Ribosomal DNA repeat unit polymorphism in six Aegilops species

Genome ◽  
1992 ◽  
Vol 35 (3) ◽  
pp. 510-515 ◽  
Author(s):  
W. K. Kim ◽  
R. L. Innes ◽  
E. R. Kerber
Keyword(s):  
Repeat Unit ◽  
Genotypic Diversity ◽  
Type A ◽  
Aegilops Species ◽  
Type B ◽  
Rdna Repeat ◽  
Coding Region ◽  
Repeat Units ◽  
Dna Repeat ◽  
Bamhi Site

Total genomic DNA of 27 accessions representing six Aegilops species was restricted with BamHI, EcoRI, and BamHI plus EcoRI, and the restriction fragments were probed with the ribosomal clones pMF2 containing the ribosomal RNA coding regions. The rDNA repeat lengths varied between 9.0 and 10.8 kb. Intraspecific variation among the 10 accessions of Ae. squarrosa var. strangulata ranged from 9.0 to 9.6 kb, suggesting a diversity of genotypes within as well as between species. These variations were not related to their geographical distributions. Each of 24 accessions had two BamHI sites in the coding region (type A), while three accessions of Ae. squarrosa var. strangulata had four BamHI sites (type B, two sites in the intergenic region). Results for these three accessions of Ae. squarrosa var. strangulata suggest genotypic diversity in this species. In BamHI restriction of each accession, a third DNA fragment, ranging between 9.0 and 10.8 kb in type A and 6.0 kb in type B, resulted from lack of digestion at the 26S BamHI site. In double digestion, all rDNA repeat units were restricted by EcoRI, yielding 3.9-, 0.9-, and 4.8-kb fragments, the last of which arose from the lack of digestion at the 26S BamHI site, estimated to occur in 5–20% of the repeat units, depending on the accession.Key words: Triticum tauschii, RFLP, diversity.

Polymorphism in ribosomal DNA repeat units of 12 Hordeum species

Genome ◽  
1989 ◽  
Vol 32 (6) ◽  
pp. 1124-1127 ◽  
Author(s):  
Stephen J. Molnar ◽  
George Fedak
Keyword(s):  
Ribosomal Dna ◽  
Repeat Unit ◽  
Unit Length ◽  
Intergenic Spacer ◽  
Rdna Repeat ◽  
Repeat Units ◽  
Dna Repeat ◽  
Rdna Repeat Unit ◽  
Bamhi Restriction Site ◽  
Hordeum Species

Total genomic DNA was isolated from leaves of individual accessions of 12 Hordeum species. SacI, HindIII, and BamHI restriction fragments hybridizing to the wheat rDNA probe pTA71 were compared. Thirteen rDNA repeat unit length variants were recovered, which combined to produce 11 distinct phenotypes. All rDNA repeat units had two SacI sites and no HindIII sites. The rDNA repeat units of H. secalinum, H. hrasdanicum, and H. distichum all had 3 BamHI sites, but in different configurations. The rDNA repeat units of the other species had at least 4 BamHI sites. Ladders of small hybridizing fragments in 8 of 9 of the latter accessions indicated the presence of occasional BamHI sites in some subrepeats within the intergenic spacer regions of the rDNA repeat units. Different distributions of BamHI restriction site maps within the Hordeum sections strengthen the concept of using variation in rDNA restriction sites as a taxonomic character.Key words: Hordeum, ribosomal DNA, polymorphism.

Cloning of the rDNA repeat unit from a British entomopathogenic nematode (Steinernematidae) and its potential for species identification

Parasitology ◽  
1993 ◽  
Vol 107 (5) ◽  
pp. 529-536 ◽  
Author(s):  
A. P. Reid ◽  
W. M. Hominick
Keyword(s):  
Entomopathogenic Nematode ◽  
Repeat Unit ◽  
Unit Length ◽  
Soil Survey ◽  
Rdna Repeat ◽  
Dna Repeat ◽  
Length Polymorphisms ◽  
Rdna Repeat Unit ◽  
Unique Restriction ◽  
Plasmid Puc18

SUMMARYThe entire ribosomal DNA repeat unit of a steinernematid species (Nashes isolate) was cloned as three separate EcoR I fragments in the plasmid pUC18. An equimolar cocktail of these three clones was used to identify Steinernema species on Southern blots as each species displays its own unique restriction fragment length polymorphisms. The clones also identified two new species isolated in a soil survey of coastal regions of Britain. One of the clones (pSn4.0) can detect length heterogeneities in the rDNA repeat unit of various isolates of some of the species, particularly the most common in the United Kingdom, S. feltiae. These differences in the rDNA repeat unit length remained constant over several years for one isolate of S. feltiae, but were different for each of the geographical isolates studied to date.

