT 29 cells. Electrophoresis in polyacrylamide gels indicates that each cell type has a different content of 5 M urea soluble proteins which are distinguishable from the histones, from the tight DNA-binding proteins and from the high-mobility-group chromosomal proteins. Antibodies against 5 M urea soluble proteins extracted from HeLa cells were produced in mice. Although each of the mice tested prior to immunization contained a detectable amount of antibodies against both the 5 M urea soluble proteins and tight DNA-binding proteins, immunization elevated the level of the antibodies in the serum over 100-fold. The antibodies do not distinguish between the 5 M urea extracts obtained from different sources because most of the antibodies are directed against antigens shared by the cells studied. Immunofluorescence studies reveal that components which cross-react with 5 M urea soluble chromosomal proteins are also present in the cytoplasm. We conclude the following. (1) 5 M urea extracts from chromatin a group of proteins which differs among cells. (2) Mice contain detectable amounts of autoantibodies against these chromosomal proteins. (3) Immunization with the 5 M urea extractable fraction elicits antibodies against a restricted number of antigenic components which are shared among the cells studied. (4) 5 M urea extractable proteins are found both in the nucleus and cytoplasm; part of these may be cytoskeletal elements. Because the antisera do not react with histones, high-mobility-group proteins and tight DNA-binding proteins, they may be used for various functional studies on the 5 M urea extractable chromosomal protein fraction.     

Experimental studies on continuous hypothermic liver perfusion with a synthetic solution containing gelatin polypeptides (Haemaccel)

A rat liver model has been developed for studying preservation by continuous hypothermic perfusion. Perfusion for 5 and 24 hr with a defined solution containing Haemaccel as colloid at a temperature of 5–7 °C was found to result in good preservation of the metabolic activity of the livers as assessed by the ability of the tissue to synthesize urea and take up galactose. In common with other continuous perfusion methods, there was increasing evidence of cell damage as perfusion progressed, and there was an associated depletion of cellular K⁺ and an increase in tissue water content. There was a considerable increase in vascular resistance, as indicated by a fall in flow rate at a constant pressure in the later stages of perfusion, similar to that which has been reported in other liver preservation experiments using plasma derivatives or Dextran. Further studies are envisaged to attempt to analyze, in a controlled fashion, the nature of the damage incurred by the liver during storage and the requirements for maintenance of a viable graft at hypothermia.     

A two-dimensional gel electrophoretic procedure for the separation of complex mixtures of 4–12S RNAs

A two-dimensional gel electrophoretic method suitable for the separation of complex mixtures of RNA species in the size range of 4 to 12 S is described. A 3.6–11% polyacrylamide gradient gel containing a gradient of 0–7 m urea was used in the first dimension, and a transverse 3.6–22.6% polyacrylamide gradient gel containing 5 m urea was used in the second dimension. The method was applied to the separation of total cytoplasmic RNAs from a cellular slime mold. In this method reproducible fingerprints were obtained by the use of visible-marker RNA.     

Effect of major liver resection on hepatic ureagenesis in humans

Changes in hepatic ureagenesis following major hepatectomy are not well characterized. We studied the relation between urea synthesis and liver mass before and after major hepatectomy in humans. Fifteen patients scheduled for resection of malignancies in otherwise healthy livers were studied. Pre- and postoperative liver volume was assessed by computerized tomography-volumetry. During surgery, a primed, continuous infusion of [(13)C]urea was administered intravenously, and arterial blood samples were obtained hourly. Indocyanine green clearance was determined before and after resection. Seven patients underwent major hepatectomy, and eight patients underwent minor [<5% functional liver volume (total volume -- tumor volume)] or no resection, serving as controls. Resected functional liver volume in the major hepatectomy group averaged 60%. Urea synthesis per gram of functional liver tissue increased 2.6-fold following major hepatectomy, maintaining whole body urea synthesis. Arterial ammonia remained unchanged throughout the study, whereas following hepatectomy a hyperaminoacidemia occurred. In conclusion, immediately following major hepatectomy, urea synthesis per gram of functional liver tissue increases rapidly and proportionately to the amount of liver tissue resected, maintaining whole body urea synthesis at preoperative levels. This rapid and complete adaptation suggests that the capacity of urea synthesis is not limiting the maximum resectable volume in otherwise healthy livers.     

Effects of exercise on nitrogen excretion, carbamoyl phosphate synthetase III activity and related urea cycle enzymes in muscle and liver tissues of juvenile rainbow trout (Oncorhynchus mykiss).

