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PubMed2003

[A and D genome evolution in Gossypium revealed using SSR molecular markers].

Genetic diversity analysis of diploid and allotetraploid cotton species was carried out using SSR molecular markers by selecting representative species having A and (or) D genome in Gossypium. Ten diploid cotton species in A and D genomes had high polymorphism and the molecular cluster was consistent with Gossypium classification previously reported by Fryxell. From molecular level, G. gossypioides belonging to D genome had low similarity matrix compared with other diploid D genome species. Diploid cotton species separately having A or D genome had their high similarity matrix. The research supported that G. gossypioides was the most original cotton species among all D genome species, different genomes in Gossypium had common origin and made evolution separately. To better understand genetic events that accompany allopolyploid formation, we add 2 cultivated allotetraploid cotton species in our research materials. However, the results showed that it was not appropriate to study evolution of A and D genome in Gossypium using cultivated allotetraploid cotton species. In order to solve the question, original arboreum, herbaceum and wild types of allotetraploid cotton species should be adopted. Further evolution research on cotton species based on the transcription level of cotton genome is being carried on.

DNA, Plant↗
PubMed2004

[Novel molecular marker systems--SRAP and TRAP and their application].

SRAP and TRAP are two kinds of newly developed molecular marker systems with the advantages of simplicity, high throughput, numerous co-dominant makers, highly reproducibility and ready to sequence, especially preferential targeting ORFs. The principle and protocol of SRAP and TRAP, which were developed in Brassica and Helianthus crops firstly, are introduced in the paper. Primer design is a key step for SRAP and TRAP, and some F-and R-primers were developed. Unlike SRAP technique, the TRAP requires cDNA or EST sequence information for fixed primer development. The annealing temperature is 35 degrees in the first 5 cycles and 50 degrees in the subsequent 30~35 cycles. The amplicons can be separated by polyacrylamide or agarose gel, and detected by autoradiography, silver or EB staining. SRAP and TRAP are applied in germplasm genetic diversity analysis, genetic map including transcriptome map construction, important trait gene tagging and gene cloning in many crops.

Acid Phosphatase↗
PubMed2005

Determinants of health-service use by low-income people.

Poverty influences health status, life expectancy, health behaviours, and use of health services. This study examined factors influencing the use of health-related services by people living in poverty. In the first phase, 199 impoverished users of health-related services in 2 large Canadian cities were interviewed by their peers. In the second phase, group interviews with people living in poverty (n = 52) were conducted. Data were analyzed using thematic content analysis. Diverse health-related services were used to meet basic and health needs, to maintain human contact, and to cope with life's challenges. Use of services depended on proximity, affordability, convenience, information, and providers' attitudes and behaviours. Use was impeded by inequities based on income status. To promote the health of people living in poverty, nurses and other health professionals can enhance the accessibility and quality of services, improve their interactions with people living in poverty, provide information about available programs, offer coordinated community-based services, collaborate with other sectors, and advocate for more equitable services and policies.

Alberta↗
PubMed1991

[Bladder replacement and continent diversion: what about metabolic complications?].

During the past several years there has been increasing interest in refunctionalizing patients who have undergone radical extirpative surgery for pelvic malignancies and patients with dysfunctional bladders. To accomplish this, intestinal segments have been successfully employed in a variety of configurations. Independent of their optimal urosurgical implementation these procedures are not without potential complications, a significant portion of which involve metabolic derangements. Besides first follow-up results of patients with bladder substitution or continent urinary diversion, analysis of experimental investigations and functionally comparable clinical conditions enables an insight into potential following physiopathological interrelationships. These concern, besides the problem of chronic metabolic acidosis, disorders of bile acid and vitamin B12 metabolism as well as the potential induction of a secondary hyperoxaluria with subsequent oxalate concrement diathesis. Furthermore, there may be a malabsorption of calcium and vitamin D with development of intestinal osteopathy due to the reduction of absorptive surface. Apart from these problems of enteral loss and deficiency manifestations, several case reports and investigations suggest that bone demineralization can occur as a consequence of chronic metabolic acidosis and patients are at risk of skeletal demineralization. The pathogenesis of this association has yet to be clarified. These physiopathological interrelationships must be considered in medical attendance of patients with intestinal substitute bladders and continent supravesical pouch systems over many years. As these procedures become more popular, it becomes important to identify any metabolic changes that may occur as their consequence.