Variation in the ribosomal DNA repeat unit within single-oospore isolates of the genus Pythium

Genome ◽  
1990 ◽  
Vol 33 (4) ◽  
pp. 585-591 ◽  
Author(s):  
Frank N. Martin
Keyword(s):  
Ribosomal Rna ◽  
Repeat Unit ◽  
Pythium Species ◽  
Coding Region ◽  
Nontranscribed Spacer ◽  
Dna Repeat ◽  
Restriction Sites ◽  
Genus Pythium ◽  
Polymorphic Forms ◽  
Isolate Variation

Restriction analyses of the DNA repeat unit coding for the production of 5.8S, 17S, and 26S ribosomal RNA (rDNA) isolated from several different Pythium species revealed polymorphic forms within a single-oospore isolate. Restriction mapping of cloned rDNA from Pythium paroecandrum indicated that two major forms were present in approximately equal ratios (A and B, 11.6 and 11.9 kb in size, respectively), which differed in the nontranscribed spacer region for numbers and locations of restriction sites for HaeIII, SalI, and KpnI and an insertion–deletion adjacent to the 3′ end of the 26S RNA coding region. The insertion–deletion makes form B 0.27 kb larger than form A. An additional insertion–deletion in both forms of approximately 60 bp in the same region makes a total of four polymorphic types in the isolate investigated. Similar results also were obtained for Pythium spinosum following restriction digestion of purified rDNA. A survey of other Pythium species indicates that the presence of polymorphic forms in the same isolate, variation in the number or polymorphic forms in different isolates of the same species, and insertions–deletions in multiples of approximately 60 bp adjacent to the 3′ end of the 26S coding region are common in the genus.Key words: Pythium spp., rDNA.

scholarly journals Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

2014 ◽  
Vol 2014 ◽  
pp. 1-15 ◽  
Author(s):  
Maxim V. Zagoskin ◽  
Valentina I. Lazareva ◽  
Andrey K. Grishanin ◽  
Dmitry V. Mukha
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Trees ◽  
Repeat Unit ◽  
Its2 Rdna ◽  
Minimum Evolution ◽  
Nucleotide Substitutions ◽  
Repeat Units ◽  
Dna Repeat ◽  
Ribosomal Repeat ◽  
Its1 And Its2

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that theMesocyclops,Thermocyclops,andMacrocyclopsgenera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals.

A rapid means of identifying wild rice species DNA using dot blots and genome-specific rDNA probes

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 391-395 ◽  
Author(s):  
C L McIntyre ◽  
B C Winberg
Keyword(s):  
Repeat Unit ◽  
Rice Genome ◽  
Intergenic Spacer ◽  
Size Class ◽  
Rdna Repeat ◽  
Wild Rice Species ◽  
Rdna Repeat Unit ◽  
Oryza Latifolia ◽  
Bamhi Site ◽  
Oryza Australiensis

Intergenic spacer fragments from the rDNA repeat unit were isolated from a single accession of each of 9 species that cover the range of genomes found in the Oryza genus (A-F). Seven of the 9 species contained 1 size class of rDNA repeat unit only, while Oryza sativa and Oryza latifolia contained 3 and 2 size classes, respectively, of which fragments were cloned for the major size class only. Oryza australiensis contained an additional BamHI site in the intergenic spacer. Dot blots were prepared and hybridised with a repeat unit from each species. Under high stringency conditions, all probes were specific to species possessing the same genome or genomes.Key words: rDNA, rice, genome-specific, dot blots.

scholarly journals The origin of the triploid in Paragonimus westermani on the basis of variable regions in the mitochondrial DNA

2003 ◽  
Vol 77 (4) ◽  
pp. 279-285 ◽  
Author(s):  
T. Agatsuma ◽  
M. Iwagami ◽  
Y. Sato ◽  
J. Iwashita ◽  
S.J. Hong ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Natural Populations ◽  
Type A ◽  
Type B ◽  
Coding Region ◽  
Variable Regions ◽  
Paragonimus Westermani ◽  
16S Sequence ◽  
Form Type ◽  
Parsimony Trees