The purpose of this study was to determine if carbamoyl phosphate synthetase III (CPSase III) and related urea cycle enzyme activities in skeletal muscle tissue of juvenile rainbow trout (Oncorhynchus mykiss) increase during short- or long-term exercise, in parallel with changes in whole-body urea excretion rates. Urea excretion was elevated by 65% in fish that swam at high-speed (50 cm/s) vs. low-speed (20 cm/s) over a 2-h period, with no significant changes in CPSase III, ornithine transcarbamoylase or glutamine synthetase activities in muscle tissue. Fish that swam for 4 days at high-speed had higher rates of ammonia excretion and GSase activity in muscle and liver tissue relative to low-speed swimmers. Calculations showed that 47-53% of excreted urea, theoretically could be accounted for by total muscle CPSase III activity in juvenile and adult trout. The data indicate that increases in the rate of urea excretion during short-term high intensity exercise are not linked to higher activities of urea cycle enzymes in muscle tissue, but this does not rule out the possibility of increased flux through muscle CPSase III and related enzymes. Furthermore, these results indicate that urea cycle enzyme activities in skeletal muscle tissue can account for a significant portion of total urea excretion in juvenile and adult trout.     

Urea tolerance and osmoregulation in Bufo viridis and Rana ridibunda

1. The tolerance and adaptation to urea solutions by terrestrial green toads (Bufo viridis) and semi-aquatic frogs (Rana Ridibunda) were studied. 2. the green toad showed tolerance to urea solution of 800 mM and the frogs showed tolerance only to about 400 mM urea solution. 3. The plasma concentrations of both species was hyperosmotic to the external medium in all the different urea solutions. 4. Blood osmolality, urea, Na+ and Cl- concentrations of B. viridis were always higher than in R. ridibunda. 5. The urea concentration in muscle of R. ridibunda was higher than the urea concentration in muscle of B. viridis. 6. The muscle tissue weight loss of B. viridis was significantly lower than R. ridibunda.     

Effect of nitrates supplied with the transpiration flow on assimilate translocation

Solutions of nitrates (0.5% KNO₃, 0.2% NH₄NO₃) or urea (0.15%) were fed under the pressure of 10⁴ Pa to 50–60-cm-long detached shoots of common flax (Linum usitatissimum L.). One hour after the start of supplying the solutions, an assimilation clip chamber was fastened to the middle part of the shoot (¹⁴C source area), and ¹⁴CO₂ was blown through in the light for 2.5 min. The analysis of distribution of ¹⁴C among the labeled products of photosynthesis produced by source leaves showed that nitrates reduced the incorporation of the label into sucrose. At the same time, the ratio of labeled sucrose to labeled hexoses decreased, and the incorporation of the label into serine greatly increased. Urea did not produce such effects. The pattern of distribution of ¹⁴C within the plant 3 h after the assimilation of ¹⁴CO₂ points to the suppression of assimilate efflux from the leaves of plants fed with nitrates. In plants supplied with water or urea, 17–20% of labeled carbon was found below the ¹⁴C source area of the shoot, in nitrate type of treatment, only 3–5% was found there. In plants supplied with nitrates, the cortex tissue below the source leaf contained more ¹⁴C in proteins and less in low-molecular substances. In the wood tissue, such a correlation was not observed. When the shoot was supplied with water or urea, the content of ¹⁴C in sucrose in the source leaves in 3 h declined from 55–60% to 38–42%. When the shoot was fed with nitrates, the share of label in sucrose increased from 50 to 62–73%. Autoradiography of the source leaves showed that, in plants supplied with water or urea, the label was predominantly accumulated in large vascular bundles, and in nitrate type of treatment, it was accumulated outside large bundles. Electron microscopy showed that, in nitrate plants, the companion cells of phloem endings were very much vacuolated.     

Contribution of several nitrogen sources to growth of Alexandrium catenella during blooms in Thau lagoon,southern France

