Mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization

In fluorescent in situ hybridization (FISH), the efficiency of hybridization between the DNA probe and the rRNA has been related to the accessibility of the rRNA when ribosome content and cell permeability are not limiting. Published rRNA accessibility maps show that probe brightness is sensitive to the organism being hybridized and the exact location of the target site and, hence, it is highly unpredictable based on accessibility only. In this study, a model of FISH based on the thermodynamics of nucleic acid hybridization was developed. The model provides a mechanistic approach to calculate the affinity of the probe to the target site, which is defined as the overall Gibbs free energy change (DeltaG degrees overall) for a reaction scheme involving the DNA-rRNA and intramolecular DNA and rRNA interactions that take place during FISH. Probe data sets for the published accessibility maps and experiments targeting localized regions in the 16S rRNA of Escherichia coli were used to demonstrate that DeltaG degrees overall is a strong predictor of hybridization efficiency and superior to conventional estimates based on the dissociation temperature of the DNA/rRNA duplex. The use of the proposed model also allowed the development of mechanistic approaches to increase probe brightness, even in seemingly inaccessible regions of the 16S rRNA. Finally, a threshold DeltaG degrees overall of -13.0 kcal/mol was proposed as a goal in the design of FISH probes to maximize hybridization efficiency without compromising specificity.     

Permeation of volatile compounds through starch films

The aim of this study was to gain insight into the factors that affect the permeation of volatiles through starch films. These films were obtained by casting gelatinized starch/water/glycerol mixtures. The films were dried and conditioned under different conditions (temperature and relative humidity) resulting in films that vary in the degree of starch crystallinity and glycerol and water content. The permeation of two model volatiles (carvone and diacetyl) at 20 degrees C and at 30, 60, or 90% relative humidity (RH) was analyzed gravimetrically. Further, the solubility of the two model compounds (under conditions where the permeation experiments were carried out) was determined. From the obtained permeation and solubility data, the diffusion coefficients of these compounds in the different starch films were calculated. The crystallinity in the starch films increased with increasing water content of the films during preparation. The water content of the resulting films in turn increased with increasing glycerol and when the films were exposed to a higher RH during drying or conditioning. For films with the same composition, the flux for diacetyl was greater than for carvone. The solubilities of diacetyl and carvone were slightly dependent on the properties of the films. It was found that with increasing starch crystallinity the diffusion coefficient for both compounds decreases, which is probably due to the impermeability of starch crystallites. Interestingly, in films with about the same extent of crystallinity, the diffusion can be described with the free volume model, with water and glycerol determining the amount of free volume.     

Morphological characteristics and performance variables of women soccer players

The purpose of this study was to describe certain morphological characteristics of women soccer players and to examine aspects of training and performance. Twenty-two anthropometric sites were used in measurements of somatotype and body composition; flexibility, agility, anaerobic power, leg muscle power, and dynamic pulmonary functions were used as performance variables. Measurements were made on 17 professional athletes and 17 age-matched sedentary women who acted as controls. The women soccer players showed less fat content and less lean body mass than did the sedentary women. The mean somatotype for the soccer players was 3.07-3.55-2.43 and for the nonathletes was 3.57-3.35-2.90. Anaerobic power, leg muscle power, and agility in the athletes were higher than in the nonathletes, whereas no differences were found in flexibility and pulmonary functions (p > 0.05). The women soccer players showed more significantly mesomorphic, less endomorphic, least ectomorphic components and higher performance level than did the sedentary women.     

Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling?

What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of continuum Langevin dynamics models of chymotrypsin inhibitor 2. We find that residue-based additive Gō-like contact energies, although native-centric, are by themselves insufficient for protein-like calorimetric two-state cooperativity. Further native biases by local conformational preferences are necessary for protein-like thermodynamics. Kinetically, however, even models with both contact and local native-centric energies do not produce simple two-state chevron plots. Thus a model protein's thermodynamic cooperativity is not sufficient for simple two-state kinetics. The models tested appear to have increasing internal friction with increasing native stability, leading to chevron rollovers that typify kinetics that are commonly referred to as non-two-state. The free energy profiles of these models are found to be sensitive to the choice of native contacts and the presumed spatial ranges of the contact interactions. Motivated by explicit-water considerations, we explore recent treatments of solvent granularity that incorporate desolvation free energy barriers into effective implicit-solvent intraprotein interactions. This additional feature reduces both folding and unfolding rates vis-à-vis that of the corresponding models without desolvation barriers, but the kinetics remain non-two-state. Taken together, our observations suggest that interaction mechanisms more intricate than simple Gō-like constructs and pairwise additive solvation-like contributions are needed to rationalize some of the most basic generic protein properties. Therefore, as experimental constraints on protein chain models, requiring a consistent account of protein-like thermodynamic and kinetic cooperativity can be more stringent and productive for some applications than simply requiring a model heteropolymer to fold to a target structure.     

