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PubMed2003

Partitioning species diversity across landscapes and regions: a hierarchical analysis of alpha, beta, and gamma diversity.

Species diversity may be additively partitioned within and among samples (alpha and beta diversity) from hierarchically scaled studies to assess the proportion of the total diversity (gamma) found in different habitats, landscapes, or regions. We developed a statistical approach for testing null hypotheses that observed partitions of species richness or diversity indices differed from those expected by chance, and we illustrate these tests using data from a hierarchical study of forest-canopy beetles. Two null hypotheses were implemented using individual- and sample-based randomization tests to generate null distributions for alpha and beta components of diversity at multiple sampling scales. The two tests differed in their null distributions and power to detect statistically significant diversity components. Individual-based randomization was more powerful at all hierarchical levels and was sensitive to departures between observed and null partitions due to intraspecific aggregation of individuals. Sample-based randomization had less power but still may be useful for determining whether different habitats show a higher degree of differentiation in species diversity compared with random samples from the landscape. Null hypothesis tests provide a basis for inferences on partitions of species richness or diversity indices at multiple sampling levels, thereby increasing our understanding of how alpha and beta diversity change across spatial scales.

Animals↗
PubMed2003

Analysis of the microbial functional diversity within water-stressed soil communities by flow cytometric analysis and CTC+ cell sorting.

Total and active cell counts within soil samples were determined by culture-independent methods using flow cytometry and preparative Nycodenz gradient centrifugation. Whole cells were purified from soil cores and total extractable cell counts assessed by SYBR Green II fluorescence, while active cell counts were determined by 5-cyano-2,3-ditolyl tetrazolium chloride reduction (CTC+ cells). Parallel microcosms, maintained at either field water capacity or subjected to drying, indicated that the total extractable cell count remained between 10(8) and 10(9) g(-1) (dry weight). In contrast, the CTC+ active count fell threefold in dried microcosms (6% of total cell count) when compared to wetted microcosms (18% of total cell count). Specifically, these data highlighted an overall deactivation of microbial biomass during water stress, with 16S rDNA analyses of flow-sorted CTC+ cells demonstrating shifts within the active diversity. Flow cytometry coupled with cell purification techniques represents a significant tool for operationally defining an active and redundant microbial component within soil communities and is demonstrated during water stress.

Bacteria↗
PubMed1987

Origins of macrophage diversity: functional and phenotypic analysis of cloned populations of mouse splenic macrophages.

Soft-agar colonies of mouse splenic macrophages were examined for surface and functional characteristics that might prove useful in studying the origin(s) of macrophage diversity. Flow cytoflurometric analysis revealed that essentially all cells in all of the colonies bore the Mac-1 and Mac-3 antigens. The colonies did not differ appreciably in their phagocytic activity or in their secretion of lysozyme, but did show different patterns of Mac-2 antigen expression. In most colonies, the cells expressed low levels of the antigen, and in the remainder they expressed a high or an intermediate level of Mac-2. The colonies also differed in their ability to present keyhole limpet hemocyanin (KLH) to an antigen-specific H-2-restricted T-cell hybridoma. About 6% of the colonies gave rise to subcultures with antigen-presenting activity. This presentation was always associated with subcultures containing a high proportion of Ia-bearing macrophages, but not all cultures with similarly high proportions of Ia-bearing cells presented KLH to the hybridoma. Indeed, the induction of Ia on all cells in all cultures increased the proportion of KLH-presenting subcultures only about twofold. The results show that not all splenic macrophages have the ability to process KLH and present it to a T-cell hybridoma. This suggests the presence of functionally specialized subpopulations of macrophages, possibly derived from distinct progenitors, in the spleens of mice.

Animals↗
PubMedDate not supplied

Some current themes in functional analysis research.

The purpose of this article is to review and discuss some current themes in functional analysis research. The paper is divided into two general sections; one section discusses clinical application of functional analysis and a second section discusses functional analysis as a research method. In the first section, current issues related to treatment logic and development are reviewed. Also, clinical limitations of functional analysis are described, including treatment and assessment implementation issues (such as time and resource constraints). In the second section, three areas of research are reviewed with suggestions for further research: the analysis of diverse response topographies, the analysis of basic behavioral processes, and the evaluation of methodological refinements.

