Evaluation of methods for determining N-acetyl-beta-D-glucosaminidase in urine of rats without purification of urine samples.

N-Acetyl-beta-D-glucosaminidase (NAG) activities in urine of rats were measured with methods recommended as procedures without the pretreatment of urine sample. Four different derivatives [4-nitrophenyl; 3-cresolsulfonephthaleinyl; 3,3'-dichlorophenylsulfonephthaleinyl; 2-methoxy-4-(2-nitrovinyl)phenyl] of N-acetyl-beta-D-glucosaminide were compared for determination. The conventional test using the 4-nitrophenyl derivative showed the highest activities and was very well correlated with the other tests. The test using the 3,3'-dichlorophenylsulfonephthaleinyl substrate is most convenient and practical to determine NAG in small animals because it is, in contrast to the other three discontinuous (endpoint) tests, a continuous (kinetic) assay which can be easily adapted to clinical chemistry analyzers.     

Changes in N-acetyl-beta-D-glucosaminidase activity in the urine and urinary albumin excretion in magnesium deficient rats

To discover the details of the effects of magnesium (Mg) deficiency on kidney function, the course of changes in N-acetyl-beta-D-glucosaminidase (NAG) activity in the urine and in urinary albumin excretion were examined in rats fed a Mg-deficient diet. NAG activity in the urine and urinary albumin excretion in rats fed the Mg-deficient diet significantly increased from 7 d until the end of the feeding period. We suggest that Mg-deficient diet rapidly induces kidney function insufficiency.     

The effect of sample size and species characteristics on performance of different species distribution modeling methods

Species distribution models should provide conservation practioners with estimates of the spatial distributions of species requiring attention. These species are often rare and have limited known occurrences, posing challenges for creating accurate species distribution models. We tested four modeling methods (Bioclim, Domain, GARP, and Maxent) across 18 species with different levels of ecological specialization using six different sample size treatments and three different evaluation measures. Our assessment revealed that Maxent was the most capable of the four modeling methods in producing useful results with sample sizes as small as 5, 10 and 25 occurrences. The other methods compensated reasonably well (Domain and GARP) to poorly (Bioclim) when presented with datasets of small sample sizes. We show that multiple evaluation measures are necessary to determine accuracy of models produced with presence-only data. Further, we found that accuracy of models is greater for species with small geographic ranges and limited environmental tolerance, ecological characteristics of many rare species. Our results indicate that reasonable models can be made for some rare species, a result that should encourage conservationists to add distribution modeling to their toolbox.     

Ixodes ticks: serum species sensitivity of anticomplement activity

Ixodid ticks feed for extended periods of up to 2 weeks or more. To complete engorgement, they must overcome their host's innate immune mechanisms of which the complement system is a major component. Using in vitro assays, salivary gland extracts of the ixodid ticks, Ixodes ricinus, I. hexagonus, and I. uriae, were shown to inhibit activity of the alternative pathway of complement. The ability of the different Ixodes species to inhibit complement activity varied with the animal species used as a complement serum source. Serum species sensitivity correlates to the reported host range of the tick species tested.     

Evaluating the performance of species richness estimators: sensitivity to sample grain size

1. Fifteen species richness estimators (three asymptotic based on species accumulation curves, 11 nonparametric, and one based in the species-area relationship) were compared by examining their performance in estimating the total species richness of epigean arthropods in the Azorean Laurisilva forests. Data obtained with standardized sampling of 78 transects in natural forest remnants of five islands were aggregated in seven different grains (i.e. ways of defining a single sample): islands, natural areas, transects, pairs of traps, traps, database records and individuals to assess the effect of using different sampling units on species richness estimations. 2. Estimated species richness scores depended both on the estimator considered and on the grain size used to aggregate data. However, several estimators (ACE, Chao 1, Jackknifel and 2 and Bootstrap) were precise in spite of grain variations. Weibull and several recent estimators [proposed by Rosenzweig et al. (Conservation Biology, 2003, 17, 864-874), and Ugland et al. (Journal of Animal Ecology, 2003, 72, 888-897)] performed poorly. 3. Estimations developed using the smaller grain sizes (pair of traps, traps, records and individuals) presented similar scores in a number of estimators (the above-mentioned plus ICE, Chao2, Michaelis-Menten, Negative Exponential and Clench). The estimations from those four sample sizes were also highly correlated. 4. Contrary to other studies, we conclude that most species richness estimators may be useful in biodiversity studies. Owing to their inherent formulas, several nonparametric and asymptotic estimators present insensitivity to differences in the way the samples are aggregated. Thus, they could be used to compare species richness scores obtained from different sampling strategies. Our results also point out that species richness estimations coming from small grain sizes can be directly compared and other estimators could give more precise results in those cases. We propose a decision framework based on our results and on the literature to assess which estimator should be used to compare species richness scores of different sites, depending on the grain size of the original data, and of the kind of data available (species occurrence or abundance data).     