AbstractTriploid, parthenogenetic forms of the lungfluke, Paragonimus westermani, occur in Japan, Korea and China. The origin(s) of triploidy has been debated over the years. Sequences of two regions in the mitochondrial DNA, i.e. partial lrRNA (16S), and a portion of the non-coding region, were obtained from natural populations of P. westermani. All triploid individuals (Japan, Korea, China) and a single tetraploid individual (China) had identical sequences in the 16S region studied. Some sequence variation was observed among diploids, with those from Taiwan being distinct from the remainder. Both neighbour joining and parsimony trees using the 16S region placed diploid individuals from southwestern Japan close to the triploids and the tetraploid. The fragment amplified from the mitochondrial non-coding region showed dimorphism. One form (type A) consisted of 239 bp comprising two identical tracts of 70 bp separated by a tract of 93 bp. The second form (Type B) consisted of only a single 70 bp tract. All diploid individuals from Taiwan, China and Korea possessed type A, while those from Japan were polymorphic; individuals from Oita and Hyogo had type B, those from Chiba had type A, but both types were found in Mie. On the other hand, all of the triploid individuals and two tetraploid individuals possessed type B. Both the form present in the non-coding region and the 16S sequence suggest an affinity between a south-eastern group of diploid populations in Japan and the triploid form. A possible mechanism responsible for the origin of the triploid is discussed.

Biological and Morphological Studies on Low-Leukemia-Strain Mice with Hodgkin's-Like Neoplasia Induced by Serial Cell-Free Transmission of Leukemic Organs of SJL/J Strain Mice

1968 ◽  
Vol 26 ◽  
pp. 210-211
Author(s):  
S. Fujinaga ◽  
K. Maruyama ◽  
C.W. Williams ◽  
K. Sekhri ◽  
L. Dmochowski
Keyword(s):  
Tissue Culture ◽  
Type A ◽  
Reticulum Cell ◽  
Type B ◽  
Viral Origin ◽  
Serial Transfer ◽  
Strain Mouse ◽  
Morphological Studies ◽  
Cell Neoplasm ◽  
Free Material

Yumoto and Dmochowski (Cancer Res.27, 2098 (1967)) reported the presence of mature and immature type C leukemia virus particles in leukemic organs and tissues such as lymph nodes, spleen, thymus, liver, and kidneys of SJL/J strain mice with Hodgki's-like disease or reticulum cell neoplasm (type B). In an attempt to ascertain the possibility that this neoplasia may be of viral origin, experiments with induction and transmission of this neoplasm were carried out using cell-free extracts of leukemic organs from an SJL/J strain mouse with spontaneous disease.It has been possible to induce the disease in low-leukemia BALB/c and C3HZB strain mice and serially transfer the neoplasia by cell-free extracts of leukemic organs of these mice. Histological examination revealed the neoplasia to be of either reticulum cell-type A or type B. Serial transfer is now in its fifth passage. In addition leukemic spleen from another SJL/J strain mouse with spontaneous reticulum cell neoplasm (type A) was set up in tissue culture and is now in its 141st serial passage in vitro. Preliminary results indicate that cell-free material of 39th tissue culture passage can reproduce neoplasia in BALB/c mice.

Anticoagulant Activity of β2-Glycoprotein I Is Potentiated by a Distinct Subgroup of Anticardiolipin Antibodies

1992 ◽  
Vol 68 (03) ◽  
pp. 297-300 ◽  
Author(s):  
Monica Galli ◽  
Paul Comfurius ◽  
Tiziano Barbui ◽  
Robert F A Zwaal ◽  
Edouard M Bevers
Keyword(s):  
Human Plasma ◽  
Anticoagulant Activity ◽  
Factor Xa ◽  
Type A ◽  
Lipid Vesicles ◽  
Dependent Manner ◽  
Type B ◽  
Distinct Subgroup ◽  
Glycoprotein I ◽  
Thrombin Formation