Behavior Therapy↗
PubMed2006

DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments.

In order to evaluate whether different DNA extraction procedures can affect estimates of benthic bacterial diversity, based on 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) fingerprinting technique, we compared two in situ lysis procedures (a SDS-based protocol and a commercial kit for DNA recovery) and one cell-extraction protocol on a variety of marine sediments. Despite the two in situ lysis procedures resulted in significantly different DNA yields (highest with the SDS in situ lysis), estimates of bacterial diversity provided a not significantly different ribotype richness, as well as similar values of the Shannon-Wiener (H') and Margalef (d) indices of biodiversity and of evenness (Pielou index, J). Conversely, the cell-extraction procedure for DNA extraction resulted always in a significantly lower ribotype richness and diversity. The analysis of similarities (anosim) among the T-RFLP electropherograms allowed concluding that ribotypes composition did not change significantly using different protocols. However, the analysis of beta-diversity (turnover diversity) revealed that a large number of ribotypes was observed exclusively with one of the three protocols utilized. When unshared ribotypes from in situ lysis and cell extraction were pooled together, total ribotype richness resulted much higher (up to 80%). Our results indicate that estimates of ribotype diversity based on a single protocol of DNA extraction can significantly underestimate the total number of bacterial ribotypes present in the benthic domain. We recommend that future studies will not only integrate different DNA extraction procedures, but also will explore the possibility of integrating two or more different genetic markers in order to increase our ability to detect the actual bacterial diversity in environmental samples.

Bacteria↗
PubMed2006

A molecular approach to the characterization of the eukaryotic communities of an extreme acidic environment: methods for DNA extraction and denaturing gradient gel electrophoresis analysis.

The diversity of the phytobenthonic community present in six acidophilic microbial mats from Río Tinto (Iberian Pyritic Belt, SW Spain) was analysed by optical microscopy and two molecular techniques, denaturing gradient gel electrophoresis (DGGE) and sequence analysis of 18S rDNA cloned gene fragments. Sixteen DNA isolation protocols as well as two commercial DNA extraction kits were tested and their efficiency compared. Purified DNA extracts were amplified by PCR using universal eukaryotic primers and the PCR products analysed by DGGE. Bead-mill homogenization was found to be superior to the other cell lysis methodologies assayed (sonication or freeze-thawing cycles) as it allowed efficiencies of cell disruption of over 95%. The methods combining bead-mill homogenization in the presence of SDS, treatment with chemical extractants (hexadecylmethylammonium bromide or guanidine isothiocyanate) and phenol extraction resulted in DNA preparations that amplified the same number of bands when analysed by DGGE as the two commercial kits assayed. The phylogenetic affiliations of the DGGE bands were determined by a BLAST search, and nine different species related to the Chlorophyta, Ciliophora, Kinetoplastida, Ascomycota, Streptophyta and Colcochaetales taxonomical groups were identified. Similar levels of diversity were found using cloning procedures. Although not all the species observed under the microscope were detected using molecular techniques, e.g. euglenas, heliozoan, or amoebae, DGGE fingerprints showed rather well the level of diversity present in the samples analysed, with limitations similar to cloning techniques.

Animals↗
PubMed1992

Antigenic diversity in Haemophilus ducreyi as shown by western blot (immunoblot) analysis.

The antigenic diversity within a panel of 63 Haemophilus ducreyi isolates was examined by Western blot (immunoblot) analysis with a pool of 238 well-characterized human antisera. When a serum pool adsorbed on a mixture of Haemophilus influenzae, H. parainfluenzae, and H. parahaemolyticus was used, the immunoprofiles suggested that prominent antigenic proteins involved in the human immune response have apparent molecular masses of 63, 42, 34 to 30, and 28.5 to 28 kDa. Preliminary subcellular localization revealed that these antigens are associated with the cellular membrane. Two subsets of antigens were discriminated by detergent extraction. There was no evidence that the antigen composition is altered by changing the growth conditions. With a serum pool adsorbed on the Haemophilus spp. mixture supplemented with Actinobacillus actinomycetemcomitans, Pasteurella ureae, Neisseria gonorrhoeae, and Escherichia coli, antigenic determinants more specific for H. ducreyi were identified. An immunodominant 28.5- to 28-kDa protein was expressed by all H. ducreyi isolates. In the range from 34 to 30 kDa, 56 isolates revealed a dominant protein with variable molecular mass. By using both proteins (28.5 to 28 kDa and 34 to 30 kDa) as immunotypic markers, seven different immunopatterns were identified. Antigenic diversity among isolates from different geographical origins as well as from a single area was observed.

