Fast quantification of nucleic acid hybrids by affinity-based hybrid collection.

A hybridization technique for the quantification of nucleic acids is described. In the method a probe pair is allowed to form hybrids with the target nucleic acid in solution. One of the probes has been modified with an affinity label, by which the formed hybrids can be isolated after the reaction. Streptavidin-agarose was used to capture hybrids containing biotinylated DNA. The hybrids were measured using radioiodine as label on the second probe. The rate of the hybridization reaction in solution is fast, allowing the whole procedure to be carried out in 3 h. The method is quantitative with a detection limit of 4 X 10(5) molecules (0.67 attomoles) target DNA. The test is insensitive to impurities in biological samples, which are analyzed without purification of the target DNA. Non-isotopic measurement of the hybrids can also be applied. In this case the hybrids are bound to microtitration wells and detected spectrophotometrically by peroxidase-catalyzed colour development.     

Isolated HeLa cell nuclei synthesize meaningful DNA.

DNA replicated at the beginning of S phase was labelled by incubating nuclei isolated from cells arrested at the G/S border with radioactive deoxyribonucleoside triphosphate in a reaction mixture sustaining DNA synthesis. By hybridization against ribosomal RNA bound to nitrocellulose, the fraction of the labelled DNA which was complementary to rRNA could be quantified, and the stability of the RNA-DNA hybrids could be estimated by sequential elution of DNA at increasing temperatures. The results obtained indicate that the isolated nuclei make "meaningful" DNA, as judged by the melting characteristics of the hybrids between rRNA and the in vitro replicated DNA. Hybridization of the labelled DNA against rRNA fractionated by electrophoresis and blotted onto nitrocellulose verified the presence of sequences complementary to 18 S and 28 S rRNA.     

Novel class of rDNA repeat units in somatic hybrids between Nicotiana and Atropa

Summary Behavior of ribosomal RNA genes in the process of somatic hybridization was analyzed using hybrids Nicotiana tabacum + Atropa belladonna. Blothybridization of parental species DNAs to ³²P-rDNA specific probes revealed two classes of ribosomal repeats in both tobacco and nightshade; their length was 11.2 kb, 10.4 kb (tobacco) and 9.4 kb, 10.2 kb (night-shade). For analysis of hybrids, labelled ³²P rDNA specific probes were hybridized to DNA of parental species and somatic hybrids digested with restriction endonucleases EcoR1, EcoRV and BamH1. A new class of ribosomal DNA repeat, absent in parental species, was found in hybrid line NtAb-1. Possible mechanisms of appearence of a new rDNA class in the process of somatic cell fusion are discussed.     

Using genomic slot blot hybridization to assess intergeneric Saccharum x Erianthus hybrids (Andropogoneae - Saccharinae).

The use of genomic slot blot hybridization enabled the differentiation of hybrids from selfs in Saccharum x Erianthus intergeneric crosses in which Saccharum was used as the female parent. Based on the genomic in situ hybridization technique, slot blots of DNA from the parents and the progeny were blocked with the Saccharum parent DNA and hybridized with the labelled male Erianthus genomic DNA. This technique allowed a rapid screening for hybrids and was sensitive enough to detect a 1/20 dilution of Erianthus in Saccharum DNA, which should enable the detection of most partial hybrids. The genomic slot blot hybridization technique was shown to be potentially useful for assessing crosses involving Saccharum species with either Old World Erianthus section Ripidium or North American Erianthus (= Saccharum) species. The effectiveness of the technique was assessed on 144 progeny of a Saccharum officinarum x Erianthus arundinaceus cross, revealing that 43% of the progeny were selfs. The importance of this test as a tool to support intergeneric breeding programs is discussed.     

