The effect of intra- and interspecific aggression on patch residence time in Negev Desert gerbils: a competing risk analysis

We observed patch-use behavior by two gerbil species in a fieldsetting and investigated how aggression and intrinsic decision-makinginteract to influence patch residence times. Results were interpretedby using a competing risk analysis model, which uniquely enabledus to estimate the intrinsic patch-leaving decisions independentlyof external interruptions of foraging bouts by aggression. Theexperiment was conducted in two 1-ha field enclosures completelysurrounded by rodent-proof fences and included allopatric (onlyGerbillus andersoni allenbyi) and sympatric (G. a. allenbyiand G. pyramidum) treatments. We predicted that increased foodpatch quality (i.e., habitat quality) should decrease intrinsicpatch-leaving rates and increase rates of aggressive interactionsinvolving the forager feeding in the patch (i.e., the occupantindividual). We also anticipated that increasing populationdensity should result in an increase in the rate of aggressiveinteractions involving the occupant individual. Our resultssupported the first two predictions, indicating a trade-offbetween foraging and aggression. However, the third predictionwas realized only for G. a. allenbyi in allopatry. Furthermore,in allopatry, occupant G. a. allenbyi individuals with highcompetitive ranks were involved in aggressive interactions atlower rates than those with low competitive ranks. However,in sympatry, patch-use behavior of occupant G. a. allenbyi individualswas mainly influenced by aggressive behavior of G. pyramidum,which did not respond to their competitive rank. Thus, it shouldpay less for G. a. allenbyi to be aggressive in sympatric populations.The observed reduction in intraspecific aggression among individualG. a. allenbyi in the presence of G. pyramidum supports thisassertion. We suggest that this reduction likely weakens thenegative effect of intra- and interspecific density on the percapita growth rate of G. a. allenbyi. Because this would changethe slope of the isocline of G. a. allenbyi, it could be animportant mechanism promoting coexistence when habitat selectionis constrained.     

Effect of enzyme concentration on apparent specific activity of hydrogenase

The effect of enzyme concentration on the H2-uptake and H2-evolving activities of the reversible hydrogenase from Thiocapsa roseopersicina was examined. In the activity range assayed by a spectrophotometric technique the apparent H2-uptake specific activity varied greatly with hydrogenase concentration. Study of H2-evolving activity measured by the H2 electrode method and compared with a gas chromatographic assay also indicated that specific activity was highly dependent on enzyme concentration. The results indicate that the widely applied hydrogenase assays give systematically erroneous specific activity values. These assays should be used only for relative measurements and the hydrogenase concentration in the reaction mixture should be kept constant. To make the data from various laboratories comparable the assay parameters should be standardized.     

Application of robotics to steady state enzyme kinetics: analysis of tight-binding inhibitors of dipeptidyl peptidase IV

Using available commercial robotics and instrumentation, we developed a fully automated and rigorous steady state enzyme kinetic assay for dipeptidyl peptidase IV (DPP IV; E.C. 3.4.14.5). The automated assay was validated with isoleucyl thiazolidide, a potent inhibitor of DPP IV with K(is)=110nM. Signal window analysis indicated that the assay had a 98% probability of detecting an inhibitor yielding 15% inhibition, with a predicted false positive rate of 0.13%. A mechanistic inhibition version of the automated assay was validated with isoleucyl 4-cyanothiazolidide, a very potent inhibitor of DPP IV. Isoleucyl 4-cyanothiazolidide was a competitive inhibitor of purified porcine DPP IV with K(is)=1 nM. Similar K(is) values were obtained for purified rat DPP IV and for DPP IV activity in human plasma from normal and diabetic donors. The pH dependence of K(is) for isoleucyl 4-cyanothiazolidide yielded a bell-shaped profile, with pK(a)=5.0 and pK(b)=7.6. To date, over 100,000 data points have been generated in profiling targeted compound libraries and in the analysis of tight-binding inhibitors of DPP IV. The data also show that robotic analysis is capable of producing full mechanistic inhibition analysis in a timely fashion to support drug discovery.     