Adsorption↗
PubMed1996

Simultaneous carriage of Candida albicans strains from HIV-infected patients with oral candidiasis: multilocus enzyme electrophoresis analysis.

Genetic diversity of 160 Candida albicans isolates from the oral cavity of 16 HIV-infected adults prior to antifungal treatment was assessed using multilocus enzyme electrophoresis (10 C. albicans colonies were randomly chosen from each specimen culture). 20 electrophoretic types were distinguished from the analysis of 21 enzyme loci (10 were polymorphic). Five patients (31%) were found to be colonized by 2 or 3 genetically distinct strains. Nevertheless, in these five cases, one strain predominated (from 7 to 9 of the 10 colonies). Some HIV + patients with oral candidiasis appear to be simultaneously infected with several genetically different C. albicans strains before antifungal treatment.

AIDS-Related Opportunistic Infections↗
PubMed2003

[Molecular-genetic polymorphisms of cultivars of common hops (Humulus lupulus L.) using ISSR-PCR analysis].

Genetic diversity among 26 Russian and European cultivars of the common hop (Humulus lupulus L.) was studied using the ISSR-PCR technique. Twenty-one primers used provided amplification of 183 DNA fragments, 106 of which (57.9%) were found to be polymorphic. The ISSR markers, specific for certain cultivars were revealed. Based on the coefficient of dissimilarity values, cluster analysis was performed and a dendrogram was constructed, on which most of the hop cultivars formed two clusters according to their origin. Advantages of the ISSR-PCR analysis in selective studies aimed at the classification and identification of common hop cultivars are discussed.

Humulus↗
PubMed1996

Epitope Mapping by Label-Free Biomolecular Interaction Analysis

The diversity of B-cell response to a large immunogen gives rise to a series of antibodies that can be used for epitope mapping of an antigen. This is based on the relative reaction pattern for all antibodies in relation to each other and other ligands to the studied protein. With the introduction of an instrument system, BIAcore, label-free real-time biomolecular interaction analysis (BIA) was made possible. It is based on biosensor technology, with a carboxymethyl-dextran-coated gold surface and an integrated fluidics for transport of liquid. The basic idea is to measure label-free binding of an analyte from a continuous flow to an immobilized ligand in real time. With an automatic approach, quantitative analysis and sequential injection characteristic biospecific binding parameters such as affinity and kinetic constants can be measured. The instrument system was adopted at an early stage for epitope mapping. With label-free detection, antibodies from tissue culture media can be analyzed without purification. Binding of both antigen and a series of antibodies can be individually determined in molar ratio by sequential injections. The quantitative aspects of BIA offer the possibility of further refined epitope mapping. The relative binding pattern for 30 monoclonal antibodies against HIV-1 p24 core protein has been analyzed. Multideterminant analysis and peptide identification of binding sites were performed. Verification of the binding pattern has also been performed in relation to mapping with ELISA as well as the binding to peptides derived from the antigen sequence. Functional domains of proteins in relation to an epitope map have been identified for Taq polymerase.

Journal Article↗
PubMed2004

A 15-year evaluation of biliopancreatic diversion according to the Bariatric Analysis Reporting Outcome System (BAROS).