Effect of losartan on the blood-brain barrier permeability in diabetic hypertensive rats

Our previous publication has stressed the benefits of losartan, an angiotensin II receptor blocker, on the permeability of blood-brain barrier (BBB) and blood pressure during L-NAME-induced hypertension. This study reports the impacts of anti-hypertensive treatment by losartan on the brain endothelial barrier function and the arterial blood pressure, during acute hypertension episode, in experimentally diabetic hypertensive rats. Systolic blood pressure measurements were taken with tail cuff method before and during administration of L-NAME (0.5 mg/ml). We induced diabetes by using alloxan (50 mg/kg, i.p). Losartan (3 mg/kg, i.v) was given to rats following the L-NAME treatment. Acute hypertensive vascular injury was induced by epinephrine (40 microg/kg). The BBB disruption was quantified according to the extravasation of the Evans blue (EB) dye. L-NAME induced a significant increase in arterial blood pressure on day 14 in normoglycemic and hyperglycemic rats (p < 0.05). Losartan significantly reduced the increased blood pressure in hypertensive and diabetic hypertensive rats (p < 0.01). Epinephrine-induced acute hypertension in diabetic hypertensive rats increased the content of EB dye dramatically in cerebellum and diencephalon (p < 0.01) and slightly in both cerebral cortex (p < 0.05). Losartan treatment reduced the increased BBB permeability to EB dye in the brain regions of diabetic hypertensive rats treated with epinephrine (p < 0.05). This study indicates that, in diabetic hypertensive rats, epinephrine administration leads to an increase in microvascular-EB-albumin efflux to brain, however losartan treatment significantly attenuates this protein's transport to brain tissue.     

Influence of vitamin E on the levels of fatty acids and MDA in some tissues of diabetic rats

This study was performed to determine whether vitamin E supplementation in streptozotocin-induced diabetic rats treated with insulin could affect the levels of fatty acid composition and malondialdehyde (MDA) of brain, liver and muscle tissues. Thirty Wistar albino rats were used during the experiments. They were randomly divided into three groups, each consisting of six individuals. The first group was diabetic, the second was control, and the third was diabetic but fed vitamin E. The level of stearic acid in brain tissues decreased (p<0.05) in the second and the third groups as compared to the first group. The percentage of arachidonic and polyunsaturated fatty acids slightly decreased (p<0.05) in the diabetic group in comparison to the second and third groups. The proportion of docosahexaenoic acid significantly increased (p<0.01) in the second and third groups in contrast to the first group. The level of docosatrienoic was slightly higher (p<0.05) in the third group than in other groups. In the liver tissues, the proportion of stearic, oleic and total monounsaturated fatty acids was slightly higher (p<0.05) in the first group than in the other groups. The level of arachidonic, docosahexaenoic, unsaturated and total polyunsaturated fatty acid slightly increased (p<0.05) in the second and third groups as compared to the first group. The level of myristic and stearic acids in muscle tissue slightly increased (p<0.05) in the first group as compared to the second and third groups. The proportion of arachidonic, docosahexaenoic and unsaturated fatty acids slightly increased (p<0.05) in the second and third groups relative to the first group. The amount of MDA was slightly higher in the diabetic group than in the other groups in all tissues. The results indicate that vitamin E supplementation, in experimental diabetes could play a role in controlling the oxidative status and altered fatty acid metabolism in tissues, thereby maintaining favourable fatty acid distribution in the tissues affected by diabetic complications.     

