PCR-RFLP Analysis of D-Loop mtDNA in Indonesian Domestic Waterfowl

<p class="IsiAbstrakIndo"><span lang="EN-GB">Phylogenetic or population genetic studies have been focused on finding genetic variations in mitochondrial DNA (mtDNA) because mutations in this region contained five times higher than other genetic materials. The aim of this research was to generate PCR-RFLP D-loop mtDNA profiles of some Indonesian domestic waterfowl. The samples were 35 local ducks, 5 muscovy duck, and 5 geese. These local ducks included on seven types of Javanese ducks in Central Java, i.e. Magelang duck, Peking duck, Pengging duck, Tegal Branjangan duck, Tegal Jarakan duck, Tegal Blorong duck, and Tegal Lemahan duck. PCR technique was used to amplify the D-loop genes, and RFLP analysis of the D-loop was performed with </span><em><span lang="EN-GB">Alu</span></em><span lang="EN-GB">I</span><em></em><span lang="EN-GB">and </span><em><span lang="EN-GB">Rsa</span></em><span lang="EN-GB">I. The results show that muscovy duck has no restriction sites in D-loop gene. Moreover, goose has a restriction </span><em><span lang="EN-GB">s</span></em><span lang="EN-GB">ite of </span><em><span lang="EN-GB">Alu</span></em><span lang="EN-GB">I in D-loop gene at 550 bp and 187 bp; and it has no restriction site of </span><em><span lang="EN-GB">Rsa</span></em><span lang="EN-GB">I. The analysis of </span><em><span lang="EN-GB">Rsa</span></em><span lang="EN-GB">I-RFLP in mtDNA </span><em><span lang="EN-GB">D-loop </span></em><span lang="EN-GB">region of ducks resulted in 1 restriction fragment pattern which can be applied in the identification of duck to differentiate it from goose and muscovy duck. PCR-RFLP analysis duck D-loop mtDNA using </span><em><span lang="EN-GB">Alu</span></em><span lang="EN-GB">I and </span><em><span lang="EN-GB">Rsa</span></em><span lang="EN-GB">I restriction enzyme resulted in 3 combinations of restriction fragment pattern shown in 3 haplotypes (A, B, and C). Genetic diversity of Indonesian domestic waterfowl population could be identified by using PCR-RFLP analysis on mtDNA </span><em><span lang="EN-GB">D-loop </span></em><span lang="EN-GB">region. So far, there are few results of research on Indonesian domestic waterfowl genetic characteristics based on PCR-RFLP mtDNA D-loop marker. Also, this research has a good contribution on genetic characterization of local duck. The characterization is an important aspect to maintain breed quality and manage the genetic resources of Indonesian germplasm and in facilitating the breeding program. </span><strong></strong></p>

Linear versus circular mitochondrial genomes: intraspecies variability of mitochondrial genome architecture in Candida parapsilosis

The yeast species Candida parapsilosis, an opportunistic pathogen, exhibits genetic and genomic heterogeneity. To assess the polymorphism at the level of mitochondrial DNA (mtDNA), the organization of the mitochondrial genome in strains belonging to the three variant groups of this species was investigated. Although these analyses revealed a group-specific restriction fragment pattern of mtDNA, strains belonging to different groups appear to have similar genes in the same gene order. An extensive survey of C. parapsilosis isolates uncovered surprising alterations in the molecular architecture of their mitochondrial genome. A screening strategy for strains harbouring mtDNA with rearranged architecture showed that nearly all strains from groups I and III possess linear mtDNA molecules terminating with arrays of tandem repeat units, while most of the group II strains have a circular mitochondrial genome. In addition, it was found that linear genophores in mitochondria of strains from different groups differ in the sequence of the mitochondrial telomeric repeat unit. The occurrence of altered forms of mtDNA among C. parapsilosis strains opens up the unique possibility to address questions concerning the evolutionary origin and replication strategy of linear and circular genomes in mitochondria.

16S Ribosomal DNA Terminal Restriction Fragment Pattern Analysis of Bacterial Communities in Feces of Rats Fed Lactobacillus acidophilus NCFM

ABSTRACT 16S ribosomal DNA terminal restriction fragment patterns from rat fecal samples were analyzed to track the dynamics ofLactobacillus acidophilus NCFM and discern bacterial populations that changed during feeding with NCFM. Lactobacillus johnsonii and Ruminococcus flavefaciens were tentatively identified as such bacterial populations. The presence ofL. johnsonii was confirmed by isolation from feces.

