[Establishment of DNA fingerprints for Chrysosplenium using SRAP Markers]

As a traditional Chinese medicinal material, Chrysosplenium is urgently needed for genetic resource investigation and protection research due to the decrease of its wild resources in recent years. After investigating the wild resources, we conducted genetic polymorphism and clustering studies of 24 species(a total of 36 samples) of Chrysosplenium using SRAP technique. The results showed that a total of 374 polymorphic bands were obtained using 18 pairs of SRAP primers to amplify these samples, on average of 20.7 bands for each primer pair. We used the biological software to analyze the population's genetic parameter and got the N_a value as 2.000 0, N_(e )value as 1.408 4, the average Nei's index as 0.263 5, and the average Shannon information index as 0.419 1. UPGMA cluster analysis showed that all the samples can be divided into three major groups at the genetic similarity coefficient of 0.70: there are 18 species(24 samples) gathered for the Ⅰ groups, 3 species or variation(7 samples) for Ⅱ groups, and 3 species(5 samples) for Ⅲ groups. The differences of these Chrysosplenium species at the molecular level are consistent with that of their geographical and ecological distribution. At the same time, we used SRAP technology to construct 36 DNA digital fingerprints of Chrysosplenium and obtained the unique molecular identification band type of each material. These results will provide effective methods and reliable basis for the identification, protection and genetic diversity analysis of the germplasm resources of Chrysosplenium, and lay a foundation for the further development and utilization of them.

Genetic analysis of clinical and vaccine strains of Bordetella pertussis by Pulsed-Field Gel Electrophoresis (PFGE), Multi Locus Sequence Typing (MLST) and serotyping

In spite of high vaccination coverage in the Expanded Program of Immunization (EPI), pertussis has not been eradicated yet and the re-emergence of the disease is still reported worldwide. The genetic divergence study of circulating clinical strains of Bordetella pertussis among the population with high vaccination coverage is a useful tool to have an insight in the understanding of genetic patterns of this bacterium and deviation of them from vaccine strains. Different methods are accessible for studying of Bordetella pertussis that can perform appropriate assessment between populations. Strains used in this study were a collection of two pertussis vaccine strains used to create killed pertussis vaccine over years at Razi Vaccine and Serum Research Institute, 10 clinical and 2 reference strains (ATCC9797 and Tohama I) in Multilocus Sequence Typing (MLST), Pulsed-Field Gel Electrophoresis (PFGE), and serotyping. The genetic profiles of vaccine working and master seeds showed no important change(s) in frequencies of fingerprint types investigated in the vaccine strains and had homogeneity in PFGE method where the clinical isolates showed diversity in genetic profile. Serotyping method showed that all of 10 clinical strains expressing Fim 3. In MLST study, seven housekeeping genes including adk, pgm, fum C, tyr B, gly A, pep A and icd were analyzed which showed no changes in the sequence of clinical and vaccine strains with 100% homology. The genes that cause pathogenicity like ptxC, tcfA and fhaB were also evaluated and the results illustrated heterogeneity in the vaccine and circulating strains.

PATTERNS OF DESCENT IN CLONAL LINEAGES AND THEIR MULTILOCUS FINGERPRINTS ARE RESOLVED WITH COMBINED GENE GENEALOGIES

Clonal lineages in the filamentous ascomycete (fungi) Sclerotinia sclerotiorum were determined by analysis of genealogies of four loci: the intergenic spacer of the nuclear ribosomal repeat (IGS; approximately 4 kb), the translation elongation factor (EF-1α; approximately 300 bp), an anonymous region (44.11; approximately 700 bp), and the calmodulin gene (CAL; approximately 400 bp). Three of the four loci are physically unlinked. The combined analysis of the four loci provided the best estimate of phylogeny, which is consistent with a pattern of some recombination among clonal lineages against a background of predominant clonality. Comparison of gene genealogies with a phylogeny inferred from DNA fingerprints and a combined phylogeny of the entire dataset identified convergent or parallel changes in fingerprints. Analysis of the entire data matrix allowed us to resolve patterns of descent among clonal lineages that could not be inferred from fingerprints alone and to discern recent episodes of divergence that were not detected in gene genealogies. Prerequisites for applying this approach to other systems are a haploid context for inferring multiple gene genealogies (such as the mitochondrial genome) that indicate limited recombination and another data matrix that identifies recently evolved genotypes.

In Silico PCR Tools for a Fast Primer, Probe, and Advanced Searching

The polymerase chain reaction (PCR) is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. The principle of this technique has been further used and applied in plenty of other simple or complex nucleic acid amplification technologies (NAAT). In parallel to laboratory "wet bench" experiments for nucleic acid amplification technologies, in silico or virtual (bioinformatics) approaches have been developed, among which in silico PCR analysis. In silico NAAT analysis is a useful and efficient complementary method to ensure the specificity of primers or probes for an extensive range of PCR applications from homology gene discovery, molecular diagnosis, DNA fingerprinting, and repeat searching. Predicting sensitivity and specificity of primers and probes requires a search to determine whether they match a database with an optimal number of mismatches, similarity, and stability. In the development of in silico bioinformatics tools for nucleic acid amplification technologies, the prospects for the development of new NAAT or similar approaches should be taken into account, including forward-looking and comprehensive analysis that is not limited to only one PCR technique variant. The software FastPCR and the online Java web tool are integrated tools for in silico PCR of linear and circular DNA, multiple primer or probe searches in large or small databases and for advanced search. These tools are suitable for processing of batch files that are essential for automation when working with large amounts of data. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and the online Java version at http://primerdigital.com/tools/pcr.html .

