Quantification of Endospore Concentrations of Pasteuria penetrans in Tomato Root Material

Six methods for quantification of the endospore concentrations of Pasteuria penetrans from tomato roots are described. Mortar disruption and machine disruption methods gave the highest estimations (endospores per gram of root material) of 83.7 and 79.0 million, respectively. These methods were significantly superior to incubation bioassay (47.7 million), enzymatic disruption (32.1 million), and enzymatic disruption + flotation (25.8 million) methods. A centrifugation bioassay method gave the lowest estimation of 12.7 million.     

Characterization of a methanogenic sludge to be used as inoculum for a high-rate reactor

The sludge of an anaerobic lagoon treating the wastewater from a factory producing baker's yeast was evaluated as inoculum for anaerobic digestion. Specific methanogenic activity tests failed to give a good estimation of the trophic groups that were evidenced by enumerations involving Most Probable Number estimations. This failure was ascribed to the toxic effects of either the acetate concentrations used or to the ammonia content of the sludge.     

Age estimation of Norway spruce using incomplete increment cores: Testing new and improved methods

Information on tree age is often vital for dendrochronological studies, especially when the Regional Curve Standardisation technique is used. Several linear and non-linear methods of tree age estimation using partial increment cores (without the presence of pith) were evaluated and modified to provide more accurate estimations than are currently used. To achieve the objective, core samples from 142 Norway spruce trees (Picea abies [L.] Karst.) were collected from an altitudinal gradient in the Western Carpathians. The samples in which the pith was included were then used for further analyses. Several known age estimation approaches were adjusted to combine the advantages of direct increment- and indirect age-diameter-based methods. Inverse differential forms of non-linear growth functions were tested and proposed as a new advanced approach for age estimation. The results show that most of the modified linear methods achieved a mean square error of less than 10% when the length of the partial core exceeded 90% of the stem radius and less than 20% when the length of the core was at least 60% of the stem radius. Using an appropriate differential form of the non-linear growth functions, a mean square error of less than 20% was reached, even when the core length was shorter than 60% of the radius. The results show that current linear methods for age estimation can only be used if the missing part of the core sample is very short, with only a few rings absent. In the case of a large number of missing rings, a differential form of non-linear functions should preferably be used instead.     

African sharptooth catfish Clarias gariepinus does not detoxify ammonia to urea or amino acids but actively excretes ammonia during exposure to environmental ammonia

The African sharptooth catfish Clarias gariepinus lives in freshwater, is an obligatory air breather, and exhibits high tolerance of environmental ammonia. This study aimed at elucidating the strategies adopted by C. gariepinus to defend against ammonia toxicity during ammonia exposure. No carbamoyl phosphate synthetase (CPS) I or III activities were detected in the liver or muscle of the adult C. gariepinus. In addition, activities of other ornithine-urea cycle (OUC) enzymes, especially ornithine transcarbamylase, were low in the liver, indicating that adult C. gariepinus does not have a "functional" hepatic OUC. After being exposed to 50 or 100 mM NH4Cl for 5 d, there was no induction of hepatic OUC enzymes and no accumulation of urea in tissues of the experimental animals. In addition, the rate of urea excretion remained low and unchanged. Hence, ammonia exposure did not induce ureogenesis or ureotely in C. gariepinus as suggested elsewhere for another obligatory air-breathing catfish of the same genus, Clarias batrachus, from India. Surprisingly, the local C. batrachus did not possess any detectable CPS I or III activities in the liver or muscle as had been reported for the Indian counterpart. There were no changes in levels of alanine in the muscle, liver, and plasma of C. gariepinus exposed to 50 or 100 mM NH4Cl for 5 d; neither were there any changes in the glutamine levels in these tissues. Yet even after being exposed to 100 mM NH4Cl for 5 d, there was no significant increase in the level of ammonia in the muscle, which constitutes the bulk of the specimen. In addition, the level of ammonia accumulated in the plasma was relatively low compared to other tropical air-breathing fishes. More importantly, for all NH4Cl concentrations tested (10, 50, or 100 mM), the plasma ammonia level was maintained relatively constant (2.2-2.4 mM). These results suggest that C. gariepinus was able to excrete endogenous ammonia and infiltrated exogenous ammonia against a very steep ammonia gradient. When exposed to freshwater (pH 7.0) with or without 10 mM NH4Cl, C. gariepinus was able to excrete ammonia continuously to the external medium for at least 72 h. This was achieved while the plasma NH4+ and NH3 concentrations were significantly lower than those of the external medium. Diffusion trapping of NH3 through boundary layer acidification can be eliminated as the pH of the external medium became more alkaline instead. These results represent the first report on a freshwater fish (C. gariepinus) adopting active excretion of ammonia (probably NH4+) as a major strategy to defend against ammonia toxicity when exposed to environmental ammonia.     