A monitoring program with a weekly sampling frequency over a 15-month period indicates that urea concentrations above a certain threshold level may trigger the blooms of Alexandrium catenella in Thau lagoon. However, urea concentrations were also sometimes related to ammonium and dissolved organic nitrogen concentrations, indicating that the role of urea may not be a direct one. An original approach is used to assess the relative contribution of several nitrogen sources (nitrate, nitrite, ammonium, urea) to growth of A. catenella by comparing nitrogen uptake rates to nitrogen-based growth rates estimated from dilution experiments during four blooms over a 4-year period (2001–2004) in Thau lagoon. Nitrate and nitrite contributed 0.1–14% and 0.1–5% respectively of growth requirements. Ammonium and urea were the main N sources fueling growth of A. catenella (30–100% and 2–59%, respectively). Indirect estimates indicated that an unidentified N source could also contribute significantly to growth at specific times. Concerning ammonium and urea uptake kinetics, half-saturation constants varied between 0.2 and 20 μgat N L⁻¹ for ammonium and between 0.1 and 44 μgat N L⁻¹ over the 4-year period, indicating that A. catenella can have a competitive advantage over other members of the phytoplankton even under low concentrations of ammonium and urea. However, the observed large changes in ammonium and urea uptake kinetics on a short time scale (days) during blooms preclude more precise estimates of those contributions to growth and require further investigation.     

Changes in hexokinase activity during muscle alteration

Changes in extractability and activity of hexokinase (HK) were studied under the action of heating and of urea on skeletal muscles of Rana temporaria L., and besides the stability of this enzyme in muscle extract to those agents in vitro was examined. Under a 15 minutes heating of muscle, a decrease in extractability (the activity calculated for 1 g of tissue) and activity (the activity calculated for 1 mg of protein) of hexokinase is first revealed at 37 degrees C. Then the enzyme extractability decreases gradually in accordance to the decrease in extractability of the total water-soluble protein; the level of hexokinase activity attained at 37 degrees does not change up to 40 degrees. At 42 degrees the activity of the enzyme is completely inhibited. Under the heating of the muscle extract, the decrease of enzyme activity takes place at 36 degrees, the level achieved being stable up to 42 degrees C. Under the action of urea on the muscle at the reversible phase of alteration (1 M urea from 5 minutes to 2 hours at room temperature, 1 M urea for 9 hours at + 4 degrees C), hexokinase activity increases, calculated for 1 g of tissue and for 1 mg of protein. Under the irreversible disappearance of muscle excitability (1 M urea during 9 hours, 2 M urea during 2 hours at room temperature) no hexokinase activity was revealed. The activation of the enzyme is discussed in connection with the data on the increase of ATP content in muscle under the urea alteration. The treatment of the enzyme in muscle extract with 1 M urea decreases its activity in 30 minutes down to 67%; the level achieved does not change during 20 hours.     

Exploring the differences and similarities between urea and thermally driven denaturation of bovine serum albumin: intermolecular forces and solvation preferences

The interactions of bovine serum albumin (BSA) with urea/water were investigated by computer simulation. It was revealed that the BSA-hydrophobic residues in urea solutions favored contact with urea more than with water. Energy decomposition analysis showed that van der Waals energy was the dominant driving force behind urea affinity for hydrophobic residues, whereas coulombic attraction was largely responsible for water affinity for these residues. Meanwhile, urea–BSA hydrogen bond energies were found to be weaker than water–BSA hydrogen bond energies. The greater strength of water–BSA hydrogen bonds than urea–BSA hydrogen bonds, and the opposing preferential interaction between the BSA and urea suggest that disruption of hydrophobic interaction predominates urea–protein denaturation. In pure water, hydrophobic residues showed aggregation tendencies at 323 K, suggesting an increase in hydrophobicity, while at 353 K the residues were partly denatured due to loss of hydrogen bonds; thus, disruption of hydrophobic interactions appeared to contribute less to thermal denaturation.     

Interactions between lignin and urea researched by molecular simulation

Molecular simulations of interactions between urea molecules and lignin polymer have been carried out with the aim of understanding the mechanism of urea slow-release behaviours in lignin–urea materials. It has been found, by docking technology and natural bond orbital analysis, that H-bonds and π-electronic conjugation effect are the main driving forces to keep urea molecules adsorbed on the lignin. In the NPT (isothermal–isobaric ensemble) simulations, mean-squared displacement results show that water molecules can promote the urea molecules gradually away from the lignin. Furthermore, in NVT (canonical ensemble) molecular dynamic simulations, results on diffusion constants of urea molecules in lignin–urea system show that diffusion constant of urea molecules in a urea–water–lignin system increases with an increase in the water content. Conclusions gained from two different kinds of simulation are in agreement with each other and are consistent with the experimental observations.     