Deciphering the factors associated with the colonization of rice plants by cyanobacteria

Cyanobacteria-rice plant interactions were analyzed using a hydroponics experiment. The activity of plant defense and pathogenesis-related enzymes, scanning electron microscopy, growth, nitrogen fixation (measured as ARA), and DNA fingerprinting assays proved useful in illustrating the nature of associations of cyanobacteria with rice plants. Microscopic analyses revealed the presence of short filaments and coiled masses of filaments of cyanobacteria near the epidermis and cortex of roots and shoot tissues. Among the six cyanobacterial strains employed, Calothrix sp. (RPC1), Anabaena laxa (RPAN8), and Anabaena azollae (C16) were the best performing strains, in terms of colonization in roots and stem. These strains also enhanced nitrogen fixation and stimulated the activity of plant defense/cell wall-degrading enzymes. A significantly high correlation was also recorded between the elicited plant enzymes, growth, and ARA. DNA fingerprinting using highly iterated palindromic sequences (HIP-TG) further helped in proving the establishment of inoculated organisms in the roots/shoots of rice plants. This study illustrated that the colonization of cyanobacteria in the plant tissues is facilitated by increased elicitation of plant enzymes, leading to improved plant growth, nutrient mobilization, and enhanced plant fitness. Such strains can be promising candidates for developing "cyanobacteria colonized-nitrogen-fixing rice plants" in the future.

Molecular Characterization of Vegetative Compatibility Group 4A and 4B Isolates of Verticillium dahliae Associated with Potato Early Dying

Forty isolates of Verticillium dahliae, collected from potato seed tubers and potato plants from various regions in North America and previously assigned to vegetative compatibility groups (VCGs) 4A or 4B, were characterized using molecular markers. The VCG 4A isolates were previously shown to be a highly virulent pathotype of potato and to interact synergistically with the root-lesion nematode Pratylenchus penetrans to cause potato early dying. All but one of the VCG 4A isolates characterized in this study lacked the subspecies-specific repetitive DNA sequence E18 and could be differentiated from the remaining isolates by restriction fragment length polymorphisms (RFLPs) in the nuclear rDNA and Trp1 loci. The E18 RFLP patterns of several VCG 4B isolates from Maine and New York were highly similar to those of VCG 4B isolates previously collected from potato and tomato fields in Ontario. The data presented here suggest that the molecular markers will be useful for the detection and classification of isolates of V. dahliae associated with potato early dying.

A Global Marker Database for Phytophthora infestans

A marker database was compiled for isolates of the potato and tomato late blight pathogen, Phytophthora infestans, originating from 41 locations which include 31 countries plus 10 regions within Mexico. Presently, the database contains information on 1,776 isolates for one or more of the following markers: restriction fragment length polymorphism (RFLP) "fingerprint" consisting of 23 bands; mating type; dilocus allozyme genotype; mitochondrial DNA haplotype; sensitivity to the fungicide metalaxyl; and virulence. In the database, 305 entries have unique RFLP fingerprints and 258 entries have unique multilocus genotypes based on RFLP fingerprint, dilocus allozyme genotype, and mating type. A nomenclature is described for naming multilocus genotypes based on the International Organization for Standardization (ISO) two-letter country code and a unique number. Forty-two previously published multilocus genotypes are represented in the database with references to publications. As a result of compilation of the database, seven new genotypes were identified and named. Cluster analysis of genotypes from clonally propagated populations worldwide generally confirmed a previously published classification of "old" and "new" genotypes. Genotypes from geographically distant countries were frequently clustered, and several old and new genotypes were found in two or more distant countries. The cluster analysis also demonstrated that A2 genotypes from Argentina differed from all others. The database is available via the Internet, and thus can serve as a resource for Phytophthora workers worldwide.

Molecular markers in plant ecology

Various methods from molecular biology reveal sequence polymorphisms in organelle and nuclear DNA that can be used as highly informative markers for the structure and dynamics of genomes at the level of populations and individuals. Molecular markers that can be determined without regard to the phenotype permit an unbiased comparison of the adaptation of organisms to their environment, its genetic basis and its effect on evolution. Several marker types used in ecological research and their uses and limitations arc briefly discussed. PCR-based methods, especially arnitrary-primer-based RAPDs, are likely to be most widely used and receive most attention. The limited use of DNA markers for overall quantitative (phenetic) comparisons of 'genetic variability' and 'generic distance' is stressed and fheir power as qualitative markers for any and all relevant regions in the genome is emphasized. Specific applications relevant to plant ecology are illustrated. These are: identification of organism and genotype even where morphology is of little help, as in mycorrhiza; identification of clones in asexually-reproducing species, even when they are widespread and intermingled; determining if genetic variation in elonal populations comes from mutations within elonal lines or from independent origins of clonal lines; reconstructing the genotype phylogeny and fruit dispersal of elonal (apomicuc) and inbred selling organisms, measuring the degree of outcrossing by offspring exclusion analysis; detecting and analyzing introgression and characterizing reeombinant genotypes in hybrid zones relative to differential adaptive responses: tracing the phylogenetic origin and extent of ecologically differentiated races or species; characterizing the genetic basis, mapping and isolating the genes responsible for special adaptive responses. In a final outlook, 1 speculate about unconventional sources of genetic variation affecting the ecological characteristics of plants that will become accessible to experimental analysis with the new molecular methods. Contents Summary 403 I. Introduction 404 II. Most ecological applications concern markers in the nuclear geonome 404 III. DNA polymorphisms differ from allozyme pohmorphisms 404 IV. Types of molecular marker 405 V. The application of markers in ecology 409 VI. From marker to character 413 VII. Outlook 414 References 414.