Search for unique segments of the ectromelia virus genome by cross blot hybridization with DNA from other orthopoxviruses]

In order to identify ectromelia virus (EMV) genome regions which may contain genes responsible for the specific pathogenicity of this virus, blot cross-hybridization of EMV DNA with those of other orthopoxviruses was performed. Two hybridization schemes were employed: one of them included hybridization of labelled cloned fragments of EMV with digests of other viral DNAs, the other, reciprocal, consisted in hybridization of labelled total DNAs of various orthopoxviruses with digests of the region of EMV DNA adjacent to the right-terminal inverted repeat. It was demonstrated that the counterpart to an approximately 8-kilobase pair portion of EMV genome flanking the inverted repeat could be detected only in the cowpox virus genome but not in the genomes of vaccinia and rabbitpox viruses. XhoI-O and XhoI-K fragments of EMV DNA contained, along with genes found in other poxviruses, certain genes which appeared to be unique for EMV. It is postulated that some of these genes may determine the specific biological properties of EMV, including its pathogenicity for mice.     

A complex of single-strand binding protein and M13 DNA as hybridization probe.

Single-stranded DNA was complexed to the single-strand binding protein (SSB) of Escherichia coli in a mass ratio of 30:1. The protein moiety of this complex can be labelled by a number of methods of which we have chosen radio-iodination and biotinylation as examples. The SSB-M13 DNA complexes, labelled to high specific activities, were used as probes in hybridization experiments in which 1.6 X 10(-18) moles of immobilized target DNA were detected. The stability of the hybrids was not severely decreased by the binding of SSB. Analysis of hybrids by electron microscopy showed that complexing of DNA with SSB could be used to allow its subsequent identification in the hybrids.     

Identification of the Genomic Constitution ofMusaL. Lines (Bananas, Plantains and Hybrids) Using Molecular Cytogenetics

The genomic constitutions of someMusaL. lines (bananas, plantainsand artificial hybrids) were identified using molecular cytogenetictechniques. Double targetin situDNA:DNA hybridization to chromosomespreads using as probes, total genomic DNA isolated from diploidMusalinesof known AA (labelled with biotin-11-dUTP) and BB (labelledwith digoxigenin-11-dUTP) genome constitution was carried out.The use of 60% acetic acid combined with heating over a flamegave high quality chromosome spreads free of cytoplasm forinsituhybridization. Total genomic A DNA labelled broad centromericregions of all 22 chromosomes of the diploid line, Calcutta4 (M. acuminataColla. ssp.burmanniccoides; A genome) with somechromosomes showing stronger hybridization. Labelled DNA fromthe B genome hybridized strongly to the centromeric regionsof all 22 chromosomes of Butohan 2 (M. balbisianaColla; B genome).The two satellited chromosomes of genome B labelled stronglywith genomic A DNA.In situhybridization of labelled A and Bgenomic DNA to metaphase chromosomes of triploid AAB and ABBcultivars discriminated between A and B genome chromosomes.The plantains Agbagba, Obino l'Ewai and Mbi Egome showed 22genome A and 11 genome B chromosomes while the cooking bananasBluggoe and Fougamou showed 11 genome A and 22 genome B chromosomes.Hybridization of labelled A and B genomic DNA to chromosomesof the hybrids showed that TMP2x 2829-62 has all 22 genome Achromosomes while TMPx 4698-1 has 33 genome A and 11 genomeB chromosomes.In situhybridization of labelled total genomicDNA to chromosomes has immense potential for identificationof chromosome origin and can be used to characterize cultivarsand hybrids produced inMusabreeding.Copyright 1997 Annals ofBotany Company Genomicin situhybridization; banana; plantain; hybrids; plant breeding; genome organization; biodiversity     

Testing hybridization hypotheses and evaluating the evolutionary potential of hybrids in mangrove plant species

Natural hybridization is of marked importance from global to local biological diversity. In mangroves, species ranges overlap extensively with one another and species share a long overlap of flowering time. Although hybridization has been suggested, patterns of hybridization and the evolutionary potential of hybrids are not yet fully understood. This study provides molecular evidence for the parental origins and status of hybrids in the dominant mangrove genus Rhizophora based on comparisons of chloroplast and nuclear phylogenies and estimations of genetic relatedness and structure from inter‐simple sequence repeat (ISSR) markers. Phylogenetic analyses indicate that almost all species can act as maternal parents to hybrids and that hybridization can be bidirectional. Bayesian analyses indicate that hybrids are simple F₁s, and no trace of backcrossing was detected within populations. Hybridization, for the most part, occurs almost only locally and dispersal of hybrid individuals is limited beyond the hybrid sites.     