A bioinformatics approach for determining sample identity from different lanes of high-throughput sequencing data

The ability to generate whole genome data is rapidly becoming commoditized. For example, a mammalian sized genome (～3Gb) can now be sequenced using approximately ten lanes on an Illumina HiSeq 2000. Since lanes from different runs are often combined, verifying that each lane in a genome's build is from the same sample is an important quality control. We sought to address this issue in a post hoc bioinformatic manner, instead of using upstream sample or "barcode" modifications. We rely on the inherent small differences between any two individuals to show that genotype concordance rates can be effectively used to test if any two lanes of HiSeq 2000 data are from the same sample. As proof of principle, we use recent data from three different human samples generated on this platform. We show that the distributions of concordance rates are non-overlapping when comparing lanes from the same sample versus lanes from different samples. Our method proves to be robust even when different numbers of reads are analyzed. Finally, we provide a straightforward method for determining the gender of any given sample. Our results suggest that examining the concordance of detected genotypes from lanes purported to be from the same sample is a relatively simple approach for confirming that combined lanes of data are of the same identity and quality.     

Determination of catecholamines in urine and plasma by on-line sample pretreatment using an internal surface boronic acid gel

An automated method of analysis of catecholamines using a new packing material, internal surface boronic acid gel, was developed. The new support is designed with a carboxymethylcellulose-bonded external surface in order to be non-adsorptive to proteins and with a phenylboronic acid-bonded internal surface to retain only catecholamines. This packing support displayed an affinity for basic or neutral catecholic compounds with no protein adsorption and enabled on-line sample pretreatment of catecholamines in urine and deproteinized plasma. The catecholamines were selectively adsorbed on the new material and separated on a reversed-phase or a cation-exchange column. These compounds were then detected electrochemically. The limits of quantitation were 1.5–3.0 ng/ml in urine and 10–15 pg/ml in plasma, at a signal-to-noise ratio of 5.     

Protein location and elemental composition of urine spheres in different avian species

We examined the internal morphology, location of protein, and identity and location of elements, in avian urate-containing spheres in 9 species of birds. The urine spheres were collected from voided samples. The spheres ranged in size from 0.5-5.0 microm, except in the domestic fowl, where they ranged up to 10 microm in diameter. The internal morphology of the spheres was examined using freeze-fracture microscopy. Protein location within the spheres was identified using fluorescein isothiocyanate (FITC). The urine spheres were analyzed for content and internal location of elements using Energy Dispersal System Analysis (EDS). Internally, the spheres consisted of a central nidus surrounded by 3-4 concentric narrow rings of protein. Elements found within the spheres included nitrogen, potassium, calcium, sodium, phosphorus, chloride and sulfur; however, only nitrogen, potassium and chloride were common in the spheres of all species. Nitrogen comprised the majority of the elemental content of the spheres (77-90%) followed by potassium (8-45%), with all other ions present in trace amounts. Unlike protein, the location of elements was random within the spheres. Protein and urate are both negatively charged and known to associate to form the spheres and as potassium is the only cation common to all spheres, it too may play a role in their formation.     

Methods of determining renin activity in individual renal glomeruli and their fragments

The author suggests a modification of the method for determination of renin activity in a single glomerulus and its fragments, based on the use of cold EDTA-treated plasma of nephrectomized animals as renin substrate source, instead of a complicated method of substrate obtaining from plasma. The renin bioassay method was somewhat simplified. All the procedures were conducted with the use of home-produced equipment. The principle of this modification can be used for clinical purposes.     