BACKGROUND: Biliopancreatic diversion (BPD) is the most effective bariatric procedure in terms of weight loss. However, analysis of the quality of life (QoL) has never been reported. The BAROS, giving a score to each operated patient on weight loss, improvement in medical conditions, QoL, complications and reoperations, has proven to be a standard reference for evaluating bariatric surgery outcomes. METHODS: In order to apply the BAROS to BPD, we sent a questionnaire to 1,800 BPD patients who had been operated between 1984 and 1998. The response-rate was 51.2%. Out of 1,709 questionnaires which actually reached their destination, we had 858 fully compiled returned. There were 615 women. 596 patients had had an ad hoc stomach (AHS) BPD, and 262 had had an ad hoc stomach ad hoc alimentary limb (AHS-AHAL) BPD. RESULTS: According to the scoring key, 3.5% were classified as a failure, 11% were fair results, 22.8% good, 39.5% very good, and 23.2% excellent results. Considering AHS BPD and AHS-AHAL BPD separately,while the mean excess weight percent loss was 70.5+/-23 and 64.7+/-17 respectively, the failure rate was 6% in the first group and 2% in the AHAL group, while 11% and 6% of cases respectively were fair results, 24% and 20% good, 36% and 47% very good, 23% and 25% excellent results. CONCLUSION: The BAROS evaluation of BPD highlights the importance of its flexibility: the new policy of adapting the procedure to individual characteristics caused a drop in the failure rate and an increase in good, very good and excellent results.

Adult↗
PubMed1995

Prevalence of genetic versus environmental factors in human female temporal organization: preliminary analysis.

Genetic diversity among ethnic groups is studied by comparing the genetic fingerprint of the examined groups. This index is constructed by aggregating the differential frequencies of various marker characteristics. Recent advances in the study of human biological rhythms may provide new indexes that will complement the genetic profile of a population. One of the rhythm parameters that is especially useful for this purpose is the acrophase (peak time location). The aim of the present study is to construct a rhythm profile based on acrophase distribution for various human groups and to estimate the contribution of genetic and environmental factors to that profile. The rhythm profiles were constructed by comparing the acrophases of 11 plasma hormones in women from three different ethnic-geographic populations (North Americans, Romanians, and Japanese) with reference to three age groups (adolescence-early postpuberty, young adulthood, and postmenopause). Genetic distances of these ethnic groups were determined by 14 genetic markers. Cluster and principal coordinates analyses were used to define the variation of the two parameters (genetic distances and acrophase dispersion). The analyses show that North Americans and Romanians are closer to each other with regard to both parameters and far apart from the Japanese. However, there was a difference between the variation presented by the first eigenvalue of the genetic profiles (94.5%) and that of the first eigenvalue of the acrophase pattern (69.1%), which means reduction in the variability (increased similarity) among the three ethnic groups according to the acrophase profiles.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗
PubMed2005

Changes in liver volume from birth to adulthood: a meta-analysis.

A diversity of equations is available for the estimation of liver volume (LV), derived from studies in populations of ethnically homogeneous individuals and using a variety of methods of measurement. The aim of this study was to integrate all published pediatric data and to define a general equation for estimating LV from birth onward. Data were collated from 5,036 subjects (birth to 18 yr old). Equations were developed based on simple regression against body surface area (BSA) and multiple regression of LV with weight, height, BSA, age, gender, race, methodology, and year of publication as covariates. These equations, together with those reported in the literature, were compared for accuracy of prediction of LV from birth to 18 yr old. The most parsimonious equation to describe LV was selected according to the Akaike information criteria (AIC), precision and bias and following visual inspection of residual errors and observed vs. predicted plots: LV = 0.722 * BSA(1.176). The multiple regression models indicated that Japanese have up to 19% larger livers compared to Caucasians for a given body weight. Radiographic and ultrasonic measurements were associated with up to 8% lower estimates of liver size compared to measurements made at autopsy. There was no evidence that gender or the year in which a study was published (1933-1999) influenced the estimation of LV. The general equation was also applied to predict adult LV, and its precision and accuracy was found to be superior to those of 10/11 published adult models. In conclusion, we have developed a more general model to predict LV in pediatric populations and young adults, and have investigated a range of covariates.

Adolescent↗
PubMed2000

Molecular diversity of Renibacterium salmoninarum isolates determined by randomly amplified polymorphic DNA analysis.

The molecular diversity among 60 isolates of Renibacterium salmoninarum which differ in place and date of isolation was investigated by using randomly amplified polymorphic DNA (RAPD) analysis. Isolates were grouped into 21 banding patterns which did not reflect the biological source. Four 16S-23S rRNA intergenic spacer (ITS1) sequence variations and two alleles of an exact tandem repeat locus, ETR-A, were the bases for formation of distinct groups within the RAPD clusters. This study provides evidence that the most common ITS1 sequence variant, SV1, possesses two copies of a 51-bp repeat unit at ETR-A and has been widely dispersed among countries which are associated with mainstream intensive salmonid culture.