USE OF SENSORY EVALUATION FOR MEASURING DEODORIZING EFFECTS OF AN AIR CONDITIONER

The application of sensory methodology for measuring deodorizing effect of an air conditioner equipped with electric plasma was introduced. Deodorizing effect was measured using chemical and sensory methods at different time (0, 30 and 60 min) and mode (control, blowing and cooling) of an air conditioner. Smoke from a roll of cigarette in a closed room was used as a source of odor and the concentrations of acetic acid and ammonia were measured as odorous chemical components. As one of the sensory methods triangle test was used and as a first step to obtain deodorizing effects by triangle test, the threshold of each panelist was obtained as the log dilution ratio of odor concentration at which the difference from odorless air was detected. The odor concentration at each time and mode was calculated using the threshold of the panel and the deodorizing effect was obtained on the basis of the odor concentration. In addition to a triangle test, scaling methods such as category scaling or magnitude estimation were used to measure deodorizing effect of an air conditioner. Deodorizing effects by scaling methods were calculated based on odor intensity with time at each mode. The regression analysis was done between the efficacy of deodorizing effect by sensory test and those by acetic acid and ammonia, the R² values of the regression equations for triangle test, category scale, and magnitude estimation were 0.84, 0.72 and 0.69, respectively. Deodorizing effect by triangle test explained the decrease of acetic acid and ammonia better than those by category scaling or magnitude estimation while high cost and time consuming labor involved in triangle tests reduced the merit. The results of this study demonstrated that various sensory methods could be used to measure deodorizing effect of air conditioners and further researches on fast and reliable methods are needed to establish the official procedures.     

Enzymatic determination of carbon (14C)-labeled glycerol in biological samples

A method for determination of glycerol-specific-radioactivity in biological samples is presented. It is based on the following steps: (a) enzymatic conversion of glycerol to dihydroxyacetone-phosphate, (b) quantitative trapping of dihydroxyacetone-phosphate in SPE amino (NH₂) columns, (c) eluation with HCl 0.5 N of dihydroxyacetone-phosphate followed by radioactivity counting and (d) estimation of the radioactivity thus trapped compared with that of enzymatically untreated aliquots of the same samples. No interferences from other ¹⁴C-labeled materials tested such as d-glucose, l-alanine, l-glutamine and d-β-hydroxybutyrate were observed. This inexpensive and high-speed method can be applied in routine multiple estimations of glycerol-specific-radioactivity in biological samples in tracer metabolic studies.     

Estimating abundance and population trends when detection is low and highly variable: A comparison of three methods for the Hermann's tortoise

Assessing population trends is a basic prerequisite to carrying out adequate conservation strategies. Selecting an appropriate method to monitor animal populations can be challenging, particularly for low-detection species such as reptiles. This study compares 3 detection-corrected abundance methods (capture–recapture, distance sampling, and N-mixture) used to assess population size of the threatened Hermann's tortoise. We used a single dataset of 432 adult tortoise observations collected at 118 sampling sites in the Plaine des Maures, southeastern France. We also used a dataset of 520 tortoise observations based on radiotelemetry data collected from 10 adult females to estimate and model the availability (g0) needed for distance sampling. We evaluated bias for N-mixture and capture–recapture, by using simulations based on different values of detection probabilities. Finally, we conducted a power analysis to estimate the ability of the 3 methods to detect changes in Hermann's tortoise abundances. The abundance estimations we obtained using distance sampling and N-mixture models were respectively 1.75 and 2.19 times less than those obtained using the capture–recapture method. Our results indicated that g0 was influenced by temperature variations and can differ for the same temperature on different days. Simulations showed that the N-mixture models provide unstable estimations for species with detection probabilities <0.5, whereas capture–recapture estimations were unbiased. Power analysis showed that none of the 3 methods were precise enough to detect slow population changes. We recommend that great care should be taken when implementing monitoring designs for species with large variation in activity rates and low detection probabilities. Although N-mixture models are easy to implement, we would not recommend using them in situations where the detection probability is very low at the risk of providing biased estimates. Among the 3 methods allowing estimation of tortoise abundances, capture–recapture should be preferred to assess population trends. © 2013 The Wildlife Society.     