Optimal patch residence time in egg parasitoids: innate versus learned estimate of patch quality

Charnovs marginal value theorem predicts that female parasitoids should exploit patches of their hosts until their instantaneous rate of fitness gain reaches a marginal value. The consequences of this are that: (1) better patches should be exploited for a longer time; (2) as travel time between patches increases, so does the patch residence time; and (3) all exploited patches should be reduced to the same level of profitability. Patch residence time was measured in an egg parasitoid Anaphes victus (Hymenoptera: Mymaridae) when patch quality and travel time, approximated here as an increased delay between emergence and patch exploitation, varied. As predicted, females stayed longer when patch quality and travel time increased. However, the marginal value of fitness gain when females left the patch increased with patch quality and decreased with travel time. A. victus females appear to base their patch quality estimate on the first patch encountered rather than on a fixed innate estimate, as was shown for another egg parasitoid Trichogramma brassicae. Such a strategy could be optimal when inter-generational variability in patch quality is high and within-generational variability is low.     

Nitrogen deficiency increases the residence time of respiratory carbon in the respiratory substrate supply system of perennial ryegrass

Plant respiration draws on substrate pools of different functional/biochemical identity. Little is known about the effect of nitrogen deficiency on those pools' sizes, half-lives and relative contribution to respiration, and consequently, of carbon residence time in respiratory metabolism. Here we studied how nitrogen fertilization affects the respiratory carbon supply system of shoots and roots of Lolium perenne , a perennial grass. Plants grown at two nitrogen supply levels in continuous light were labelled with ¹³CO₂/¹²CO₂ for intervals ranging from 1 h to 1 month. The rate and isotopic composition of shoot, root and plant respiration were measured, and the time-courses of tracer incorporation into respired CO₂ were analysed by compartmental modelling. Nitrogen deficiency reduced specific respiration rate by 30%, but increased the size of the respiratory supply system by 30%. In consequence, mean residence time of respiratory carbon increased with nitrogen deficiency (4.6 d at high nitrogen and 9.2 d at low nitrogen supply). To a large extent, this was due to a greater involvement of stores with a long half-life in respiratory carbon metabolism of nitrogen-deficient plants. At both nitrogen supply levels, stores supplying root respiration were primarily located in the shoot, probably in the form of fructans.     

Design methodology accounting for the effects of porous medium heterogeneity on hydraulic residence time and biodegradation in horizontal subsurface flow constructed wetlands

Horizontal flow constructed wetlands are engineered systems capable of eliminating a wide range of pollutants from the aquatic environment. Nevertheless, poor hydrodynamic behavior is commonly found resulting in preferential pathways and variations in both (i) the hydraulic residence time distribution (HRTD) and, consequently, (ii) the wetland's treatment efficiency. The aim of this work was to outline a methodology for wetland design that accounts for the effect of heterogeneous hydraulic properties of the porous substrate on the HRTD and treatment efficiency. Biodegradation of benzene was used to illustrate the influence of hydraulic conductivity heterogeneity on wetland efficiency. Random, spatially correlated hydraulic conductivity fields following a log-normal distribution were generated and then introduced in a subsurface flow numerical model. The results showed that the variance of the distribution and the correlation length in the longitudinal direction are key indicators of the extent of heterogeneity. A reduction of the mean hydraulic residence time was observed as the extent of heterogeneity increased, while the HRTD became broader with increased skewness. At the same time, substrate heterogeneity induced preferential flow paths within the wetland bed resulting in variations of the benzene treatment efficiency. Further to this it was observed that the distribution of biomass within the porous bed became heterogeneous, rising questions on the representativeness of sampling. It was concluded that traditional methods for wetland design based on assumptions such as a homogeneous porous medium and plug flow are not reliable. The alternative design methodology presented here is based on the incorporation of heterogeneity directly during the design phase. The same methodology can also be used to optimize existing systems, where the HRTD has been characterized with tracer experiments.     

