Direct and indirect estimates of the selfing rate in small and large individuals of the bumblebee pollinated Cynoglossum officinale L (Boraginaceae)

We measured the relationship between selfing rates and flower number in an experimental population of bumblebee pollinated Cynoglossum officinale , with plants differing in flower number. Results were compared with the prediction of a model based on pollen dynamics and pollinator behaviour. The selfing rate, as measured by multilocus oligonucleotide DNA fingerprinting, increased with flower number and ranged from 0% to 70%. Flowers on large plants received an equal number of visits from bumblebees as flowers on small plants. On large plants more flowers in a row were visited, inducing geitonogamy. The overall relationship between selfing rate and number of flowers can be explained by pollen dynamics and pollinator behaviour without invoking postpollination processes such as differential pollen tube growth and abortion.     

A nonradioactive screening method for cloning genes encoding sequence-specific DNA binding proteins.

We have developed a novel nonradioactive screening method for cloning genes encoding sequence-specific DNA binding proteins. This method is derived from previously described protocols developed for the same purpose by using radioactively labeled DNA probes containing protein recognition sequences. This nonradioactive strategy relies upon the use of a small hapten, digoxigenin. Fusion proteins expressed from the recombinant bacteriophage lambda gt11/lambda ZAP are immobilized on nitrocellulose filters and probed with digoxigenin-labeled double-stranded DNA as a ligand. The specifically bound DNA probes can be detected through sequential incubations with antibody-enzyme conjugate and enzyme substrates. This technique has been successfully utilized to isolate several cDNA clones encoding DNA binding proteins.     

Modification of DNA with dihydrazide of succinic acid for preparation of hybridization probes

A two-step chemical method of introduction of nonradioactive labels in DNA was proposed. At first step DNA is modified by succinic dihydrazide at pH 5.0 and 95 degrees C, or at pH 4.5 and 37 degrees C in presence of sodium bisulfite. Then FITC or biotin are joined to the hydrazide groups. DNA modified in this way were shown to be effective hybridisation probes.     

Use of biotinylated DNA probes in screening cells obtained from cervical swabs for human papillomavirus DNA sequences

A nonradioactive DNA-detection procedure using biotinylated DNA probes in the screening of cells from cervical swabs for DNA sequences homologous to human papillomavirus (HPV) DNA was tested. This alternative DNA-detection method yielded results comparable to those obtained with radioisotope-labeled DNA probes in 32 cases tested. This procedure obviates the special precautions required for radioisotope materials. Accordingly, this technique can be made available to many laboratories, and conclusive evidence as to the relation of HPV infection to cervical cancer may thus be accumulated.     

Fine-scale estimation of outcrossing in western redcedar with microsatellite assay of bulked DNA

Western redcedar (Thuja plicata, Cupressaceae) is a self-fertile conifer with a mixed mating system and significant variation for outcrossing among populations. In this paper, we conducted a fine-scale study of mating system variation to identify correlates of outcrossing in natural populations. We examined variation for outcrossing within and among individual trees, and describe a new method to estimate outcrossing using bulked DNA samples. Bulking (assaying DNA tissues from several individuals simultaneously) increases the experimental power without increasing the experimental effort. We sampled 80 trees from four natural populations in southwestern British Columbia. From each tree, we sampled from up to six crown positions (three heights and inner vs outer branches). From each position, two samples of three seedlings each were bulked before DNA extractions. Using four microsatellite loci, we obtained outcrossing rates for each tree and for each of the six crown positions. We found individual tree selfing rates to increase with tree height in all four populations, but selfing rates did not differ among crown positions. The higher selfing rate of larger trees is probably due to their greater proportional contribution to local pollen clouds. Individual tree outcrossing rates ranged from 22 to 100% and the population outcrossing rates from 66 to 78%. Missed alleles due to bulking and the estimation method used both cause a downward bias in outcrossing rates, so that these estimates are probably lower than the actual outcrossing rates. Nevertheless, the trends we observed are not affected by systematic biases of estimation.     

Nonradioactive labeling with chemically modified cytosine tails by the polymerase chain reaction.