Technologies and methods for sample pretreatment in efficient proteome and peptidome analysis

Although great progresses have been made in proteomics during the last decade, proteomics is still in its infancy. Extreme complexity of proteome sample and large dynamic range of protein abundance overwhelm the capability of all currently available analytical platforms. Sample pretreatment is a good approach to reduce the complexity of proteome sample and decrease the dynamic range. In this article, we present an overview of different technologies and methods for sample pretreatment in efficient proteome and peptidome analysis. Methods for isolation of rare amino acid-containing peptides, terminal peptides, PTM peptides and endogenous peptides are reviewed. In addition, two automated sample pretreatment technologies, i.e. automated sample injection and on-line digestion, are also covered.     

Antimicrobial activity in urine: effect on leukocyte count and bacterial culture results

A total of 500 urine specimens collected from non-hospitalized patients were investigated for leukocyte count by microscopy, bacterial recovery by culture, and detection of antimicrobial activity by disc diffusion. Results indicated that 21% of the specimens contained leukocytes > or = 50/cu mm, whereas 14.4% of specimens revealed significant bacterial growth. The use of Staphylococcus aureus ATCC 29737 as a test bacterium detected the antimicrobial activity in 19.2% of the urine specimens, while the use of two clinical isolates of Escherichia coli detected this activity in fewer specimens. Evidence is provided which indicates that bacterial growth inhibitors in urine are mainly due to the intake of antibiotics by patients. These inhibitors confused the interpretation of urine culture results as they were found to play a major role in the occurrence of sterile pyorrhea and in reducing the number of specimens yielding significant bacterial growth.     

Age related changes of N-acetyl-beta-D-glucosaminidase and L-alanine aminopeptidase in mouse kidney, urine and plasma

Age and sex dependent differences of N-acetyl-beta-D-glucosaminidase (NAG) and L-alanine aminopeptidase (AAP) activities in kidney, urine and plasma of male and female mice were studied. The sex difference in NAG activity appeared between 27 and 38 days of age with the manifestation of significant differences in body weight and kidney growth. NAG activity in male kidneys was 3-fold that in females and its urinary level in mature males was over 10-fold higher. Androgenic regulation was found not only in the NAG contents in the kidneys and in the urinary excretion but also in the plasma NAG level, which showed higher in females. On the other hand, AAP activity in kidney, urine and plasma did not show much sex differences. Age related changes in AAP activity were not found except in the kidney and marked androgenic regulation was also not found in AAP. These results indicate that NAG and AAP, which are both urinary enzymes used as indicators of renal lesions, may be regulated differently.     

Use of a culture of human peripheral blood lymphocytes for determining the mutagenic activity of urine

The present study shows that the culture of human peripheral lymphocytes may be used as target cells for detecting the whole urine mutagenic activity. It is established that urine from healthy control cigarette smokers and from non-smoking greenhouse workers contacting with a complex of different pesticides significantly increased frequency of chromosome aberrations in the approbated test-system. The data obtained give evidence for the presence of genetically active substances in organisms of the examined individuals.     

Age-dependent excretion of alanine aminopeptidase, alkaline phosphatase, gamma-glutamyltransferase and N-acetyl-beta-D-glucosaminidase in human urine

Urinary excretion of alanine aminopeptidase, alkaline phosphatase, gamma-glutamyltransferase and N-acetyl-beta-D-glucosaminidase was determined in gel-filtered samples of morning random urine specimens of 442 subjects of various ages (5 days to 58 years). Enzyme excretion related to urinary creatinine (enzyme/creatinine ratio; U/mmol creatinine) significantly decreased with increasing age. Sex-related differences of some enzyme excretions were found in age groups over 6 years. From these investigations, we calculated upper reference intervals (97.5 percentiles) for 5 age-dependent groups of children and adolescents and for one group of adults.     

Arginine and methylated arginines in human plasma and urine measured by tandem mass spectrometry without the need for chromatography or sample derivatisation

A method for the simultaneous analysis of asymmetric dimethylarginine, symmetric dimethylarginine, monomethylarginine and arginine in human plasma and urine, with short analysis time and isotopic internal standardisation for each analyte is described. The method requires neither sample derivatisation nor the need for chromatographic separation of analytes. The method described shows good precision and accuracy and is suited for both research purposes and implementation in the busy, routine clinical laboratory. In addition the synthesis and utilisation of isotopically labelled symmetric dimethylarginine and monomethylarginine is described for the first time, avoiding the use of surrogates such as homoarginine for internal standardisation.