Animals↗
PubMed1994

Staphylococcal protein A induces biased production of Ig by VH3-expressing B lymphocytes.

Staphylococcal protein A (SPA) is known to bind preferentially to the VH3 family of Ig heavy chain variable gene products. The current studies were conducted to examine the functional capacity of SPA to induce Ig production by VH3-expressing human B cells preferentially. Human peripheral blood B cells stimulated with anti-CD3-activated T cells or the Wood 46 strain of Staphylococcus aureus, which lacks SPA, expressed IgM containing all VH families, as detected by reverse transcription-PCR. In contrast, stimulation with SPA containing S. aureus or SPA-Sepharose resulted in biased expression of VH3 containing IgM. Similarly, cord blood B cells that require costimulation for Ig production induced by anti-CD3-activated T cells produced only VH3 containing IgM on costimulation with SPA containing S. aureus. The sequences of 21 VH3 IgM gene products derived from different B cell sources were determined and found to include at least nine members of the VH3 family, which were both in germ-line configuration and somatically mutated. Use of DH and JH was diverse. Analysis of these VH3 gene products revealed conserved residues in FR1 and 3'CDR2/FR3, which are candidates to play a role in SPA-mediated activation of VH3-expressing B cells. Like T cell superantigens, SPA probably interacts with residues in the partially solvent exposed regions of the heavy chain molecule outside the classical Ag binding site and provides a signal that can lead to Ig production by human B cells expressing VH3.

Amino Acid Sequence↗
PubMed2005

Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques.

Comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16S rRNA gene clone library and improved cultivation-based techniques. Our study demonstrated that the use of gellan gum as a gelling reagent instead of agar was more effective at increasing culturability, cultivating a diverse array of novel microbes, and reducing the gaps of the results between molecular and cultivation-based analyses.

Bacteria↗
PubMed2006

RAPD analysis of genetic diversity and population genetic structure of Stipa krylovii Reshov. in Inner Mongolia steppe.

Random amplified polymorphic DNA (RAPD) analysis was used to characterize the genetic diversity and population genetic structure of Stipa krylovii populations in Inner Mongolia steppe of North China. Thirteen 10 bp oligonucleotide primers, which generated 237 RAPD bands, were used to analyze 90 plants of five populations from three regions, meadow steppe, typical steppe and desert steppe, from the east to the west. The genetic diversity of Stipa krylovii that was revealed by observed number of alleles (na), expected number of alleles (ne), Nei's diversity index (h), Shannon's diversity index (H), amplificated loci, polymorphic loci and the percentage of polymorphic loci (PPB) increased from the east to the west. The Pearson's correlation analysis between genetic diversity parameters and ecological parameters indicated that the genetic diversity of Stipa krylovii was associated with precipitation and cumulative temperature variations along the longitude (humidity were calculated by precipitation and cumulative temperature). Dendrogram based on Jaccard's genetic distance showed that the individuals from the same population formed a single sub-group. Although most variation (56.85%) was within populations, there was high genetic differentiation among populations of Stipa krylovii, high differentiation within and between regions by AMOVA analysis. Either Nei's unbiased genetic distance (G(ST)) or gene flow (Nm) among pairwise populations was not correlated with geographical distance by Mantel's test (P > 0.05), suggesting that there was no consistency with the isolation by distance model in these populations. Natural selection may have played a role in affecting the genetic diversity and population structure, but habitat destruction and degradation in northern grassland in China may be the main factor responsible for high genetic differentiation among populations, within and among regions.

China↗
PubMed1994

The leg of Drosophila as a model system for the analysis of neuronal diversity.