We developed a modified nonradioactive method for the detection of DNA. This method makes use of the polymerase chain reaction for preparation of probes; that is, a DNA fragment inserted in the polylinker region of an M13 or pUC vector is amplified with primers that have a modified cytosine tail at the 5' terminus (C-tailed primers). By this method, large amounts of labeled probes can be obtained easily. After hybridization, modified cytosine tails can be detected immunologically. DNA labeled by this method could be used in plaque hybridization. We could detect 0.05 pg of dot-blotted labeled DNA in 30 min with an enzyme-catalyzed chemiluminescence reaction.     

Comparison of three nonradioactive and a radioactive DNA probe for the detection of target DNA by DNA hybridization

The specificity and sensitivity of three methods for the preparation and detection of nonradioactive probe DNA (biotin-nick translation, biotin-photolabel, and antigen-chemical linkage) were evaluated and compared with a nick-translated³²P-labeled DNA probe in DNA hybridization studies. The DNA probes were prepared from a restriction fragment (HindIII-3) from bacteriophage P1 DNA, and target DNA consisted of purified phage P1 DNA or P1 prophage DNA in lysogens ofEscherichia coli. A probe concentration of 50 ng/ml resulted in clear detection with the three nonradioactiveHindIII-3 DNA probes, whereas the specificity of the³²P-HindIII-3 DNA probe was satisfactory at a concentration of 25 ng/ml. However, the detection of false positives was greater with the³²P-labeled probe. The sensitivity of the radiolabeled DNA probe was marginally greater than that of the nonradioactive probes in dot blot hybridizations with purified phage P1 DNA. However, when the preparation time, ease of use, safety, duration of storage, and expense were compared for the four methods of labeling, the nonradiolabeled probes were generally superior to the radiolabeled probe.     

Synthesis of peptide nucleic acid-peptide chimeras carrying the c-myc tag-sequence

Summary The preparation of peptide nucleic acids (PNA) carrying a c-myc tag-peptide sequence is described. These PNA-peptide chimeras have higher affinity to complementary DNA than unmodified oligonucleotides. Moreover, they can be used as nonradioactive probes with sensitivity similar to other nonradioactive methods.     

异羟基洋地黄毒甙元(Digoxigenin)标记的探针在乙型肝炎病毒核酸杂交中的应用

应用异羟基洋地黄毒甙元标记的探针,检测了人和鸭的血清及肝脏中的乙型肝炎病毒核酸,并与~(32)P标记的同位素探针做了比较。结果证明,该探针的特异性和敏感性与同位素探针一致(0.2pg)。它可用于各种核酸杂交试验,如打点杂交、Southern和Northern转印杂交试验等。恰当地从标本中提取待测核酸,是应用该探针的重要条件。     

热启动PCR快速制备地高辛标记探针

介绍了一种在热启动PCR中,以Dig-11-dUTP部分代替dTTP,从少量基因组DNA中快速制备大量的地高辛标记的探针的方法,此探针灵敏度达0.03pg,并只和相关的DNA特异杂交.     

High-sensitivity hybridization assay for quantitation of residual E. coli DNA

Impurity assays for recombinant protein therapeutics are essential to ensure batch-to-batch consistency and to meet the FDA's criteria for a well-characterized biopharmaceutical. For determination of residual host cell DNA, membrane hybridization assays utilizing radiolabeled DNA probes prepared from the host cell's genomic DNA have traditionally been used for products derivedfrom bacterial expression systems to obtain the required low picogram sensitivity. Nonradioactive methods, while desirable to eliminate radioactive waste disposal and safety issues, typically suffer from poor sensitivity and high backgrounds. We report the development of a suitably sensitive, nonradioactive assay to quantitate residual E. coli DNA levels in purified protein drugs by means of a slot-blot hybridization method. The assay utilizes digoxigenin-labeled E. coli DNA probes and SuperSignal chemiluminescent substrate. The optimized chemiluminescent hybridization assay has both low background and high sensitivity, allowing routine detection of 2.5 pg E. coli DNA. The method can be tailored for detection/quantitation of DNA contamination in recombinant protein products expressed in E. coli or other bacterial expression systems.     

Gene rearrangements detected by nonradioactive digoxigenin-labeled DNA probes.