Animals↗
PubMed2005

Effects of variable docking conditions and scoring functions on corresponding protein-aligned comparative molecular field analysis models constructed from diverse human protein tyrosine phosphatase 1B inhibitors.

The effects of variable docking conditions and scoring functions on corresponding protein-aligned comparative molecular field analysis (CoMFA) models have been assessed. To this end, a group of diverse inhibitors were docked into the active site of human protein tyrosine phosphatase 1B (h-PTP 1B). The docked structures were utilized to construct corresponding protein-aligned CoMFA models by employing probe-based (H+, OH, CH3) energy grids and genetic partial least squares (G/PLS) statistical analysis. A total of 48 different docking configurations were evaluated, of which some succeeded in producing self-consistent and predictive CoMFA models. However, the best CoMFA model coincided with docking the un-ionized ligands into the hydrated form of the binding site via the PLP1 scoring function and restricted docking settings (r2(LOO) = 0.647, r2(PRESS) against 27 test compounds = 0.617). Interestingly, the most significant CoMFA models were orthogonal and corresponded to significantly different docked conformers/poses. To utilize the predictive potentials of the best CoMFA models collectively, it was decided to combine them in a single quantitative structure-activity relationship (QSAR) model. The combination model illustrated excellent statistical properties (r2(LOO) = 0.890, r2(PRESS) against 27 test compounds = 0.750).

Binding Sites↗
PubMed2005

Use of capillary array electrophoresis single-strand conformational polymorphism analysis to estimate genetic diversity of candidate genes in germplasm collections.

Capillary array electrophoresis single-strand conformation polymorphism (CAE-SSCP) analysis provides a reliable high-throughput method to genotype plant germplasm collections. Primers designed for highly conserved regions of candidate genes can be used to amplify DNA from plants in the collection. These amplified DNA fragments of identical length are turned into useful markers by assaying sequence differences by CAE-SSCP analysis. Sequence differences affect the electrophoretic mobility of single-stranded DNA under non-denaturing conditions. By collecting the mobility data for both strands assayed at two temperatures, alleles can be defined by mobility alone. For a germplasm collection with an unknown number of alleles at a locus, such mobility data of homozygotes can be used to determine the number of unique alleles without the necessity of cloning and sequencing each allele.

Alleles↗
PubMed2001

Genetic diversity within the genus Trichinella as shown by cleavage fragment length polymorphism analysis.

The genetic diversity within the genus Trichinella was studied using cleavage fragment length polymorphism (CFLP) analysis. The CFLP method generates specific fingerprints based on single nucleotide mutations. By this method the amplified intergenic regions of the 5S rRNA genes of the eight different genotypes of Trichinella were analysed. The CFLP pattern of T. spiralis was completely different compared with the sylvatic species T. britovi, T. nativa, T. nelsoni, and the genotypes Trichinella T5, Trichinella T6 and Trichinella T8. The T. pseudospiralis intergenic region can be differentiated by size from the other species of Trichinella.

Animals↗
PubMed1975

Ileal conduit urinary diversion in children: computer analysis of followup from 2 to 16 years.

A 2 to 16-year followup of 96 ileal conduit urinary diversions in children is discussed. To assess the effect of time on renal function and structure we divided the patients into recent and remote operative groups. Patients with a longer followup (average 11.3 years) had a significantly greater incidence of pyelographic deterioration, particularly from preoperative normal status, compared to patients in the short followup group (average 4.5 years). Preoperative pyelonephritis was associated with a small but significant percentage of patients who progressed to poor renal function. Three potentially preventable and correctable late complications--stomal stenosis, excessive conduit length and ureteroileal obstruction--were associated with significant long-term deterioration in either renal function or pyelographic appearance. By using ileal conduit urinary diversion in children we attempt to provide a lifelong solution to urologic and social problems. The pyelographic deterioration rates would suggest that the solution is not perfect. Alternative forms of treatment need similar assessment for comparison. Patients who have ileal conduit urinary diversion need vigilant lifelong followup with accurate assessment of renal function, infection and pyelographic status to prevent or arrest renal deterioration.

Blood Urea Nitrogen↗