Repeated DNA sequences in mycobacteria

In tuberculosis, it is often important to establish the source of infection and to determine whether disease is due to a new strain of Mycobacterium tuberculosis or to relapse. To cope with the resurgence of tuberculosis and atypical mycobacterioses in AIDS patients, on the one hand, and to overcome the limitations of classical bacteriological procedures on the other, the development of rapid, sensitive, and reliable diagnostic and epidemiologic tools is highly desirable. Molecular typing methods are often based on repeated genes such as those for rRNA. Ribotyping is of limited use with pathogenic mycobacteria. as the slow-growers possess a single rRNA operon, while the fast-growers have two. This problem has been overcome by the discovery and study of repeated DNA elements in mycobacterial genomes, as these provide an alternative pathway for diagnostic and epidemiological investigations.     

Repeated DNA sequences in fungi

Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10-20% repeated DNA sequences. There are approximately 100-110 copies of repeated DNA sequences of approximately 4 × 10⁷ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5°C difference of T_e50 (temperature at which 50% duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA.     

小麦族植物DNA重复序列研究

近些年来从小麦族植物中分离到了许多DNA重复序列,并对其组织结构特点,物种分布特异性和在染色体上的分布特征做了广泛的研究,其中一些重复序列已被成功地用于检测遐入小麦的外源染色质和小麦族有关种属的进化研究,本文就以上诸方面进行了简要介绍。     

Repeated sequences on mitochondrial DNA ofSpirodela oligorhiza

Summary Mitochondrial DNA ofSpirodela oligorhiza (duck weed) was analyzed with restriction enzymes. The genome size appears to be at least 250 kbp. Four different PstI fragments were cloned. These four clones contain a sequence which is reiterated about 100-fold on theSpirodela mitochondrial DNA. Hybridization analysis showed that a similar sequence is present onZea mays mitochondrial DNA, although much less reiterated here. The presence of these reiterated sequences might contribute to the physical heterogeneity of plant mitochondrial DNA.     

Repeated nucleotide sequences in human main band DNA

Male and female human placenta DNA was fractionated in an Ag+-Cs2SO4 density gradient. The different fractions along the gradient were analyzed by Hae III endonuclease digestion. Within the main band DNA on the light side a component having a Hae III digestion pattern similar to that of human satellite III DNA has been identified. This component which might be defined as a cryptic satellite accounts for at least 3% of the total human DNA and has a different position than human satellite III in Ag+-Cs2SO4.     

Repeated sequences in the DNA of the eukaryotic genome

Long DNA molecules from a cucumber satellite, the cucumber main band, mung bean, and Chinese hamster ovary (CHO) were digested with mung bean nuclease I, which was used as a probe for high AT regions. The digests were viewed under the electron microscope, and the distribution of sizes for the fragments of nuclease-treated plant DNA showed that the main band cucumber and the mung bean have regions along their genomes spaced at approximately 0.3 to 0.4 μ that are sensitive to the nuclease. The satellite from the cucumber contains these sites at intervals generally of 0.1 μ or less, whereas CHO DNA has these regions at intervals of 0.05 to 1.40 μ in length. The long DNA from the main band of the cucumber and the CHO were also partially melted in formamide at 37°C to denature preferentially the regions along the DNA molecules that are rich in AT. Measurements of the distances from the center of each loop to the center of the adjacent loops showed that these distances for the main band cucumber DNA tended to occur at approximately every 0.4 μ, whereas the corresponding distances for the Chinese hamster DNA were less regular, occurring every 0.1 to 1.0 μ.     

The Central American land bridge as an engine of diversification in New World doves

Aim The closure of the Central American land‐bridge connection between North and South America 3.5 million years ago was a major biogeographic event that allowed considerable interchange of the previously isolated faunas of these continents. However, the role that this connection may have had in diversification of North and South American faunas is less well understood. The goal of this study was to evaluate the potential role of the formation of this land connection in generating diversity, through repeated rare dispersal events followed by isolation. Location North and South America. Methods We evaluated the role of the Central American land‐bridge connection in avian diversification using a molecular phylogeny based on four gene regions for mid‐sized New World doves. Diversification events were dated using a Bayesian relaxed clock analysis and internal calibration points for endemic island taxa with known island ages. Results The reconstructed phylogenetic tree was well supported and recovered monophyly of the genera Leptotila and Zenaida, but the quail‐doves (Geotrygon) were paraphyletic, falling into three separate lineages. The phylogeny indicated at least nine dispersal‐driven divergence events between North and South America. There were also five dispersal events in the recent past that have not yet led to differentiation of taxa (polymorphic taxa). Main conclusions Most of these dispersal‐driven diversification events occurred at the time of or after the formation of the Central American land bridge, indicating that this land connection played a role in facilitating divergence via dispersal of doves between continents.     