Determination of iodide amounts in urine and water by isotope dilution analysis

Urinary iodide and iodine in drinking water were determined in 318 healthy children aged 0 to 18 yr living in Izmir and environmental rural and urban areas in the western part of Turkey. The method is based on substochiometric isotope dilution analysis. Iodide was precipitated by substoichiometric amounts of AgNO₃. Iodide-131 was used as a tracer. Electrophoresis was performed to separate Ag¹³¹I from excess¹³¹I-. The Ag¹³¹I zone was cut off the electrophoresis paper and counted with a Nal(Tl) scintillation counter. Count rates were plotted versus added KI concentrations. The unknown iodide amount was found by using these linear plots. Iodide concentration ranges were within 1.8 –100.45 Μg/L in the analyzed drinking water samples. The mean value was 44.14 ±17.33 Μg/L and the median was 58.08 Μg/L. Urinary iodide concentration ranges were 0.22 –142.22 Μg/L. The median of the distribution was 37.71 Μg/L and the mean was 40.30 ±24.05 Μg/L. The results show that the examined area suffers moderate iodine deficiency.     

Synthesis,in vitro and in vivo giardicidal activity of nitrothiazole-NSAID chimeras displaying broad antiprotozoal spectrum

We designed and synthesized five new 5-nitrothiazole-NSAID chimeras as analogues of nitazoxanide, using a DCC-activated amidation. Compounds 1–5 were tested in vitro against a panel of five protozoa: 2 amitochondriates (Giardia intestinalis, Trichomonas vaginalis) and 3 kinetoplastids (Leishmania mexicana, Leishmania amazonensis and Trypanosoma cruzi). All chimeras showed broad spectrum and potent antiprotozoal activities, with IC₅₀ values ranging from the low micromolar to nanomolar order. Compounds 1–5 were even more active than metronidazole and nitazoxanide, two marketed first-line drugs against giardiasis. In particular, compound 4 (an indomethacin hybrid) was one of the most potent of the series, inhibiting G. intestinalis growth in vitro with an IC₅₀ of 0.145 μM. Compound 4 was 38-times more potent than metronidazole and 8-times more active than nitazoxanide. The in vivo giardicidal effect of 4 was evaluated in a CD-1 mouse model obtaining a median effective dose of 1.709 μg/kg (3.53 nmol/kg), a 321-fold and 1015-fold increase in effectiveness after intragastric administration over metronidazole and nitazoxanide, respectively. Compounds 1 and 3 (hybrids of ibuprofen and clofibric acid), showed potent giardicidal activities in the in vitro as well as in the in vivo assays after oral administration. Therefore, compounds 1–5 constitute promising drug candidates for further testing in experimental chemotherapy against giardiasis, trichomoniasis, leishmaniasis and even trypanosomiasis infections.     

Kinetics, mechanism, and time course analysis of lipase-catalyzed hydrolysis of high concentration olive oil in AOT-isooctane reversed micelles

Candida rugosa lipase has been used to investigate the hydrolysis of high concentration olive oil in the AOT-isooctane reversed micellar system at W(o) = 10, pH 7.1, and 37 degrees C. Results from this work show the hydrolytic reaction obeys Michaelis-Menten kinetics up to the initial substrate concentration of 1.37M, with turnover number k(cat) and Michaelis constant K(M) of 67.1 mumol/min mg enzyme and 0.717M, respectively. A competitive inhibition by the main product, oleic acid, has been found with a dissociation constant K(I) for the complex EP* of 0.089M. The rate equation was further analyzed in the time course reaction and was found in agreement with the experimental results for lower substrate concentrations, up to 0.341M. Large deviation occurred at high substrate concentrations, which may be due to the effects of large consumption of water on kinetics, on the formation of glycerol, and on the deactivation of lipase in the hydrolysis reaction as well.     

