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Restriction fragment length polymorphism tools is an R application which supports a complete workflow of polymerase chain reaction-restriction fragment length polymorphism ( PCR- RFLP), dealing with the problems which accompany analysis when PCR- RFLP is used in diversity studies. Large numbers of different RFLP samples obtained from multiple electrophoresis runs might lead to limitations or misidentifications due to the need for band matching in most existing software applications. Due to the common problem of variation in the density of bands (i.e. distances between bands or visual intensity) in the electropherograms, it is desirable to have options for handling samples with uncertain or faint bands. As a further step in the workflow, scientists often use DNA sequencing to identify individual genotypes, so that the use of specific software to combine these tasks might be helpful. With this background, we here present an application that supports a complete workflow, starting with the analysis of single species samples by PCR- RFLP, to PCR- RFLP genotype identification based on a reference data set and DNA sequencing followed by similarity analysis. RFLPtools is a freely available, platform-independent application which provides analysis functions for DNA fragment molecular weights (e.g. by RFLP analysis), including similarity calculations without the need for band matching. As it is written for the statistical software R, other statistical analyses might also be easily applied. [ABSTRACT FROM AUTHOR]

We describe here two open-ended laboratory investigations for an undergraduate laboratory course that uses students' DNA as templates for quantitative real-time PCR and for traditional PCR followed by RFLP analysis. Students are captivated by the immediacy of the application and the relevance of the genotypes and traits, lactase persistence or nonpersistence, under study. Concepts ranging from nucleotide polymorphisms to natural selection can be demonstrated and reinforced by these laboratories. Students have a high degree of success with the laboratories and both objective and self-assessments of student learning indicate that concepts and techniques are better understood following implementation of these laboratory investigations. [ABSTRACT FROM AUTHOR]

The article discusses the molecular identification of two endangered pigeon species (Columbidae) in Canary Islands. The distribution and diet of the pigeons are analyzed using faecal samples to identify the target species. It states that pigeon species such as C. bollii and C. junoniae share the same features body sizes and food resources. Both endemic pigeon species in the Canary Islands which share the same laurel forest areas were successfully identified by the HaeIII restriction profiles of PCR-amplified products through faecal sampling. Furthermore, the pigeon species are said to be of conservation concern, but due to their arboreal habits and cautious nature, their ecology is poorly understood. [ABSTRACT FROM AUTHOR]

We report the development of a simplified procedure for restriction fragment length polymorphism (RFLP) analysis of mushrooms. We have adapted standard molecular techniques to be amenable to an undergraduate laboratory setting in order to allow students to explore basic questions about fungal diversity and relatedness among mushroom species. The streamlined protocols allowed students to practice important molecular techniques within the context of self-designed investigative projects. This laboratory experience provided opportunities for students to practice strategies for examining molecular diversity among species. [ABSTRACT FROM AUTHOR]

Since 1990, massive cucumber mosaic cucumovirus (CMV) outbreaks of various symptomatology, especially on tomato, have been observed all over Greece. To characterize local virus populations, 40 CMV isolates of different origin and symptomatology in the field and glasshouse were examined for subgroup identification and presence of satellite RNA (satRNA). The IC-PCR method was used to amplify part of the coat protein gene of the isolates; the products were submitted to RFLP analysis using EcoRI and MspI restriction enzymes. Most isolates gave the characteristic pattern attributed to CMV subgroup I, confirming the results obtained by serotyping with monoclonal antibodies. Some Greek isolates, however, possessed additional EcoRI and MspI sites unusual for subgroup I isolates, and the patterns obtained, especially for MspI, could be confused with those of subgroup II. These data suggest that restriction enzyme analysis of amplified PCR products used for strain characterization needs to be treated with caution, especially for viruses such as CMV showing genomic heterogeneity. IC-PCR was also developed for satRNA amplification and the results agreed with those of molecular hybridization with a dig-DNA probe. A satRNA was carried by 77% of the isolates. [ABSTRACT FROM AUTHOR]

Two types of fungi based on the light required for induction of conidiophore formation are known as 'photo-induced' and 'non-photo-induced' sporulators. Conidial development in a 'photo-induced' strain of Bipolaris oryzae (formerly, Helminthosporium oryzae) is controlled by antagonistic action of blue and near-UV radiation mediated through the 'mycochrome' system at two developmental stages: conidiophore induction and conidiophore maturation. Otherwise, conidial development in a 'non-photo-induced' strain of B. oryzae, unlike that in the 'photo-induced' strain, is controlled by antagonistic action of blue and near-UV radiation at the conidiophore maturation stage alone. In this study, we collected fungi, B. oryzae, from brown lesion spots on rice leaves cultivated in paddy fields, and investigated the possible existence of a new ecotype different from known 'photo-induced' and 'non-photo-induced' sporulators. We also investigated the sensitivity of conidial development of each isolate to blue and near-UV radiation. The isolates were identified as B. oryzae by morphology of hyphae and conidia and the symptomatic brown lesion spots on rice leaves caused by each isolate. There was no distinction between 'photo-induced' and 'non-photo-induced' strains on rDNA base. Moreover, the existence of a new type of 'non-photo-induced' sporulator different from the one presently known was confirmed. In this newly identified sporulator, conidial development was not affected by light irradiation. Among 153 isolates, one isolate belonged to a previously known 'non-photo-induced' sporulator, five isolates belonged to a new 'non-photo-induced' sporulator ecotype, and over 95% of the isolates were 'photo-induced' sporulators. Among 'photo-induced' strains, there were several subtypes having different sensitivities to near-UV radiation required for inducing conidiophore formation. [ABSTRACT FROM AUTHOR]

This paper reviews recent developments in the use of molecular probes for analyzing the genetic makeup of somatic hybrids. Successful application of somatic hybridization to the interspecific transfer of traits encoded in the nucleus is still having limited success. A major difficulty is hybrid infertility, particularly in hybrids between sexually incompatible species. The formation of asymmetric hybrids is being explored as an approach for improving hybrid fertility. Evaluation of the degree of chromosome elimination and chromosome stability and instability in asymmetric hybrids is difficult when the traditional approaches of chromosome counting and isozyme analysis are used. Two new approaches are resolving this difficulty. The use of species-specific repetitive DNA probes in dot blotting and in situ hybridization to chromosomes is providing quantitative data on chromosome elimination and allows detection of translocations. Use of restriction fragment length polymorphism (RFLP) probes for analysis of hybrids between genetically mapped species makes it possible to account for the presence or absence of individual chromosomes and chromosome arms. Wider use of such molecular probes should greatly improve our understanding of the genetics of both symmetric and asymmetric somatic hybrids and may lead to new strategies for the effective interspecific transfer of nucleus-encoded traits by protoplast fusion. [ABSTRACT FROM AUTHOR]