The neurons innervating insect sense organs vary in number, shape, dendritic morphology, axonal projections and connectivity, providing abundant material for the genetic analysis of neuronal diversity. Here we describe the leg of Drosophila as a potential model system for this analysis. The leg of Drosophila comprises a variety of sense organs arranged in a precise and reproducible pattern. The cell bodies of the sensory neurons are located near the organ they innervate, which greatly facilitates their identification and accessibility. The development of the leg from its progenitor structure, the imaginal disc, is known in good detail. In particular, the time of appearance and of divisions of the sense organ precursors is known. The origin and mode of formation of the leg nerve (through which all sensory axons project into the central nervous system) has been described. The central projections of some of the sensory neurons have been examined by horseradish peroxidase backfill or DiI labelling. Finally, the expression of several genes that control the differentiation of various types of sensory neurons can be manipulated at will. We illustrate these different aspects, and discuss the potentials and shortcomings of this system.

Animals↗
PubMed1999

Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities.

An automated method of ribosomal intergenic spacer analysis (ARISA) was developed for the rapid estimation of microbial diversity and community composition in freshwater environments. Following isolation of total community DNA, PCR amplification of the 16S-23S intergenic spacer region in the rRNA operon was performed with a fluorescence-labeled forward primer. ARISA-PCR fragments ranging in size from 400 to 1,200 bp were next discriminated and measured by using an automated electrophoresis system. Database information on the 16S-23S intergenic spacer was also examined, to understand the potential biases in diversity estimates provided by ARISA. In the analysis of three natural freshwater bacterial communities, ARISA was rapid and sensitive and provided highly reproducible community-specific profiles at all levels of replication tested. The ARISA profiles of the freshwater communities were quantitatively compared in terms of both their relative diversity and similarity level. The three communities had distinctly different profiles but were similar in their total number of fragments (range, 34 to 41). In addition, the pattern of major amplification products in representative profiles was not significantly altered when the PCR cycle number was reduced from 30 to 15, but the number of minor products (near the limit of detection) was sensitive to changes in cycling parameters. Overall, the results suggest that ARISA is a rapid and effective community analysis technique that can be used in conjunction with more accurate but labor-intensive methods (e.g., 16S rRNA gene cloning and sequencing) when fine-scale spatial and temporal resolution is needed.

Bacteria↗
PubMed1999

THE THREE DS OF PCR-BASED GENOMIC ANALYSIS OF PHYTOBACTERIA: Diversity, Detection, and Disease Diagnosis.

The advent of molecular biology in general and the polymerase chain reaction in particular have greatly facilitated genomic analyses of microorganisms, provide enhanced capability to characterize and classify strains, and facilitate research to assess the genetic diversity of populations. The diversity of large populations can be assessed in a relatively efficient manner using rep-PCR-, AFLP-, and AP-PCR/RAPD-based genomic fingerprinting methods, especially when combined with computer-assisted pattern analysis. Genetic diversity maps provide a framework to understand the taxonomy, population structure, and dynamics of phytobacteria and provide a high-resolution framework to devise sensitive, specific, and rapid methods for pathogen detection, plant disease diagnosis, as well as management of disease risk. A variety of PCR-based fingerprinting protocols such as rDNA-based PCR, ITS-PCR, ARDRA, T-RFLPs, and tRNA-PCR have been devised, and numerous innovative approaches using specific primers have been adopted to enhance both the detection and identification of phytobacteria. PCR-based protocols, combined with computer-based analysis, have provided novel fundamental knowledge of the ecology and population dynamics of bacterial pathogens, and present exciting new opportunities for basic and applied studies in plant pathology.

Journal Article↗
PubMed2004

Evaluation of a plasmid-based 16S-23S rDNA intergenic spacer region array for analysis of microbial diversity in industrial wastewater.