Hybridization and gene flow between a day- and night-flowering species of Zaluzianskya (Scrophulariaceae s.s., tribe Manuleeae)

Despite apparent ethological isolation based on specialized pollination systems, hybridization between day-flowering Zaluzianskya microsiphon and night-flowering Z. natalensis has been proposed due to intermediate individuals found in sympatric populations of these species. The extent of this putative hybridization was investigated using inter-simple sequence repeat (ISSR) markers and principal components analysis (PCA) of morphological traits. The species are genetically similar, but show some intra- and interspecific variation in band frequencies. Neighbor-joining analyses of the ISSR data demonstrated that although the species largely formed distinct groups, several individuals from the sympatric populations of each species and the "hybrids" clustered together rather than with members of their own species. These results are consistent with hybridization, although they could also indicate historical similarity. Nine loci were present only in individuals of Z. microsiphon, the "hybrids," and sometimes the sympatric individuals of Z. natalensis. In contrast, only one locus showed the reverse pattern. This suggests unidirectional gene flow from Z. microsiphon to Z. natalensis, which is also supported by population-level examinations of four loci. Ordination revealed separate phenotype clusters for each species, with hybrid individuals located in between but often closer to the Z. natalensis cluster. One hypothesis is that hybrids are backcrossing with Z. natalensis, leading to introgression of Z. microsiphon genetic material.     

Nucleic acid hybridization: from research tool to routine diagnostic method

The nucleic acid hybridization reaction is extremely specific and thus a valuable tool for the identification of genes or organism of interest. The increasing use of nucleic acid hybridization in applied fields like diagnostic medicine has led to the development of more convenient hybridization assays than those originally used in basic research. In conventional nucleic acid hybridization methods immobilized nucleic acids are detected on a filter by a radiolabelled probe. Sandwich hybridization is a simple test format for the analysis of unpurified biological material, but has the disadvantage of a slow reaction rate. Solution hybridization methods are fast and easy to perform provided that a method to separate the formed hybrids from the reaction mixture is available. In non-isotopic detection the nucleic acid probe is modified with a chemical group, which is identified with a labelled detector molecule after hybridization. The low sensitivity of detection is the main problem in nucleic acid hybridization methods. Procedures to amplify the detectable signal or the amount of detectable nucleic acid sequences are potential solutions to this problem. The new hybridization methods have successfully been used for some applications, but still need to be combined into well performing tests to be applicable to any desired purpose.     

Interspecific hybridization increases transposition rates of Osvaldo.

Several authors have postulated that genetic divergence between populations could result in genomic incompatibilities that would cause an increase in transposition in their hybrids, producing secondary effects such as sterility and therefore starting a speciation process. It has been demonstrated that transposition largely depends on intraspecific hybridization for P, hobo, and I elements in Drosophila melanogaster and for several elements, including long terminal repeat (LTR) and non-LTR retrotransposons, in D. virilis. However, in order to demonstrate the putative effect of transposable elements on speciation, high levels of transposition should also be induced in hybrids between species that could have been originated by this process and that are still able to interbreed. To test this hypothesis, we studied the transposition of the LTR retrotransposon Osvaldo in Drosophila buzzatii-Drosophila koepferae hybrids. We used a simple and robust experimental design, analyzing large samples of single-pair mate offspring, which allowed us to detect new insertions by in situ hybridization to polytene chromosomes. In order to compare transposition rates, we also used a stock recently obtained from the field and a highly inbred D. buzzatii strain. Our results show that the transposition rate of Osvaldo is 10(-3) transpositions per element per generation in all nonhybrid samples, very high when compared with those of other transposable elements. In hybrids, the transposition rate was always 10(-2), significantly higher than in nonhybrids. We show that inbreeding has no effect on transposition in the strains used, concluding that hybridization significantly increases the Osvaldo transposition rate.     