In vivo analysis of compound activity and mechanism of action using epistasis in Drosophila

The recent establishment of high-throughput methods for culturing Drosophila provided a unique ability to screen compound libraries against complex disease phenotypes in the context of whole animals. However, as compound studies in Drosophila have been limited so far, the degree of conservation of compound activity between Drosophila and vertebrates or the effectiveness of feeding as a compound delivery system is not well known. Our comprehensive in vivo analysis of 27 small molecules targeting seven signaling pathways in Drosophila revealed a high degree of conservation of compound activity between Drosophila and vertebrates. We also investigated the mechanism of action of AY9944, one of the Hh pathway antagonists that we identified in our compound feeding experiments. Our epistasis analysis of AY9944 provided novel insights into AY9944’s mechanism of action and revealed a novel role for cholesterol transport in Hh signal transduction.     

Composition and mean residence time of molecular weight fractions of organic matter extracted from two soils under different forest species

The organic matter extracted from various mineral horizons of two forest soils, one under silver fir (Abies alba Mill.), the other under European beech (Fagus sylvatica L.), was fractionated by dialysis into three fractions, 100–1000, 1000–8000, and >8000Da. On a C basis, in all horizons the recovered organic matter amounted to less than a half of the total and was mainly composed of molecules >8000Da. The 100–1000Da fraction had a principal elemental composition profoundly different from the other two fractions, which, instead differed from each other significantly only for the S content and the molar ratio of C with N. No significant difference in this regard was found between soils. The richness in O and some typical absorption bands in the FT-IR spectra indicated that the 100–1000Da fraction had a lot of carboxyl moieties. The spectroscopic (¹³C NMR) investigation showed that the 1000–8000 and >8000Da fractions had a prevalently aliphatic nature and signals attributable to polysaccharides (O-alkyl C) revealed overall a high presence of non-humic biopolymers. These latter were significantly more abundant, suggesting a lower degree of humification, in the >8000Da fraction than in the 1000–8000Da fraction. Comparing soils, that under beech appeared significantly richer in O-alkyl C than that under fir. The organics extracted from the A horizon of both soils had positive ¹⁴C values, indicating recent synthesis mainly due to the present forest cover. The mean residence time (MRT) of the combined 100–1000Da and 1000–8000Da fractions and the >8000Da fraction increased with depth, even to about 5000 years in the more than 1-m deep BC horizons under beech. In some cases, and especially in the soil under fir, despite higher values of ¹³C denoting stronger microbial decomposition, the 100–8000Da fraction showed a higher MRT than that of the >8000Da fraction, perhaps due to its ascertained lower content of non-humic biopolymers.     

Residence time and food contact time effects on transfer of Salmonella Typhimurium from tile, wood and carpet: testing the five-second rule

AIMS: Three experiments were conducted to determine the survival and transfer of Salmonella Typhimurium from wood, tile or carpet to bologna (sausage) and bread. METHODS AND RESULTS: Experiment 1. After 28 days, 1.5 to 2.5 log(10) CFU cm(-2) remained on tile from and the more concentrated media facilitated the survival of S. Typhimurium compared with the more dilute solutions. Experiments 2 and 3. The bacterial transfer rate to food decreased as the bacterial residence time on the surface increased from 2, 4, 8 to 24 h with transfers of 6.5, 4.8, 4.6 and 3.9 log CFU ml(-1) in the rinse solutions, respectively. Over 99% of bacterial cells were transferred from the tile to the bologna after 5 s of bologna exposure to tile. Transfer from carpet to bologna was very low (<0.5%) when compared with the transfer from wood and tile (5-68%). CONCLUSIONS: (i) Salmonella Typhimurium can survive for up to 4 weeks on dry surfaces in high-enough populations to be transferred to foods and (ii) S. Typhimurium can be transferred to the foods tested almost immediately on contact. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrated the ability of bacteria to survive and cross-contaminate other foods even after long periods of time on dry surfaces, thus reinforcing the importance of sanitation on food contact to minimize the risk of foodborne illness.     