Repeated DNA sequences and species relatedness in the genusEquisetum

The kinetics with which DNA reassociates and the thermal stability of rapidly reassociating (repetitive) DNA sequences have been monitored for six species in the genusEquisetum. Using the kinetic complexity for each of two repeated DNA sequence components as the basis for comparison, species in the subgenusEquisetum (E. arvense, E. fluviatile andE. telmateia) form one group and species in the subgenusHippochaete (E. hyemale, E. laevigatum andE. scirpoides) form another group. Using the difference in thermal stability between native and reassociated repetitive DNA for comparison, the same grouping of species is obtained.     

Pliocene climatic change in insular Southeast Asia as an engine of diversification in Ficedula flycatchers

Aims Insular Southeast Asia and adjacent regions are geographically complex, and were dramatically affected by both Pliocene and Pleistocene changes in climate, sea level and geology. These circumstances allow the testing of several biogeographical hypotheses regarding species distribution patterns and phylogeny. Avian species in this area present a challenge to biogeographers, as many are less hindered by barriers that may block the movements of other species. Widely distributed Southeast Asian avian lineages, of which there are many, have been generally neglected. Ficedula flycatchers are distributed across Eurasia, but are most diverse within southern Asia and Southeast Asian and Indo‐Australian islands. We tested the roles of vicariance, dispersal and the evolution of migratory behaviours as mechanisms of speciation within the Ficedula flycatchers, with a focus on species distributed in insular Southeast Asia. Methods Using a published molecular phylogeny of Ficedula flycatchers, we reconstructed ancestral geographical areas using dispersal vicariance analysis, weighted ancestral area analysis, and a maximum likelihood method. We evaluated the evolution of migratory behaviours using maximum likelihood ancestral character state reconstruction. Speciation timing estimates were calculated via local molecular clock methods. Results Ficedula originated in southern mainland Asia, c. 6.5 Ma. Our analyses indicate that two lineages within Ficedula independently and contemporaneously colonized insular Southeast Asia and Indo‐Australia, c. 5 Ma. The potential impact of vicariance due to rising sea levels is difficult to assess in these early colonization events because the ancestral areas to these clades are reconstructed as oceanic islands. Within each of these clades, inter‐island dispersal was critical to species’ diversification across oceanic and continental islands. Furthermore, Pliocene and Pleistocene climatic change may have caused the disjunct island distributions between several pairs of sister taxa. Both vicariance and dispersal shaped the distributions of continental species. Main conclusions This study presents the first evaluation, for Ficedula, of the importance of vicariance and dispersal in shaping distributions, particularly across insular Southeast Asia and Indo‐Australia. Although vicariant speciation may have initially separated the island clades from mainland ancestors, speciation within these clades was driven primarily by dispersal. Our results contribute to the emerging body of literature concluding that dynamic geological processes and climatic change throughout the Pliocene and Pleistocene have been important factors in faunal diversification across continental and oceanic islands.     

Foldamers with hybrid biological and synthetic sequences as selective DNA fluorescent probes

Foldable polymers with alternating single-strand deoxyribonucleic acid (ssDNA) and planar fluorescent organic chromophores can self-organize into folded nanostructures and hence are hybrid foldamers with biological sequences and synthetic properties. The biological sequence provides highly specific molecular recognition properties, while the physical properties of synthetic chromophores offer sensitive fluorescence detection. In this paper, we describe that rational designed hybrid foldamers exhibit potential in the detection of polynucleotides. Under strictly controlled laboratory conditions, fluorescence measurements indicate that configuration change due to binding of polynucleotides with one or two mismatched bases can be readily distinguished. These results shed light on the design and construction of nanostructured foldamers with actuator and sensory properties, which may find important applications as biological probes.     

Repeated sequences as genetic markers in pooled tissue samples

We show, using the PDR1 element of pea, that dispersed repeated sequences of moderate copy number can be used simply and efficiently to generate markers linked to a trait of interest. Inspection of hybridization patterns of repeated sequences to DNA mixtures of pooled genotypes is a sensitive way of detecting such markers. The large number of bands in tracks of digests of these mixtures allows the simultaneous sampling of loci at many places in the genome, and the many unlinked loci serve as internal controls. It is also shown that intensity ratios calculated from these band differences can be used to give a rough estimate of linkage distance.     