Isolation and characterization of plasma membranes from the fungus Podospora anserina

This paper describes a method for separating and isolating plasma membranes from the septated fungus Podospora anserina. Plasma membranes were isolated from protoplasts (young cell plasma membranes) and mycelia (both young and aged cell plasma membranes). The procedure of fractionation consisted of a combination of differential and isopycnic centrifugations. Characterization of cellular membranes and enrichment of the fractions with plasmalemma were carried out by assays on enzymatic activities. A plasma membrane fraction was isolated in a buoyant density peak of 1.087 g/cm3, where three enzymatic activities bound to plasma membrane, adenylate cyclase, chitin synthase, and beta-glucan synthase at low affinity for UDP-Glc, peaked together. Good purity of this fraction was determined by the absence or the very low level of other enzymatic activities used as markers for intracellular membranes, i.e., succinate dehydrogenase, alpha-mannosidase, NADPH cytochrome c reductase, and beta-glucan synthase at high affinity for UDP-Glc activities.     

Metabolic capacity for L-citrulline synthesis from ammonia in rat isolated colonocytes.

Ammonia is present at high concentration in the colon lumen and is considered a colon cancer suspect. Furthermore, ammonia usually eliminated by the liver in the ornithine cycle is considered highly toxic to cerebral function when present in excess in the blood plasma. Therefore, the metabolic pathways involved in ammonia metabolism in colonocytes were studied in the present study. Rat colonocytes were found equipped with low carbamoylphosphate synthase I activity, high ornithine carbamoyltransferase and arginase activities and low argininosuccinate synthase activity. High (10 and 50 mmol/l) NH4Cl concentrations but not low concentrations (1 and 5 mmol/l) were found able to increase respectively 3- and 10-fold the conversion of radioactive L-arginine to L-citrulline. In contrast, very low capacity for L-citrulline conversion to L-arginine is found in colonocytes. It is concluded that an incomplete ornithine cycle is operative in colonocytes which results in ammonia stimulated L-citrulline production. The contribution of this metabolic pathway in relation to ammonia detoxication by colonocytes is discussed.     

Estimation of chlorophyll a distribution in the photosynthetic pigment systems I and II of the blue-green alga Anabaena variabilis.

Chlorophyll a distribution in pigment systems I and II was estimated with the blue-green alga Anabaena variabilis by two methods: first, with intact cells using delayed light emission as an index reaction; second, by measuring the 2,6-dichlorophenolindophenol-Hill reaction and the cytochrome c photooxidation in membrane fragments. The first estimation indicated that 0.053+/-0.014 of total chlorophyll a functions as a component of pigment system II, and the second method 0.086+/-0.012. Though the values were somewhat different in the two methods, both estimations indicated that pigment system II chlorophyll a occupies a very small fraction of total chlorophyll a.     

SuperFine: fast and accurate supertree estimation

Many research groups are estimating trees containing anywhere from a few thousands to hundreds of thousands of species, toward the eventual goal of the estimation of a Tree of Life, containing perhaps as many as several million leaves. These phylogenetic estimations present enormous computational challenges, and current computational methods are likely to fail to run even on data sets in the low end of this range. One approach to estimate a large species tree is to use phylogenetic estimation methods (such as maximum likelihood) on a supermatrix produced by concatenating multiple sequence alignments for a collection of markers; however, the most accurate of these phylogenetic estimation methods are extremely computationally intensive for data sets with more than a few thousand sequences. Supertree methods, which assemble phylogenetic trees from a collection of trees on subsets of the taxa, are important tools for phylogeny estimation where phylogenetic analyses based upon maximum likelihood (ML) are infeasible. In this paper, we introduce SuperFine, a meta-method that utilizes a novel two-step procedure in order to improve the accuracy and scalability of supertree methods. Our study, using both simulated and empirical data, shows that SuperFine-boosted supertree methods produce more accurate trees than standard supertree methods, and run quickly on very large data sets with thousands of sequences. Furthermore, SuperFine-boosted matrix representation with parsimony (MRP, the most well-known supertree method) approaches the accuracy of ML methods on supermatrix data sets under realistic conditions.     