Isolation and Characterization of FiveErwinia amylovora Bacteriophages and Assessment of Phage Resistance in Strains of Erwinia amylovora

ABSTRACT Phages able to infect the fire blight pathogen Erwinia amylovora were isolated from apple, pear, and raspberry tissues and from soil samples collected at sites displaying fire blight symptoms. Among a collection of 50 phage isolates, 5 distinct phages, including relatives of the previously described phages φEa1 and φEa7 and 3 novel phages named φEa100, φEa125, and φEa116C, were identified based on differences in genome size and restriction fragment pattern. φEa1, the phage distributed most widely, had an approximately 46-kb genome which exhibited some restriction site variability between isolates. Phages φEa100, φEa7, and φEa125 each had genomes of approximately 35 kb and could be distinguished by their EcoRI restriction fragment patterns. φEa116C contained an approximately 75-kb genome. φEa1, φEa7, φEa100, φEa125, and φEa116C were able to infect 39, 36, 16, 20, and 40, respectively, of 40 E. amylovora strains isolated from apple orchards in Michigan and 8, 12, 10, 10, and 12, respectively, of 12 E. amylovora strains isolated from raspberry fields (Rubus spp.) in Michigan. Only 22 of 52 strains were sensitive to all five phages, and 23 strains exhibited resistance to more than one phage. φEa116C was more effective than the other phages at lysing E. amylovora strain Ea110 in liquid culture, reducing the final titer of Ea110 by >95% when added at a ratio of 1 PFU per 10 CFU and by 58 to 90% at 1 PFU per 105 CFU.

Virulence parameters in the characterization of strains of Entamoeba histolytica

Differences in virulence of strains of Entamoeba histolytica have long been detected by various experimental assays, both in vivo and in vitro. Discrepancies in the strains characterization have been arisen when different biological assays are compared. In order to evaluate different parameters of virulence in the strains characterization, five strains of E. histolytica, kept under axenic culture, were characterized in respect to their, capability to induce hamster liver abscess, erythrophagocytosis rate and cytopathic effect upon VERO cells. It was found significant correlation between in vitro biological assays, but not between in vivo and in vitro assays. Good correlation was found between cytopathic effect and the mean number of uptaken erythrocytes, but not with percentage of phagocytic amoebae, showing that great variability can be observed in the same assay, according to the variable chosen. It was not possible to correlate isoenzyme and restriction fragment pattern with virulence indexes since all studied strains presented pathogenic patterns. The discordant results observed in different virulence assays suggests that virulence itself may not the directly assessed. What is in fact assessed are different biological characteristics or functions of the parasite more than virulence itself. These characteristics or functions may be related or not with pathogenic mechanisms occurring in the development of invasive amoebic disease

Genotype and Parental Combination Influence Efficiency of Cybrid Induction in Citrus by Electrofusion

Interspecific hybridizations by electrofusion of embryogenic callus cells from `Seminole' tangelo (Citrus reticulata Blanco × C. paradisi Macf.), `Hazzara (Abohar)', or `Ohta' ponkan (C. reticulata Blanco) and leaf cells from `Lisbon' lemon [C. limon (L.) Burm. f.] or rough lemon (C. jambhili Lush.), respectively, were performed. Electrofusion of `Seminole' tangelo and `Lisbon' lemon, `Hazzara (Abohar)' and rough lemon, and `Ohta' ponkan and rough lemon resulted in 33, 43, and 36 plants, respectively. Seven to 10 plants in each combination were selected randomly and used to investigate nuclear and cytoplasmic genomes. Regenerated plants derived from electrofusion of `Seminole' tangelo and `Lisbon' lemon, and `Hazzara (Abohar)' and rough lemon possessed the same restriction fragment pattern for nuclear rDNA as that of the mesophyll parents and the same mitochondrial DNA (mtDNA) restriction pattern as that of the respective suspension parents, indicating that they were cybrids. In contrast, all the plants resulting from a combination between `Ohta' ponkan and rough lemon were confirmed by nuclear rDNA and mtDNA analysis to be somatic hybrids. The analysis of chromosome number supported the results of Southern blot hybridization. The results suggest that specific cell lines, parental combinations, or both can increase the efficiency of inducing cybrids in Citrus by electrofusion.