Residence time and kinetic efficiency analysis of extracellular signal-regulated kinase 2 inhibitors

The RAS/RAF/MEK/ERK signal transduction cascade plays an important role in the regulation of critical cellular processes such as cell proliferation, migration, and differentiation. The up-regulation of this pathway can negatively affect cell homeostasis and is responsible for the development of various forms of cancer and inflammation processes. Therefore, there is a strong interest in pursuing drug programs targeting some of the enzymes involved in this pathway. In addition to the determination of K_i, K_d, IC₅₀, and/or EC_50, a more thorough kinetic analysis can provide useful information for the selection of the best lead series during the early stage of the drug discovery process. This study describes a medium-throughput fluorescent probe displacement assay for the rapid determination of the k_off constant, residence time, and kinetic efficiency for ERK (extracellular signal-regulated kinase) inhibitors. Using this method, we have identified several inhibitors that we have subjected to further kinetic analysis by comparing k_off constants determined for these time-dependent inhibitors using either the active or inactive form of ERK2.     

Purification of carbonic anhydrase-II from sheep liver and inhibitory effects of some heavy metals on enzyme activity

In this study; sheep carbonic anhydrase-II (SCA-II) (E.C: 4.2.1.1) was purified from sheep liver and in vitro effects of heavy metals on the enzyme was examined. SCA-II isozyme was purified with about 203 purification fold, a specific activity of 2320 EU/mg-protein and a yield of 72 by using Sepharose-4B-L tyrosine-sulfanilamide affinity gel chromatography. Purity of the SCA-II enzyme was verified by SDS-PAGE technique and subunit molecular mass of the enzyme was found as 29?kDa. In addition to this, inhibitory effects of some metal ions on the enzyme were examined. In this study, sheep liver tissue was chosen; because the liver is an organ in which metal wastes of air, water and food are collected and it is easy to obtain the liver tissue. Because of the very important duties of CA enzyme on living beings, the effect of metals on the CA enzyme was investigated.     

Notable difference in anti-HIV activity of integrase inhibitors as a consequence of geometric and enantiomeric configurations

While some examples are known of integrase inhibitors that exhibit potent anti-HIV activity, there are very few cases reported of integrase inhibitors that show significant differences in anti-HIV activity that result from distinctions in cis- and trans-configurations as well as enantiomeric stereostructure. We describe here the design and synthesis of two enantiomeric trans-hydroxycyclopentyl carboxamides which exhibit notable difference in anti-HIV activity. This difference is explained through their binding interactions within the active site of the HIV-1 integrase intasome. The more active enantiomer 3 (EC₅₀ 25 nM) was relatively stable in human liver microsomes. Kinetic data revealed that its impact on key cytochrome P450 isozymes, as either an inhibitor or an activator, was minor, suggesting a favorable CYP profile.     

Day-to-day variation in nitrogenase activity of Alnus incana explained by weather variables: a multivariate time series analysis

A modelling system is described that indicates the extent to which day-to-day variations in nitrogenase activity in young Alnus incana (L.) Moench, grown in defined conditions in the field, may be affected by weather conditions both during and prior to the day of measurement. Nitrogenase activity (acetylene reduction activity, ARA) was measured weekly on intact field-grown grey alder (A. incana) plants, 0.15–0.42 m tall at planting, nodulated with Frankia. The measurements were done at noon on two groups of plants in 1987 and on two other groups in 1988. Each group was made up of five or six plants. Seven weather variables: daily sunshine hours, daily mean, maximum and minimum air temperature, daily mean and 1300 h relative humidity, and daily rainfall were used. The relation between log(ARA/leaf area) and the weather variables were analysed using a PLS model (partial least squares projection to latent structures). The advantage of PLS is that it can handle x-variables that are correlated. Data from 1987 were chosen as a training set. Multivariate PLS time series analysis was made by adding, in a stepwise manner, the weather data up to 5 d before the day of measurement. This procedure gave six models with n * 7 x-variables (n= 1–6). With the models from the time series analysis of 1987 data, true predictions of ARA per leaf area were made from weather data 1988 (test set 1) and from ‘early-season’ weather data from 1987 and 1988 (test set 2). The variation in ARA/leaf area could be predicted from the weather conditions. The predictions of the two test sets improved when the weather conditions one and two days before the day of measurements were added to the model. The further addition of weather data from 3 to 5 d before the day of measurement did not improve the model. The good predictions of ARA/leaf area show that the alders responded to the variable weather conditions in the same way in 1988 as in 1987, despite the ten-fold difference in size (leaf area) at the end of the growing season. Among the weather variables, air temperature and the daily sunshine hours were positively correlated to ARA, while relative air humidity and rainfall were negatively correlated to ARA. The daily minimum temperature and rainfall appeared to have least impact on ARA. By use of PLS, we could extract information out of a data set containing highly correlated x-variables, information that is non-accessible with conventional statistical tools such as multiple regression. When making measurements of nitrogenase activities under field conditions, we propose that attention should be paid to the weather conditions on the days preceding the day of measurement. The day-to-day variation in nitrogenase activity is discussed with reference to known effects of stress factors under controlled conditions.     