Treatment options in extravasation injury: an experimental study in rats

Local skin necrosis after extravasation of doxorubicin hydrochloride (Adriamycin), a widely used chemotherapeutic agent, is a common problem in cancer patients. Even though several treatment options have been proposed for extravasation injury, there is still controversy regarding the management of such lesions. The aim of this study was to compare the efficacy of saline infiltration, vitamin C infiltration, suction technique, and early surgical excision as a treatment in a rat extravasation model. The authors planned their study in two stages. In stage 1, the lowest effective dose of doxorubicin at which a homogeneous skin necrosis was formed and the method of administration were investigated. Intradermal and subpannicular injections were made for six rats, using six different concentrations of doxorubicin (0.33, 0.5, 0.66, 1.0, 1.33, and 1.5 mg/ml). In stage 1, the intradermal injection produced homogeneous and uniform tissue necrosis. In stage 2, the efficacy of saline infiltration (group 1), vitamin C infiltration (group 2), suction (group 3), suction and saline washout (group 4), suction and vitamin C washout (group 5), and early surgical excision (group 6) was compared. The treatment options were applied 2 hours after doxorubicin injection. At the end of the seventh day, the presence and size of ulcers at the injection site were calculated. Fourteen days after injection, a histopathologic examination was performed for each treatment and control group. In groups 1 and 3, there was no statistically significant difference in the size of necrosis compared with the control groups. In groups 2, 4, and 5, the size of necrosis was smaller compared with the control groups, and this was statistically significant. Furthermore, in group 4 (suction and saline washout) and group 5 (suction and vitamin C washout), the calculated area of necrosis was smaller compared with other treatment groups, and this was statistically significant. The findings supported the assertion that suction and saline or vitamin C washout reduce necrotic tissue size in extravasation injury.     

Biosorption of chromium(VI) from aqueous solution by cone biomass of Pinus sylvestris

Biosorption of chromium(VI) on to cone biomass of Pinus sylvestris was studied with variation in the parameters of pH, initial metal ion concentration and agitation speed. The biosorption of Cr(VI) was increased when pH of the solution was decreased from 7.0 to 1.0. The maximum chromium biosorption occurred at 150 rpm agitation. An increase in chromium/biomass ratio caused a decrease in the biosorption efficiency. The adsorption constants were found from the Freundlich isotherm at 25 degrees C. The cone biomass, which is a readily available biosorbent, was found suitable for removing chromium from aqueous solution.     

Enhanced stress tolerance in Escherichia coli and Nicotiana tabacum expressing a betaine aldehyde dehydrogenase/choline dehydrogenase fusion protein

In Escherichia coli the osmoprotective compound glycine betaine is produced from choline by two enzymes; choline dehydrogenase (CDH) oxidizes choline to betaine aldehyde and then further on to glycine betaine, while betaine aldehyde dehydrogenase (BADH) facilitates the conversion of betaine aldehyde to glycine betaine. To evaluate the importance of BADH, a BADH/CDH fusion enzyme was constructed and expressed in E. coli and in Nicotiana tabacum. The fusion enzyme displayed both enzyme activities, and a coupled reaction could be measured. The enzyme was characterized regarding molecular weight and the dependence of the enzyme activities on environmental factors (salt, pH, and poly(ethylene glycol) addition). At high choline concentrations, E. coli cells expressing BADH/CDH were able to grow to higher final densities and to accumulate more glycine betaine than cells expressing CDH only. The intracellular glycine betaine levels were almost 5-fold higher for BADH/CDH when product concentration was related to CDH activity. Also, after culturing the cells at high NaCl concentrations, more glycine betaine was accumulated. On medium containing 20 mM choline, transgenic tobacco plants expressing BADH/CDH grew considerably faster than vector-transformed control plants.     

Purification of glucose 6-phosphate dehydrogenase from chicken erythrocytes. investigation of some kinetic properties

Glucose 6-phosphate dehydrogenase (G6PD) was purified from chicken erythrocytes, and some characteristics of the enzyme were investigated. The purification procedure was composed of three steps: hemolysate preparation, ammonium sulfate precipitation, and 2',5'-ADP Sepharose 4B affinity gel chromatography. Thanks to the three consecutive procedures, the enzyme, having the specific activity of 20.862 EU/mg proteins, was purified with a yield of 54.68% and 9,150-fold. Optimal pH, stable pH, optimal temperature, molecular weight, and KM and Vmax values for NADP+ and glucose 6- phosphate (G6-P) were also determined for the enzyme. In addition, Ki values and the type of inhibition were determined by means of Line-Weaver-Burk graphs obtained for such inhibitors as ATP, ADP, NADH, and NADPH.