The configurations of immunoglobulin, T-cell receptor beta chain and bcl-2 genes were analyzed in lympho-proliferative disorders using nonradioactive digoxigenin-labeled probes. The studies demonstrated the reliability of digoxigenin-labeled probes for the detection of single-copy genes after Southern blotting of genomic DNA: 1 microgram and sometimes even 0.2 microgram of restriction endonuclease-digested DNA could be detected either by JH, C beta or bcl-2 probes. The intensity of the signal was consistently satisfactory, and there was no background problem. Control experiments showed neither false-positive nor false-negative results caused by the use of the nonradioactive detection system.     

Human papillomavirus DNA detection in Papanicolaou-stained cervical smears with a nonradioactive, in situ hybridization assay.

Archived Papanicolaou-stained cervical smears from women with different cervical pathologies were processed for human papillomavirus (HPV) DNA detection and typing with an in situ hybridization (ISH) assay that employed commercial biotinylated HPV DNA probes. Two HPV DNA probes were utilized: one included HPV genotypes 6/11 and the other, 16/18. The method yielded positive results for HPV DNA 6/11 in 5 cases with condylomata acuminata (100%) and in 2 of 47 with flat warty lesions (4.2%), whereas HPV DNA 16/18 was detected in 29/47 of the latter group (61.7%). In cases with cervical intraepithelial III or invasive squamous cell carcinoma the yield was lower: positive results for HPV DNA 16/18 were obtained in only one of the five cases with one or the other cervical pathology (20%). An analysis of the results showed that the sensitivity of the assay correlated with evidence in the Papanicolaou specimens of pathognomonic cell injury from HPV infection. In the presence of such cytologic features, HPV DNA typing was possible in 37/52 cases (65.4%). In view of the modest difficulty and relatively quick execution of the nonradioactive ISH assay, the authors believe that Papanicolaou cervical smears with cytologic changes of HPV infection could be processed by this method in order to acquire information on the HPV type or types involved in the cervical infection.     

Amplification of kinetoplast DNA as a tool in the detection and diagnosis of Leishmania

This paper demonstrates how the polymerase chain reaction can be used to increase the sensitivity of detection of Leishmania parasites by DNA hybridization methods through the amplification of the minicircle target sequence. The oligonucleotide primers used are able to direct the amplification of all Leishmania strains tested. In addition, the PCR products from L. mexicana and L. braziliensis strains can be distinguished by hybridization with kDNA probes. The method is sensitive enough to detect the kDNA from a single organism and this sensitivity allows the use of nonradioactive hybridization methods. This method can be used to detect Leishmania from human biopsy material.     

The influence of floral display size on selfing rates in Mimulus ringens

Pollinators often visit several flowers in sequence on plants with large floral displays. This foraging pattern is expected to influence the rate of self-fertilization in self-compatible taxa. To quantify the effects of daily floral display on pollinator movements and selfing, we experimentally manipulated flower number in four replicate (cloned) arrays of Mimulus ringens (Scrophulariaceae), each consisting of genets with unique combinations of homozygous marker genotypes. Four display classes (two, four, eight and 16 flowers) were present in each array. Pollinator visitation rate per flower and seed set per fruit were unaffected by display. However, flower number strongly influenced the frequency of within-plant pollinator movements, which increased from 13.8% of probes on two-flower displays to 77.6% of probes on 16-flower displays. The proportion of within-plant movements was significantly correlated with selfing (r = 0.993). The increase from 22.9% selfing on two-flower displays to 37.3% selfing on 16-flower displays reflects changes in the extent of geitonogamous self-pollination. We estimate that approximately half of all selfing on 16-flower displays resulted from geitonogamy. Selfing also varied dramatically among fruits within display classes. Nested ANOVA indicates that differences among flowers on two-flower ramets accounted for 45.4% of the variation in selfing, differences among genets accounted for 16.1% of the variation, and statistical and sampling error accounted for 38.5% of the variation. Differences among flowers within ramets may reflect the order of sequential floral probes on a display.     

A hydroxylapatite batch assay for quantitation of cellular DNA damage.