Assessment of protein model structure accuracy estimation in CASP13: Challenges in the era of deep learning

Scoring model structure is an essential component of protein structure prediction that can affect the prediction accuracy tremendously. Users of protein structure prediction results also need to score models to select the best models for their application studies. In Critical Assessment of techniques for protein Structure Prediction (CASP), model accuracy estimation methods have been tested in a blind fashion by providing models submitted by the tertiary structure prediction servers for scoring. In CASP13, model accuracy estimation results were evaluated in terms of both global and local structure accuracy. Global structure accuracy estimation was evaluated by the quality of the models selected by the global structure scores and by the absolute estimates of the global scores. Residue-wise, local structure accuracy estimations were evaluated by three different measures. A new measure introduced in CASP13 evaluates the ability to predict inaccurately modeled regions that may be improved by refinement. An intensive comparative analysis on CASP13 and the previous CASPs revealed that the tertiary structure models generated by the CASP13 servers show very distinct features. Higher consensus toward models of higher global accuracy appeared even for free modeling targets, and many models of high global accuracy were not well optimized at the atomic level. This is related to the new technology in CASP13, deep learning for tertiary contact prediction. The tertiary model structures generated by deep learning pose a new challenge for EMA (estimation of model accuracy) method developers. Model accuracy estimation itself is also an area where deep learning can potentially have an impact, although current EMA methods have not fully explored that direction.     

Influence of mutational and sampling factors on the estimation of demographic parameters in a "continuous" population under isolation by distance

In numerous species, individual dispersal is restricted in space so that "continuous" populations evolve under isolation by distance. A method based on individual genotypes assuming a lattice population model was recently developed to estimate the product Dsigma2, where D is the population density and sigma2 is the average squared parent-offspring distance. We evaluated the influence on this method of both mutation rate and mutation model, with a particular reference to microsatellite markers, as well as that of the spatial scale of sampling. Moreover, we developed and tested a nonparametric bootstrap procedure allowing the construction of confidence intervals for the estimation of Dsigma2. These two objectives prompted us to develop a computer simulation algorithm based on the coalescent theory giving individual genotypes for a continuous population under isolation by distance. Our results show that the characteristics of mutational processes at microsatellite loci, namely the allele size homoplasy generated by stepwise mutations, constraints on allele size, and change of slippage rate with repeat number, have little influence on the estimation of Dsigma2. In contrast, a high genetic diversity (approximately 0.7-0.8), as is commonly observed for microsatellite markers, substantially increases the precision of the estimation. However, very high levels of genetic diversity (>0.85) were found to bias the estimation. We also show that statistics taking into account allele size differences give unreliable estimations (i.e., high variance of Dsigma2 estimation) even under a strict stepwise mutation model. Finally, although we show that this method is reasonably robust with respect to the sampling scale, sampling individuals at a local geographical scale gives more precise estimations of Dsigma2.     

Improving Collective Estimations Using Resistance to Social Influence

Groups can make precise collective estimations in cases like the weight of an object or the number of items in a volume. However, in others tasks, for example those requiring memory or mental calculation, subjects often give estimations with large deviations from factual values. Allowing members of the group to communicate their estimations has the additional perverse effect of shifting individual estimations even closer to the biased collective estimation. Here we show that this negative effect of social interactions can be turned into a method to improve collective estimations. We first obtained a statistical model of how humans change their estimation when receiving the estimates made by other individuals. We confirmed using existing experimental data its prediction that individuals use the weighted geometric mean of private and social estimations. We then used this result and the fact that each individual uses a different value of the social weight to devise a method that extracts the subgroups resisting social influence. We found that these subgroups of individuals resisting social influence can make very large improvements in group estimations. This is in contrast to methods using the confidence that each individual declares, for which we find no improvement in group estimations. Also, our proposed method does not need to use historical data to weight individuals by performance. These results show the benefits of using the individual characteristics of the members in a group to better extract collective wisdom.     

Measurement of ammonia and glutamine in cell culture media by gas sensing electrodes

Summary This paper describes the use of a commercially available off-line gas sensing electrode for determination of ammonia and glutamine in cell culture media. The measurement technique was tested in different media preparations with different serum concentrations. The glutamine decomposition was studied as a function of pH for cell culture medium and the results were compared to those obtained by conventional methods,i.e., HPLC. Finally, glutamine and ammonia metabolism were studied during the cultivation of a hybridoma cell line.     

Influence of food ration, copper exposure and exercise on the energy metabolism of common carp (Cyprinus carpio)

The present study was conducted to extend the understanding of the combined physiological effects of different food rations in combination with sublethal levels of copper in common carp (Cyprinus carpio). Fish acclimated to low (0.5% body weight) and high (5% body weight) food rations were exposed to 1 microM copper for a period of 28 days and kept for a further 14 days in copper free water to examine their recovery. Measurements of oxygen consumption, ammonia excretion and ammonia accumulation in plasma and muscle were done at various time intervals during the experimental period. Overall, oxygen consumption and ammonia excretion rates were significantly affected by food ration in both copper free and copper exposed fish. Additional challenges, such as copper exposure and/or exercise, significantly increased plasma and muscle ammonia in the fish fed a high food ration. Muscle ammonia levels in general responded slower (first increase after 72 h) and recovered within 2 weeks of exposure. There was a significant correlation between plasma ammonia levels, muscle ammonia levels and ammonia excretion rates. Influence of copper in terms of ammonia excretion and plasma ammonia accumulation was observed in high ration fish but low ration fish remained unaffected. This clearly indicates that ammonia metabolism was significantly influenced by copper in this group of fish showing that during unfavourable environmental conditions a high amount of food supply may turn deleterious to fish.     