Nickel and the metabolism of urea by Lemna paucicostata Hegelm. 6746

With urea as sole nitrogen source, the addition of 5×10^-5 M nickel sulfate to axenic cultures of Lemna paucicostata 6746 approximately doubles the rate of vegetative growth. Under a standard light-dark schedule, Ni²⁺ changes the daily pattern of respiratory CO₂ output on urea from one having a single daily peak to one with two daily peaks which resembles that on ammonium or nitrate as sole nitrogen source. It also increases CO₂ output by as much as 3-fold on a fresh-weight basis. These data represent the first confirmation in an intact higher plant of proposals, based on enzymology and tissue culture responses, for a role of Ni²⁺ in urea metabolism. Further, they indicate the possible existence of two distinct pathways of urea utilization.     

Theoretical study on the structures and properties of mixtures of urea and choline chloride

In this work, we investigated in detail the structural characteristics of mixtures of choline chloride and urea with different urea contents by performing molecular dynamic (MD) simulations, and offer possible explanations for the low melting point of the eutectic mixture of choline chloride and urea with a ratio of 1:2. The insertion of urea molecules was found to change the density distribution of cations and anions around the given cations significantly, disrupting the long-range ordered structure of choline chloride. Moreover, with increasing urea concentration, the hydrogen bond interactions between choline cations and Cl^? anions decreased, while those among urea molecules obviously increased. From the hydrogen bond lifetimes, it was found that a ratio of 1:2 between choline chloride and urea is necessary for a reasonable strength of hydrogen bond interaction to maintain the low melting point of the mixture of choline chloride with urea. In addition, it was also deduced from the interaction energies that a urea content of 67.7 % may make the interactions of cation–anion, cation–urea and anion–urea modest, and thus results in the lower melting point of the eutectic mixture of choline chloride and urea. The present results may offer assistance to some extent for understanding the physicochemical properties of the eutectic mixture of choline chloride and urea, and give valuable information for the further development and application of deep eutectic solvents.     

Determination of glucose,urea and penicillin using enzyme-pH-electrodes

Conventional hydrogen ion glas electrodes have been used for the preparation of enzyme-pH-electrodes by either entrapping the enzymes within polyacrylamide gels around the electrode or as liquid layer trapped within a cellophane membrane. The enzymes were glucose oxidase, urase and penicillinase.The pH response to glucose concentration was about linear within 10^?1–10^?3 M glucose and for urea linear within 5·10^t—–5·10^?5M. The pH response to penicillin was about linear in the range from 10^?3–10^?2 M resulting in a pH shift of 1.4 units; reproduceable pH response was obtained down to concentrations of 3·10^?5 M.Studies as to the effect of buffer using an urease–pH-electrode showed a buffer concentration of 10^?2 M a substantial shift of about one pH-unit in the range of 10^?4 to 10^?2 M urea. Both urease- and penicillinase–pH-electrodes were tested as to stability showing no decrease in pH response except at high substrate concentration (1·10^?2 M) over a period of 2–3 weeks kept at room temperature.     

The crab-eating frog, Rana cancrivora, up-regulates hepatic carbamoyl phosphate synthetase I activity and tissue osmolyte levels in response to increased salinity

The crab-eating frog Rana cancrivora is one of only a handful of amphibians worldwide that tolerate saline waters. They typically inhabit brackish water of mangrove forests of Southeast Asia, but live happily in freshwater and can be acclimated to 75% seawater (25 ppt) or higher. We report here that after transfer of juvenile R. cancrivora from freshwater (1 ppt) to brackish water (10 -->20 or 20 -->25 ppt; 4-8 d) there was a significant increase in the specific activity of the key hepatic ornithine urea cycle enzyme (OUC), carbamoyl phosphate synthetase I (CPSase I). At 20 ppt, plasma, liver and muscle urea levels increased by 22-, 21-, and 11-fold, respectively. As well, muscle total amino acid levels were significantly elevated by 6-fold, with the largest changes occurring in glycine and beta-alanine levels. In liver, taurine levels were 5-fold higher in frogs acclimated to 20 ppt. There were no significant changes in urea or ammonia excretion rates to the environment. As well, the rate of urea influx (J(in) (urea)) and efflux (J(out) (urea)) across the ventral pelvic skin did not differ between frogs acclimated to 1 versus 20 ppt. Taken together, these findings suggest that acclimation to saline water involves the up-regulation of hepatic urea synthesis, which in turn contributes to the dramatic rise in tissue urea levels. The lack of change in urea excretion rates, despite the large increase in tissue-to-water gradients further indicates that mechanisms must be in place to prevent excessive loss of urea in saline waters, but these mechanisms do not include cutaneous urea uptake. Also, amino acid accumulation may contribute to an overall rise in the osmolarity of the muscle tissue, but relative to urea, the contribution is small.