Repeated DNA sequences found in the large spacer of Vicia faba rDNA

In the large spacer of the rDNA of Vicia faba, multiples of a 0.32 kilobasepair (kb) sequence reiterate to various degrees. We sequenced the repetitious region consisting of the repeating sequences and its flanking regions using two cloned plasmids, which contain V. faba rDNA segments encompassing the whole region of the large spacer. The repetitious region was found to consist of multiple complete copies and one truncated copy of a 325 bp repeat unit and to be flanked by direct repeat sequences of about 150 bp. The set of direct repeats located at either side of the repetitious region differed from each other with about 10% sequence heterogeneity. However, nucleotide sequences of the direct repeats were well conserved between the two clones examined. Southern blot hybridization indicated a widespread distribution within the whole V. faba genome of some related sequences with high homologies to the 325 bp repeat unit and to the direct repeats.     

Repeated sequences in the DNA of Drosophila and their localization in giant chromosomes

It is shown by isopycnic density gradient centrifugation that the DNAs of the sibling species Drosophila hydei, Drosophila neohydei and Drosophila pseudoneohydei differ regarding the numbers and proportions of satellite DNA bands. An overwhelming proportion of all repetitive nucleotide sequences of the DNA is contained in these satellite fractions. The majority of the satellites are species specific despite the close phylogenetic and cytological relationship between the three species studied. — By in situ hybridization experiments it is demonstrated that the various satellite sequences occupy different positions within the chromosomes. All types of localization patterns, from a wide spread occurrence in all chromosomes to an apparent restriction to kinetochore regions of single chromosomes, have been observed. Main band DNA, on the other hand, in its hybridization behavior reflects the DNA distribution according to the banding pattern in giant chromosomes. Generally satellite sequences seem to be included in -heterochromatic chromosome regions but no relation to the heterochromatin of the Y-chromosome was found. — Renaturation studies support various evidence that satellite sequences occur in tandemly repetitious units. At least some of this repetitious material seems to be linked to non-satellite DNA sequences or to DNA of other satellites.     

Repeated DNA sequences in the distal long arm of the human X chromosome

Summary Two DNA probes from within a single large insert from a recombinant phage-DNA library that was constructed from flow-sorted chromosomes enriched for the human X chromosome were shown to hybridize with repeated X-specific and autosomal DNA sequences. The X-chromosomal repeated sequences were assigned to the distal long arm of the X chromosome by both hybrid mapping and in situ hybridization. Fine mapping places these repeats in a region of Xq28 between DX13 (DXS15, in distal Xq28) and factor VIII (F8C, in proximal Xq28). The location of the X-specific repeats makes them potentially useful for future investigations of discases mapping to the distal long arm of the X chromosome, such as the fragile X syndrome.     

Molecular dating of the diversification of Phyllostominae bats based on nuclear and mitochondrial DNA sequences

Times of divergence among the three tribes included within the subfamily Phyllostominae were estimated using a Bayesian approach to infer dates of divergence based on mitochondrial and nuclear sequence data. The subfamily Phyllostominae is particularly attractive for such analysis, as it is one of the few groups of bats to have fossil specimens. Our molecular time analyses suggest that diversification among tribes and genera of phyllostomine bats occurred during the Early to Mid-Miocene, and was coincident with diversification events in two co distributed taxa: Caviomorph rodents and New World monkeys.     

Repeated sequences from theArabidopsis thaliana genome function as enhancers in transgenic tobacco

Sixteen segments ofArabidopsis thaliana DNA that function as enhancers in transgenic tobacco plants were isolated using the pROA97 enhancer cloning vehicle and library transformation ofNicotiana tabacum. The sequences were compared for AT content, homology, repeated motifs, and expression pattern in transgenicN. tabacum. The sequences were average with respect to the AT content ofA. thaliana DNA. They could be placed into seven homology groups. Five of the sequences are single-copy sequences. The remaining eleven sequences represent two homology groups. Homology Group I contains seven sequences with minor differences. Homology Group II contains four sequences with minor differences. Two repeated motifs were identified (5′-CCTCT-3′ and 5′-AAGGAT-3′). Both repeated motifs are found in other plant enhancers, and in the promoter region of the cauliflower mosaic virus 35S gene. In the 35S gene TATA region, the motifs can form two alternative stem-loop structures. The TATATAA sequence is located in the loop region of both stem-loop structures.