Repeat swimming performance and its implications for inferring the relative fitness of asexual hybrid dace (Pisces: Phoxinus) and their sexually reproducing parental species

While theories explaining the evolution and maintenance of sex are abundant, empirical data on the costs and benefits of asexual relative to sexual reproduction are less common. Asexually reproducing vertebrates, while few, provide a rare opportunity to measure differences in fitness between asexual and sexual species. All known asexually reproducing vertebrates are of hybrid origin, and hybrid disadvantage (i.e., reduced hybrid fitness) is thought to facilitate long-term coexistence between asexual and sexual species. We used repeat swimming performance as a proxy for fitness to compare the fitness of asexual hybrid dace (Pisces: Phoxinus) and their sexually reproducing parental species, finescale dace (Phoxinus neogaeus) and northern redbelly dace (Phoxinus eos). We tested the prediction that, given the widespread coexistence of these hybrid and parental dace, the parental species should show equivalent and perhaps superior repeat performance relative to hybrids. A repeat constant acceleration test (U(max)) was conducted at both acclimation temperature (16 °C) and at an elevated temperature (25 °C) to simulate the combined influence of a repeat swim and acute temperature change that fish might experience in the wild. The asexual hybrids performed more poorly than at least one of the parental species. There was a negative effect of temperature on repeat swimming performance in all fish, and the repeat performance of hybrids was more severely affected by temperature than that of finescale dace. No difference in the effect of temperature on repeat performance was detected between hybrids and northern redbelly dace. These results suggest that hybrids suffer physiological costs relative to the parentals or at least that the hybrids do not gain advantage from hybrid vigor, which probably contributes to the coexistence of asexual and sexual species in this system.     

Rapid, high fidelity analysis of simple sequence repeats on an electronically active DNA microchip

We describe a method for the discrimination of short tandem repeat (STR) alleles based on active microarray hybridization. An essential factor in this method is electronic hybridization of the target DNA, at high stringency, in <5 min. High stringency is critical to avoid slippage of hybrids along repeat tracts at allele-specific test sites in the array. These conditions are attainable only with hybridization kinetics realized by electronic concentration of DNA. A sandwich hybrid is assembled, in which proper base stacking of juxtaposed terminal nucleotides results in a thermodynamically favored complex. The increased stability of this complex relative to non-stacked termini and/or base pair mismatches is used to determine the identification of STR alleles. This method is capable of simultaneous and precise identification of alleles containing different numbers of repeats, as well as mutations within these repeats. Given the throughput capabilities of microarrays our system has the potential to enhance the use of microsatellites in forensic criminology, diagnostics and genetic mapping.     

A Bayesian analysis of gene flow from crops to their wild relatives: cultivated (Lactuca sativa L.) and prickly lettuce (L. serriola L.) and the recent expansion of L. serriola in Europe

Interspecific gene flow can lead to the formation of hybrid populations that have a competitive advantage over the parental populations, even for hybrids from a cross between crops and wild relatives. Wild prickly lettuce (Lactuca serriola) has recently expanded in Europe and hybridization with the related crop species (cultivated lettuce, L. sativa) has been hypothesized as one of the mechanisms behind this expansion. In a basically selfing species, such as lettuce, assessing hybridization in natural populations may not be straightforward. Therefore, we analysed a uniquely large data set of plants genotyped with SSR (simple sequence repeat) markers with two programs for Bayesian population genetic analysis, STRUCTURE and NewHybrids. The data set comprised 7738 plants, including a complete genebank collection, which provided a wide coverage of cultivated germplasm and a fair coverage of wild accessions, and a set of wild populations recently sampled across Europe. STRUCTURE analysis inferred the occurrence of hybrids at a level of 7% across Europe. NewHybrids indicated these hybrids to be advanced selfed generations of a hybridization event or of one backcross after such an event, which is according to expectations for a basically selfing species. These advanced selfed generations could not be detected effectively with crop‐specific alleles. In the northern part of Europe, where the expansion of L. serriola took place, the fewest putative hybrids were found. Therefore, we conclude that other mechanisms than crop/wild gene flow, such as an increase in disturbed habitats and/or climate warming, are more likely explanations for this expansion.     