A batch elution procedure is described for quantitative measurement of DNA damage. The technique is based on alkaline unwinding of cellular DNA and separation of singlestranded from duplex forms by step elution from hydroxylapatite with phosphate formamide. The method is rapid, permits large numbers of samples to be handled simultaneously, and consistently yields recoveries of >95% of total chromatographed DNA. Because as many as 1 × 10⁷ cells per batch may be analyzed, quantitation of the eluted DNA by nonradioactive methods is feasible. The method is standardized with respect to the unwinding constant β, the alkaline DNA unwinding unit Mng, and the DNA-damaging efficiency of ionizing irradiation.     

Pollinator visitation patterns strongly influence among-flower variation in selfing rate

Background and Aims

Adjacent flowers on Mimulus ringens floral displays often vary markedly in selfing rate. We hypothesized that this fine-scale variation in mating system reflects the tendency of bumble-bee pollinators to probe several flowers consecutively on multiflower displays. When a pollinator approaches a display, the first flower probed is likely to receive substantial outcross pollen. However, since pollen carryover in this species is limited, receipt of self pollen should increase rapidly for later flowers. Here the first direct experimental test of this hypothesis is described.

Methods

In order to link floral visitation sequences with selfing rates of individual flowers, replicate linear arrays were established, each composed of plants with unique genetic markers. This facilitated unambiguous assignment of paternity to all sampled progeny. A single wild bumble-bee was permitted to forage on each linear array, recording the order of floral visits on each display. Once fruits had matured, 120 fruits were harvested (four flowers from each of five floral displays in each of six arrays). Twenty-five seedlings from each fruit were genotyped and paternity was unambiguously assigned to all 3000 genotyped progeny.

Key Results

The order of pollinator probes on Mimulus floral displays strongly and significantly influenced selfing rates of individual fruits. Mean selfing rates increased from 21 % for initial probes to 78 % for the fourth flower probed on each display.

Conclusions

Striking among-flower differences in selfing rate result from increased deposition of geitonogamous (among-flower, within-display) self pollen as bumble-bees probe consecutive flowers on each floral display. The resulting heterogeneity in the genetic composition of sibships may influence seedling competition and the expression of inbreeding depression.Key words: Autogamy, bee, Bombus fervidus, floral display, geitonogamy, mating system, monkeyflower, Mimulus ringens, paternity analysis, pollen carryover, pollinator visitation sequence, self-fertilization     

Preparation of enzyme-conjugated DNA probe and application to the universal probe system.

A general procedure for the cross-linking of enzyme to DNA has been developed for use as a nonradioactive probe. In this method, DNA is transaminated with diaminopropane to introduce primary amino groups into the cytosine residues. Then the amino groups are converted to thiol groups using a heterobifunctional cross-linker. The thiolated DNA is conjugated with the maleimide-introduced enzyme. With this method, alkaline phosphatase was cross-linked to a single-stranded DNA (sspUCRf1). The conjugate was able to detect 5 pg of target DNA (pUCf1 plasmid, 3.2 kbp) fixed onto the nitrocellulose membrane, using a colorimetric assay. The enzyme-conjugated DNA was applied to "the universal probe system," which consisted of two single-stranded DNA probes (a primary probe and a labeled secondary probe). Using alkaline phosphatase-conjugated sspUCRf1 DNA as the secondary probe, the c-myc gene and HBV DNA were detected effectively on Southern and dot-blot hybridization.     

Nonradioactive detection of nucleic acid by the universal probe system

A convenient and nonradioactive method for DNA hybridization tests termed the "Universal probe system" has been developed. This method is based on the principle of sandwich hybridization. This system consists of two single-stranded DNA probes (a primary probe and a biotin-labeled secondary probe). The primary probe is prepared from a chimeric phage-plasmid vector containing the complementary sequence to a target gene. The secondary probe has a sequence complementary to the vector portion of the primary probe and is labeled with biotin via the transamination reaction. An advantage of this method is that the single-stranded primary probe can be prepared with ease by using the chimeric phage-plasmid vector system, thereby avoiding tedious labeling of individually different probes. As the primary probe is not modified with biotin and other labels, it conserves the sequence to be hybridized with a target. Accordingly, the primary probe containing a relatively short hybridizing region (ca. 50 bp) can efficiently hybridize with the target. In fact, the universal probe is sensitive enough to detect a single-copy human gene on Southern blots.