REML estimation of variance parameters in nonlinear mixed effects models using the SAEM algorithm

Nonlinear mixed effects models are now widely used in biometrical studies, especially in pharmacokinetic research or for the analysis of growth traits for agricultural and laboratory species. Most of these studies, however, are often based on ML estimation procedures, which are known to be biased downwards. A few REML extensions have been proposed, but only for approximated methods. The aim of this paper is to present a REML implementation for nonlinear mixed effects models within an exact estimation scheme, based on an integration of the fixed effects and a stochastic estimation procedure. This method was implemented via a stochastic EM, namely the SAEM algorithm. The simulation study showed that the proposed REML estimation procedure considerably reduced the bias observed with the ML estimation, as well as the residual mean squared error of the variance parameter estimations, especially in the unbalanced cases. ML and REML based estimators of fixed effects were also compared via simulation. Although the two kinds of estimates were very close in terms of bias and mean square error, predictions of individual profiles were clearly improved when using REML vs. ML. An application of this estimation procedure is presented for the modelling of growth in lines of chicken.     

Segmental norepinephrine and dopamine levels in cat spinal cord

Tissue levels of norepinephrine in the uninjured cat were determined by a fluorimetric or enzymatic radiometric assay technique. There were no significant differences of NE levels between the two techniques. The highest concentrations of NE were found in the cervical (.170 ug/g) and lumbar (.232 ug/g) enlargements and appear to be related to the relative amount of grey and white matter present at these levels. Dopamine levels, as determined by the enzymatic radiometric assay technique, were found to be low in those spinal segments measured (less than 0.030 ug/g). DA appears to be similarly distributed as norepinephrine in the spinal segments. Barbiturate or nitrous oxide anesthetic agents did not result in significant differences in NE determinations at cervical or thoracic segments. Variability of reported NE and DA levels from other studies appears to be related to differences in assay technique.     

Short-term physiological changes in turbot and seabream juveniles exposed to exogenous ammonia

Seabream and turbot juveniles (40-520 g) were exposed to constant exogenous NH5-N concentrations (1.27-4.27 mmol/l; pH, 8.15). In 96 hr acclimated fish, plasma TA-N (total ammonia nitrogen) contents were positively correlated to ambient ammonia concentrations. The LD50 were 2.2-2.5 mmol/l TA-N in both species. There were no marked osmoregulatory disturbances and plasma urea-N, thyroid hormones levels and gill (Na-K)-ATPase activities were only affected at the highest concentrations. Liver GOT, GPT and GIDH activity dose-response were low and species dependent. In cannulated and non-cannulated turbot exposed to half 96 hr LC50 (lethal ambient concentration for 50% of the population), there was a rapid, pronounced and prolonged increase in plasma TA-N, followed by an immediate decline when exogenous ammonia supply was stopped. Maximum loading and unloading were observed within 1-3 hr. Plasma cortisol levels indicated a stressful situation in exposed fish (150 ng/ml) and a quick recovery capacity. In dose and time response experiments, the most relevant physiological indicator of ammonia stress was blood TA-N content. Other parameters tested led either to transient or low amplitude responses except when fish approached death.     

Estimation of the absolute density of adult Ixodes persulcatus ticks according to the results of collecting per flag-hour (Ixodidae)

The results of two methods of estimation of abundance of adult Ixodes persulcatus ticks, the absolute (at the sample plots) and the relative (per flag-hour) estimations, were compared. Collecting of ticks and estimation of their abundance was conducted during 9 years at the forests of the Far East and Pre-Ural region. The total of 1995 plots (100 sq. m each) were studied and 865 flag-hours were carried out. A good correlation of the data, obtained by these methods, was revealed. The average number of adult ticks, collected per flag-hour, approximately corresponds to the average number of ticks, activated during the season at 100 sq. m. The possibility of corresponding re-calculation of the results of estimation per flag-hour into the parameters of tick population density was evaluated. It was shown that such re-calculation gives good results. Their inexactitude usually doesn't exceed the statistical error of the parameters, obtained by the estimation of tick density at sample plots.