Repeat motifs of tau bind to the insides of microtubules in the absence of taxol

The tau family of microtubule-associated proteins has a microtubule-binding domain which includes three or four conserved sequence repeats. Pelleting assays show that when tubulin and tau are co- assembled into microtubules, the presence of taxol reduces the amount of tau incorporated. In the absence of taxol, strong binding sites for tau are filled by one repeat motif per tubulin dimer; additional tau molecules bind more weakly. We have labelled a repeat motif with nanogold and used three-dimensional electron cryomicroscopy to compare images of microtubules assembled with labelled or unlabelled tau. With kinesin motor domains bound to the microtubule outer surface to distinguish between alpha- and beta-tubulin, we show that the gold label lies on the inner surface close to the taxol binding site on beta-tubulin. Loops within the repeat motifs of tau have sequence similarity to an extended loop which occupies a site in alpha-tubulin equivalent to the taxol-binding pocket in beta-tubulin. We propose that loops in bound tau stabilize microtubules in a similar way to taxol, although with lower affinity so that assembly is reversible.     

Genome reorganization in Nicotiana asymmetric somatic hybrids analysed by in situ hybridization

In situ hybridization was used to examine genome reorganization in asymmetric somatic hybrids between Nicotiana plumbaginifolia and Nicotiana sylvestris obtained by fusion of gamma-irradiated protoplasts from one of the parents (donor) with non-irradiated protoplasts from the other (recipient). Probing with biotinylated total genomic DNA from either the donor or the recipient species unequivocally identified genetic material from both parents in 31 regenerant plants, each originating from a different nuclear hybrid colony. This method, termed genomic in situ hybridization (GISH), allowed intergenomic translocations containing chromosome segments from both species to be recognized in four regenerants. A probe homologous to the consensus sequence of the Arabidopsis thaliana telomeric repeat (5'-TTTAGGG-3')n, identified telomeres on all chromosomes, including 'mini-chromosomes' originating from the irradiated donor genome. Genomic in situ hybridization to plant chromosomes provides a rapid and reliable means of screening for recombinant genotypes in asymmetric somatic hybrids. Used in combination with other DNA probes, it also contributes to a greater understanding of the events responsible for genomic recovery and restabilization following genetic manipulation in vitro.     

Comparison between chromosomal and nuclear sap RNA from Chironomus tentans salivary gland cells by RNA/DNA hybridization

Newly-synthesized, high molecular weight RNA from salivary gland polytene chromosomes and from the nuclear sap was investigated by RNA/DNA hybridization. Salivary glands were incubated for 90 min with radioactive nucleosides and afterwards fixed. Chromosomes and nuclear sap were subsequently isolated by microdissection. Labelled RNA, extracted from three different chromosomal fractions and from the nuclear sap, was subjected to different hybridization procedures under conditions which primarily allow repeated nucleotide sequences to interact.In one type of experiments RNA was hybridized by a microtechnique to filter-bound DNA at increasing RNA/DNA input ratios. Nuclear sap RNA saturated 0.25−0.30% of the DNA, while the chromosomal RNA fractions had not reached a plateau even after hybridization with 0.5−1% of the DNA. Thus chromosomal RNA appears to contain sequences which are absent from, or present in only low concentration in, the nuclear sap. Nuclear sap RNA hybrids also showed a higher thermal stability than chromosomal RNA hybrids, which may reflect a higher precision of base-pairing in hybrids formed by nuclear sap RNA.In a second type of experiments the time dependence of hybrid formation was investigated. The hybridization rate for nuclear sap RNA was about three times as high as the corresponding rate for chromosomal RNA. This result indicates a relative enrichment of rapidly hybridizing RNA sequences in the nuclear sap.The difference in hybridization properties between chromosomal and nuclear sap RNA may be due to a predominance in the nuclear sap of RNA from a special chromosomal puff, the Balbiani Ring 2 (BR2), which has been shown to contain highly repeated DNA sequences. A comparison between the hybridization properties of nuclear sap RNA and BR2 RNA indicated that 55–70% of nuclear sap RNA may be derived from BR2.The specific hybridization rate of chromosomal RNA points to an average multiplicity of about 30 for its complementary DNA sequences. On the basis of the present and previous results it is suggested that the repeated DNA is arranged in families of related sequences and that sequences belonging to a particular family are distributed in different chromosomes.     