A plasmid-based 16S-23S rDNA intergenic spacer region (ISR) array was developed and optimized for analysis of microbial diversity within complex environmental samples. Plasmid probes with 16S-23S rDNA ISR inserts (800-1500 bp) from industrial wastewater treatment plant (WWTP) microorganisms were arrayed onto glass slides. Hybridization of fluorescently labeled target sequences from two clones from the ISR WWTP library to arrayed probes showed that there was a good linear relationship between hybridization intensity and ISR similarity (r(2)=0.82). Hybridization was highly specific (average background from arrayed probes with less than 80% similarity in ISR sequence was less than 7%). Strong fluorescence intensity corresponded to near-perfect match clones (99% or greater similarity in ISR sequence). A majority of probes (79%) showed no background hybridization. However, weak background (less than 50% for arrayed probes with 90% and 95% similarity in the 16S rRNA genes) was observed from closely related microorganisms. Background fluorescence from the negative control (plasmid vector with no insert) was similar to water and dimethyl sulfoxide (DMSO)-negative controls. Hybridization using fluorescently labeled ISR sequences from a mixed community sample produced strong fluorescent signals with no background from negative controls. A Cy5-labeled reference standard, part of the vector and present in every spotted probe, was used to normalize hybridization values. These results indicate that arrayed plasmid containing ISR probe insert sequences provides specificity and sensitivity for microbial community analysis in a high-throughput array format.

Base Sequence↗
PubMed1997

Analysis of genetic diversity at the DQA loci in African cattle: evidence for a BoLA-DQA3 locus.

We describe the development of a polymerase chain reaction (PCR)-based approach for analysis of genetic diversity at the DQA loci in African Bos indicus and Bos taurus cattle. This approach, equally effective in European and Asian cattle breeds, detects the presence or absence of DQA1 and most duplicated DQA2 genes. Nucleotide and predicted amino acid sequence analysis of the highly polymorphic second exons, in addition to analysis of the locus-specific and relatively non-polymorphic transmembrane, cytoplasmic, and 3-prime untranslated regions, has provided evidence for considerable diversity between each of the duplicated DQA2 genes. Therefore, we propose the designation BoLA-DQA3 for the previously unpublished alleles at the second DQA2 locus. Fourteen distinct PCR restriction fragment length polymorphism (RFLP) patterns, each identifying families of alleles at three DQA loci, can be distinguished. Nucleotide sequence analysis of new PCR-RFLP patterns from 193 Kenyan Boran, Ethiopian Arsi (B. indicus), and Guinean N'Dama (B. taurus) cattle identified 13 DQA1 alleles within eight major allelic families, five DQA2 alleles within a single allelic family, and seven DQA3 alleles within three major allelic families.

Alleles↗
PubMed1999

Analysis of genotypic diversity and relationships among Pseudomonas stutzeri strains by PCR-based genomic fingerprinting and multilocus enzyme electrophoresis.

Molecular fingerprinting procedures including random amplified polymorphic DNA-PCR (RAPD), repetitive extragenic palindromic PCR (rep-PCR) with REP, ERIC, and BOX primers and multilocus enzyme electrophoresis (MLEE) were used for genotypic characterization of 16 P. stutzeri strains originally isolated from marine, waste water, clinical and soil samples. A distinct genotype of each strain and overall great genotypic diversity were found within P. stutzeri. Cluster analysis (UPGMA) of the electrophoretic patterns of all PCR-based methods used resulted in concordant grouping of 8 strains. With the other strains conflicting clustering was noticed. The variability of clustering in PCR-based analyses suggested the occurrence of chromosomal rearrangements. When RAPD-, rep-PCR and MLEE fingerprints were used in a cluster analysis of combined electrophoretic patterns, the P. stutzeri strains could be differentiated into seven distinct genotypic groups. These results supported the subdivision of the species in several genomovars and reproduced, with higher resolution, the strain grouping after 16S rRNA phylogenetic reconstruction. The combined use of several fingerprint-based genotypic analyses results in higher resolutive strain clustering by UPGMA than each of the single ones analyzed separately. Additionally, this combination of individual typings proved to be reliable of the determination of the great genotypic diversity and relationships among the P. stutzeri strains.

Base Sequence↗
PubMed2001

[Analysis of genetic diversity of Bama miniature pigs and Guizhou miniature pigs by RAPD].

RAPD analysis was performed with 31 selected single primers to study genetic diversity of two strains of miniature pigs, The percentages of polymorphisic loic in or between two strains of miniature pigs were 30.9%, 29.2% and 25.7% respectively, and the average genetic distances in and between two strains of miniature pigs were 0.120, 0.072, and 0.067 respectively. These results suggested that genetic diversity and genetic variability were poorer in and between two strains of miniature pigs than ordinary breeds' pigs.

