Internal Transcribed Spacer Gene Research Articles

Polymerase Chain Reaction Detection of Cytauxzoon felis From Field-Collected Ticks and Sequence Analysis of the Small Subunit and Internal Transcribed Spacer 1 Region of the Ribosomal RNA Gene

Cytauxzoon felis produces a disease in domestic cats in the Midwest (U.S.A.), which often leads to a fatal outcome. Although the clinical disease process is well described, there are still many unanswered questions about this organism. For example, it is unknown whether species of ticks other than Dermacentor variabilis can serve as vectors for transmission. With recent reports of surviving cats from limited geographic areas, another relevant question is the potential for genetically less virulent organism strains. This study evaluated 352 individual or pooled tick samples (1,362 total ticks) for the presence of C. felis small subunit ribosomal RNA and internal transcribed spacer 1 (ITS-1) region genes using a polymerase chain reaction (PCR). These ticks were collected from dogs and cats in several Missouri counties, including 10 from cats diagnosed with cytauxzoonosis. Only 3 positive C. felis samples were identified in Amblyomma americanum nymphs, and there was very limited genetic variation noted in both genes. The small number of positive samples did not allow the study to determine which PCR analysis was more sensitive. This is the first known report of ITS-1 gene identification and sequencing for C. felis. It is also the first published investigation of genetic variation in C. felis.

DNA extraction and ITS2 (internal transcribed spacer 2) gene sequences of some Brazilian freshwater copepods

DNA extraction and ITS2 (internal transcribed spacer 2) gene sequences of some Brazilian freshwater copepods

Identification of Trichophyton rubrum by Nested PCR Analysis from Paraffin Embedded Specimen in Trichophytia Profunda Acuta of the Glabrous Skin

Trichophytia profunda acuta of the glabrous skin (TPAGS) arose in a 67-year-old Japanese man. The patient presented indurated erythematous plaques and nodules on his left forearm. Direct microscopic examination of the scale in KOH preparation was negative for fungal elements, and culture for dermatophytes was also negative. Although fungal infection could not be proven in hematoxillin-eosin stained sections, deep-cut sections of the biopsied skin lesion with PAS stain revealed the ectothrix presence of fungal elements. Nested PCR was done with Trichophyton specific primers directed to internal transcribed spacer gene 1 (ITS1), using template DNA obtained from formalin fixed, paraffin embedded skin sections. A single band corresponding to T. rubrum was obtained, and the etiological agent was thus identified. KOH tests and cultures may often turn out unsuccessful, perhaps reflecting the hair follicle dominant fungus growth in TPAGS. Although these tests are most important for diagnosis of TPAGS, nested PCR using paraffin embedded skin sections may be an alternative method to identify the etiological agent.

Genetic Profiling ofHypericum(St. John’s Wort) Species by Nuclear RibosomalITSSequence Analysis

A PCR-based DNA amplification method was applied to genetically distinguish the popular dietary supplement Hypericum perforatum L. (common St. John's Wort) from other related Hypericum species. Nuclear ribosomal gene sequences of the internal transcribed spacer (ITS) region were analyzed for 50 Hypericum taxa native to the Old and New Worlds, representing 11 of the 36 currently accepted taxonomic sections. This study provides a genetic method for authentication of commercial H. perforatum preparations. In addition, these data allow a preliminary assessment of phylogenetic relationships within the genus, revealing three strongly supported monophyletic clades, plus several secondary monophyletic groupings. Using ITS gene sequences, we were able to distinguish H. perforatum from all other species of Hypericum included in this study.

Genotypic characteristics of two serotypes of Bartonella henselae.

The study of 16S rRNA gene sequences of all isolates of Bartonella henselae obtained in our laboratory and others from human patients or cats has revealed two genotypes according to the sequence of the 16S rRNA gene. Two isolates of these genotypes have previously been related to two different serotypes, and lack of cross-protection of the two serotypes has been demonstrated in cats. We investigated the grouping of eight strains of B. henselae on the basis of 16S ribosomal DNA, 35-kDa protein, Pap 31 protein, and internal transcribed spacer (ITS) gene sequencing; sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) profiles; and monoclonal antibody reactivity studies. Houston-1, 90-615, and SA2 strains showed the same patterns in SDS-PAGE, but they differed from the patterns of B. henselae isolates URBHLLY8, URBHLIE9, Cat6, Fizz, and CAL-1. Nine monoclonal antibodies derived from BALB/c mice immunized with B. henselae Houston-1 strain reacted only with strains Houston-1, 90-615, and SA2, and not with any other Bartonella strains. The two serogroups corresponded with two genotypes based on differences in the sequences of the genes encoding 16S rRNA, 35-kDa protein, and Pap 31 protein. Sequences of ITS genes were highly divergent among strains, as each had a unique sequence and the subdivision was not supported by DNA-DNA relatedness study. Study of 22 additional strains of B. henselae isolated from French bacteremic cats demonstrated that they all belong to one or the other of the proposed serotype or genotype.

Molecular phylogeny and biogeography of Linanthus (Polemoniaceae)

To better understand the evolutionary history of Linanthus (Polemoniaceae) and its relatives, molecular phylogenies based on DNA sequence data from the internal transcribed spacer (ITS) region of nrDNA and the chloroplast gene matK were estimated using several methods. Our data suggest two separate and well-supported lineages of Linanthus in close association with two other genera-Leptodactylon and Phlox. These results agree with previous molecular systematic work on the Polemoniaceae, but do not support the traditional classification of the genus as a natural group, nor do they support the sectional classification within the genus. With a distribution centered primarily in western North America and a high degree of endemism in the California Floristic Province, it has been suggested by Raven and Axelrod that the origin and diversification of Linanthus and its relatives were tied to the development of a summer-dry climate in western North America, which began around 13-15 million years ago (mya). Increased drying during the Pliocene (1.2-5 mya) has also been hypothesized by Axelrod to have led to an increase in plant speciation in California and adjacent areas. Divergence times within the Linanthus lineages were estimated from the ITS and matK gene trees. A log-likelihood ratio test could not reject clock-like evolution for the matK data; however, the clock was strongly rejected for the ITS data set. Although ITS molecular evolution was not clock-like, the estimated times of divergence were similar to those of the matK data set. Within both lineages of Linanthus there seems to have been considerable diversification that has occurred since the Pliocene.

PCR-RFLP pattern of three kinds of Metagonimus in Korea.

We tried to compare the three kinds of Metagonimus species, M. yokogawai, Metagonimus Miyata type, and M. takahashii, which were known to be distributed in Korea with polymerase chain reaction based-restriction fragment length polymorphism (PCR-RFLP) patterns. We amplified the internal transcribed spacer 1 (ITS1) site of ribosomal RNA and mitochondrial cytochrome c oxidase I (mCOI) gene. The restriction patterns of ITS1 gene with Rsa I, Alu I and Msp I showed multiple fragmented bands of different sizes between three kinds of Metagonimus. In case of mCOI gene, Rsa I and Alu I enzymes produced differentially fragmented band patterns. According to the parsimony analysis of PCR-RFLP patterns, the estimated genetic divergence between M. yokogawai and Metagonimus Miyata type was 0.034880, between Metagonimus Miyata type and M. takahashii was 0.028098, between M. yokogawai and M. takahashii was 0.018179. It is suggested that Metagonimus Miyata type may be separate species and evolutionize at the older time than the other two species.