SummaryPlasmas of 16 patients positive for both IgG anticardiolipin (aCL) antibodies and lupus anticoagulant (LA) antibodies were subjected to adsorption with liposomes containing cardiolipin. In 5 of these plasmas both the anticardiolipin and the anticoagulant activities were co-sedimented with the liposomes in a dose-dependent manner, whereas in the remaining cases only the anticardiolipin activity could be removed by the liposomes, leaving the anticoagulant activity (LA) in the supernatant plasma. aCL antibodies purified from the first 5 plasmas were defined as aCL-type A, while the term aCL-type B was used for antibodies in the other 11 plasmas, from which 2 were selected for this study.Prolongation of the dRVVT was produced by affinity-purified aCL-type A antibodies in plasma of human as well as animal (bovine, rat and goat) origin. aCL-type B antibodies were found to be devoid of anticoagulant activity, while the corresponding supernatants containing LA IgG produced prolongation of the dRVVT only in human plasma.These anticoagulant activities of aCL-type A and of LA IgG's were subsequently evaluated in human plasma depleted of β2-glycoprotein I (β2-GPI), a protein which was previously shown to be essential in the binding of aCL antibodies to anionic phospholipids. Prolongation of the dRVVT by aCL-type A antibodies was abolished using β2-GPI deficient plasma, but could be restored upon addition of β2-GPI. In contrast, LA IgG caused prolongation of the dRVVT irrespective of the presence or absence of β2-GPI.Since β2-GPI binds to negatively-charged phospholipids and impedes the conversion of prothrombin by the factor Xa/Va enzyme complex (Nimpf et al., Biochim Biophys Acta 1986; 884: 142–9), comparison was made of the effect of aCL-type A and aCL-type B antibodies on the rate of thrombin formation in the presence and absence of β2-GPI. This was measured in a system containing highly purified coagulation factors Xa, Va and prothrombin and lipid vesicles composed of 20 mole% phosphatidylserine and 80 mole% phosphatidylcholine. No inhibition on the rate of thrombin formation was observed with both types of aCL antibodies when either β2-GPI or the lipid vesicles were omitted. Addition of β2-GPI to the prothrombinase assay in the presence of lipid vesicles causes a time-dependent inhibition which was not affected by the presence of aCL-type B or non-specific IgG. In contrast, the presence of aCL-type A antibodies dramatically increased the anticoagulant effect of β2-GPI. These data indicate that the anticoagulant activity of aCL-type A antibodies in plasma is mediated by β2-GPI.

Feeding behaviour and bioerosion: the ecological role of the rock-boring urchin, Echinometra mathaei (de Blainville, 1825), in Okinawa reef flat

2013 ◽  
Vol 1 (1) ◽  
pp. 10
Author(s):  
Noar Muda Satyawan ◽  
Shelly Tutupoho ◽  
Yusli Wardiatno ◽  
Makoto Tsuchiya
Keyword(s):  
Feeding Behaviour ◽  
Reef Flat ◽  
Type A ◽  
Gut Contents ◽  
Biological Processes ◽  
Type B ◽  
Night Time ◽  
Echinometra Mathaei ◽  
Benthic Ecosystems

Erosion rate on corals due to activities of other biota is called bioerosion. The rock-boring urchin, Echinometra mathaei, when it is abundant, plays a significant role in benthic ecosystems, including biological processes like coral erosion. During feeding, E. mathaei erodes calcium carbonate besides grazing on algae living on coral, so it plays an important role in both organic and inorganic carbons in coral reefs. The urchin E. mathaei actively feeds during the night time (nocturnal grazer). Although in Okinawa four types (A-D) of the urchin exist, the research only focused on the types A and B. Type A of E. mathaei produced 0.44951 g feces per day on average while type B produced 0.38030 g feces per day. CaCO3 analysis in feces and gut contents showed bioerosion rate of E. mathaei type A was 0.64492 g/individu/day, and 0.54436 g/individu/day in type B. There were no significant differences in bioerosion impact of E. mathaei type A and B© Laju erosi pada karang yang disebabkan oleh biota, dikenal dengan bioerosi. Bulu babi jenis Echinometra mathaei, ketika melimpah, menjadi sangat berpengaruh terhadap ekosistem bentik termasuk proses biologi seperti erosi karang. Selama aktivitas makan, E. mathaei menggerus kalsium karbonat dalam proporsi yang besar di samping alga yang tumbuh menempel pada karang sehingga memiliki peran penting dalam siklus karbon organik dan anorganik di ekosistem terumbu karang. Bulu babi E. mathaei aktif mencari makan pada malam hari (nocturnal grazer). Meskipun di Okinanawa ada 4 tipe (A-D), pada eksperimen kali ini memfokuskan pada tipe A dan B saja. Tipe A E. mathaei rata-rata memproduksi 0,44951 g feses/hari dan tipe B memproduksi 0,38030 g feses/hari. Berdasarkan analisis CaCO3 yang dilakukan pada feses dan isi lambung, laju bioerosi yang disebabkan oleh E. mathaei tipe A sebesar 0,64492 g/individu/hari sedangkan tipe B sebesar 0,54436 g/individu/hari. Tidak terdapat perbedaan dampak bioerosi yang signifikan antara E. mathaei tipe A dan B©

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