Animals↗
PubMed2024

Genetic characterization and selection of litter size traits of Guizhou Black goat and Meigu goat.

The aim of this study is to explore the genetic characteristics of Guizhou Black goats and Meigu goats and their relationship to reproductive performance through population structure analysis, genetic diversity assessment, and selection signal analysis. Blood samples of 19 Guizhou Black goats and 11 Meigu goats were collected for whole-genome high-throughput sequencing. Using PCA and ADMIXTURE analyses, their population structure and genetic relationships were revealed. Further genetic diversity analysis showed that although there is significant population differentiation, the levels of genetic diversity are similar. Subsequently, these goats were categorized into high-yield and low-yield groups based on their litter sizes, with 15 goats in each group. Then, a selection signal analysis was performed using FST and π ratios for 33,563 SNP loci. The results identified six candidate genes, including KCNIP4, GFRA2, and DGKH, which are significantly associated with high litter performance. These findings enhanced our understanding of the genetic characteristics and population structure of Guizhou Black goats and Meigu goats. Moreover, they provide an important theoretical foundation and scientific basis for further breeding improvements.

Animals↗
PubMed2024

Metagenome-based diversity and functional analysis of culturable microbes in sugarcane.

UNLABELLED: Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane's tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia, Pseudomonas, Paraburkholderia, and Chryseobacterium. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields. IMPORTANCE: This work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields.

Saccharum↗
PubMed2003

[Killer Ig-like receptor gene content diversity and haplotype analysis in Chinese Han population in Shanghai].

OBJECTIVE: To detect the diversity of killer Ig-like receptor(KIR) gene content and the combination of haplotypes in Chinese Han population in Shanghai area. METHODS: DNA samples from 87 randomly unrelated healthy individuals in Shanghai Han population were genotyped with SSP/PCR method. RESULTS: (1) Frequencies of KIR genes: All of 18 known KIRs genes, such as 2DL1-5, 2DS1-5, 3DL1-3, 3DS1, KIR1D and the pseudogenes X, Xv and Z(KIR2DP1) were observed in Shanghai Hans. All individuals contain 3DL3, 2DL4, 3DL2 and 3DL1; the most common genes were 2DL3, Z, 2DL1 and X; the following were 2DS4, 1D, 2DL5, 2DS1, 3DS1 and 2DS5; the next were 2DS2, 2DL2, 2DS3 and Xv. (2) Frequencies of KIR gene haplotypes; there were 13 haplotypes detected in 87 Han individuals, among them, the most frequent one was type 2 (haplotypeA-2DS4). (3) Frequencies of KIR genotypes: 18 kinds of the combinations of the haplotypes were observed; the most frequent ones were AJ(2,2), AF (1,2). Also, In this study were identified five new genotypes FZ1 2 9 , FZ2 1 16 , FZ3 6 17 , FZ4 4 13 and FZ5 2 6 ,which had not been observed in Caucasians so far. CONCLUSION: These findings suggest that there are distinctive frequencies of KIR gene content, haplotype as well as genotype in Chinese Han population in Shanghai area.

China↗
PubMed1996

Hierarchical analysis of nucleotide diversity in geographically structured populations.

Existing methods for analyzing nucleotide diversity require investigators to identify relevant hierarchical levels before beginning the analysis. We describe a method that partitions diversity into hierarchical components while allowing any structure present in the data to emerge naturally. We present an unbiased version of NEI's nucleotide diversity statistics and show that our modification has the same properties as WRIGHT's FST. We compare its statistical properties with several other FST estimators, and we describe how to use these statistics to produce a rooted tree of relationships among the sampled populations in which the mean time to coalescence of haplotypes drawn from populations belonging to the same node is smaller than the mean time to coalescence of haplotypes drawn from populations belonging to different nodes. We illustrate the method by applying it to data from a recent survey of restriction site variation in the chloroplast genome of Coreopsis grandiflora.

Chloroplasts↗