Trophic status based on nutrient concentration scales and primary producers community of tropical coastal lagoons influenced by groundwater discharges

Changes in the rate of primary production as an indication of trophic status of aquatic ecosystems have been one of the major indicators of their health. Despite different approaches been devised for evaluating this process, few are useful for comparison and generalization of their results. The coastal zone ecosystems of Yucatan (SE Mexico) exhibit hydrological variability closely associated with the groundwater discharges, which are the only freshwater sources in the coastal ecosystems. In order to learn about the trophic status of karstic tropical coastal lagoons, three of them (Celestun, Chelem and Dzilam) located in Yucatan (SE, Mexico) were monitored for inorganic nutrients, Chl-a, phytoplankton and macrophyte productivity. The nitrate concentrations suggest that the trophic status was influenced by fresh water springs, being meso-eutrophic in Celestun, oligotrophic in Chelem, and mesotrophic in Dzilam. In the case of ammonium ions, the three lagoons were mesotrophic, indicating that processes such as remineralization play an important role in the trophic dynamic of these shallow ecosystems. According to phosphate concentrations, Celestun and Dzilam were mesotrophic, and Chelem was oligotrophic. External inputs of phosphate and bioturbation by waterfowl may be responsible of these differences. Primary productivity at Celestun was greater than at Chelem and Dzilam lagoons and the contribution by seagrasses was significant in all three. It is found that indices based on nutrient concentration and phytoplankton biomass are useful as an indication of trophic status in groundwater influenced coastal lagoons. Moreover, estimations on the total system productivity, and the relative contribution of each primary producer, is a holistic approach useful for understanding trophic dynamic in shallow tropical coastal ecosystems.     

Purification and characterization of dihydropyrimidine dehydrogenase enzyme from sheep liver and determination of the effects of some anaesthetic and antidepressant drugs on the enzyme activity

Dihydropyrimidine dehydrogenase (DPD, E.C. 1.3.1.2) was purified from sheep liver with a yield of 16.7%, purification fold of 407.5 and specific activity of 0.705?EU/mg proteins. The purification procedure consisted of ammonium sulphate fractionation, DEAE ion exchange chromatography and 2′,5′-ADP Sepharose-4B affinity chromatography. The molecular weight determined by SDS-PAGE and was found 111?kDa. Optimum pH, ionic strength temperature and stable pH were determined as 8.0, 0.9?mM, 50?°C and 6.0, respectively. The kinetic parameters (K_m and V_max) of the enzyme were determined with NADPH as 22.97?μM and 0.17?EU/mL, respectively. The same parameters were determined with uracil as 17.46?μM and 0.14?EU/mL, respectively. Additionally, in vitro inhibitory effects of some antidepressant drugs including escitalopram, fluoxetine, mirtazapine, haloperidol and some anaesthetic drugs including propofol and lidocaine were investigated against DPD. In addition, IC₅₀ values for each active drug obtained for escitalopram, fluoxetine, mirtazapine, haloperidol, propofol and lidocaine were determined as 1736.11, 13.24, 86.65, 99.03, 0.21 and 15.07?μM, respectively.