Evaluation of the analytical performances of avidin-modified carbon sensors based on a mediated horseradish peroxidase enzyme label and their application to the amperometric detection of nucleic acids

In this study, neutravidin-coated screen-printed carbon sensors were fully characterized and further used for the amperometric detection of specific DNA sequences of human cytomegalovirus (HCMV DNA). For this purpose, we took advantage of an earlier established relationship between the amount of HRP affinity immobilized on the surface of the electrode and the steady-state current recorded in the presence of H₂O₂ as substrate and the single electron donor [Os^III(bpy)₂pyCl]²⁺ as cosubstrate. After incubating a saturating concentration of biotinylated horseradish peroxidase (Bio-HRP) onto the neutravidin-modified sensors, a surface concentration of active HRP of 3.6 pmol cm⁻² was calculated from the measurement of the electrocatalytic plateau current value. This result indicates that monolayers of neutravidin were adsorbed on the screen-printed carbon sensors. These neutravidin-covered platforms were then used to immobilize biotinylated nucleic acid targets. After hybridization with a complementary digoxigenin-labeled detection probe, the extent of hybrids formed was determined with an anti-digoxigenin HRP conjugate. The biosensor assay was applied to the detection of a synthetic oligonucleotide target, and then to the determination of an amplified viral DNA sequence. Monolayers of HRP-labeled oligonucleotide hybrids were immobilized onto the sensing surface whereas one third of the surface was covered with HCMV DNA hybrids. On the other hand, detection limits of 200 pM and 1 nM were obtained for the short oligonucleotide and the longer DNA targets, respectively. Finally, we demonstrated that the sensitivity of the electrochemical assay could be significantly improved by using high concentrations of the reduced form of the mediator [Os^II(bpy)₂pyCl]⁺, thus allowing one to detect as low as 30 pM of amplified HCMV DNA fragment.     

Interspecific hybridization between diploid species of Lotus (Leguminosae)

An interspecific hybridization study has been carried out between seven diploid species of Lotus (L. alpinus Schleich., L. japonicus (Regel) Larsen, L. filicaulis Dur., L. schoelleri Schweinf., L. krylovii Schischk. and Serg., L. tenuis Waldst. et Kit., and L. corniculatus var. minor Baker) closely related to L. corniculatus L. A total of 139 interspecific hybrids were produced in 16 combinations of the 7 species. Nine of these crosses were produced for the first time and four were obtained by means of embryo-culture. The growth habit, number of florets per umbel, flower color expression, HCN reaction and 15 metrical traits were compared between parents and hybrids. The relative case with which some hybrids were produced suggested that during the early evolutionary history of the genus species diversification could have originated through interspecific hybridization and subsequent gene differentiation. In some crosses, the hybrids resembled one parent more closely than the other. This close morphological affinity between the hybrids and one of their parents would make it extremely difficult to detect such hybrids in natural populations and probably aceounts for the prevailing belief that there is little or no hybridization in nature.     

Viral genome integration with nuclear DNA in chronic viral infection]

A possibility of the integration of tick-borne encephalitis virus RNA in the host cell genome is studied under the condition of long-term chronic infection of HEp-2 cells. Molecular hybridization of viral RNA, labelled with 3H-uridine, and of DNA from intact and chronically infected cells was performed in 50% formamide with 0,4 M NaCl with subsequent investigation of the hybridization product by means of equilibrium centrifugation in CsSO4. 0,3 and 0,5 mg of DNA were used in hybridization experiments. It is shown that RNA obviously forms hybrids with DNA from chronically infected cells, whose density varied from 1,55 to 1,46 g/ml, depending on the proportion of RNA and DNA in the hybrids. When the amount of DNA increased, the number of DNA-RNA hybrids increased as well. It is concluded that in nuclear DNA of cells chronically infected with tick-borne encephalitis virus, there are DNA sites, homologous to viral RNA, which are absent in intact cells.