Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning

To accelerate gene isolation from plants by positional cloning, vector systems suitable for both chromosome walking and genetic complementation are highly desirable. Therefore, we developed a transformation-competent artificial chromosome (TAC) vector, pYLTAC7, that can accept and maintain large genomic DNA fragments stably in both Escherichia coli and Agrobacterium tumefaciens. Furthermore, it has the cis sequences required for Agrobacterium-mediated gene transfer into plants. We cloned large genomic DNA fragments of Arabidopsis thaliana into the vector and showed that most of the DNA fragments were maintained stably. Several TAC clones carrying 40- to 80-kb genomic DNA fragments were transferred back into Arabidopsis with high efficiency and shown to be inherited faithfully among the progeny. Furthermore, we demonstrated the practical utility of this vector system for positional cloning in Arabidopsis. A TAC contig was constructed in the region of the SGR1 locus, and individual clones with ca. 80-kb inserts were tested for their ability to complement the gravitropic defects of a homozygous mutant line. Successful complementation enabled the physical location of SGR1 to be delimited with high precision and confidence.

FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains

Distinctive from that of the animal system, the basic plan of the plant body is the continuous formation of a structural unit, composed of a stem with a meristem at the top and lateral organs continuously forming at the meristem. Therefore, mechanisms controlling the formation, maintenance, and development of a meristem will be a key to understanding the body plan of higher plants. Genetic analyses of filamentous flower (fil) mutants have indicated that FIL is required for the maintenance and growth of inflorescence and floral meristems, and of floral organs of Arabidopsis thaliana. FIL encodes a protein carrying a zinc finger and a HMG box-like domain, which is known to work as a transcription regulator. As expected, the FIL protein was shown to have a nuclear location. In situ hybridization clearly demonstrated that FIL is expressed only at the abaxial side of primordia of leaves and floral organs. Transgenic plants, ectopically expressing FIL, formed filament-like leaves with randomly arranged cells at the leaf margin. Our results indicate that cells at the abaxial side of the lateral organs are responsible for the normal development of the organs as well as for maintaining the activity of meristems.

A sequence-ready contig map of the top arm of Arabidopsis thaliana chromosome 3

A fine physical map of the top arm of Arabidopsis thaliana chromosome 3 has been constructed by ordering P1, TAC and BAC clones using the sequences of a variety of DNA markers and end-sequences of clones. The marker sequences used in this study were derived from 58 DNA markers, 93 YAC end-sequences, and 807 end-sequences of P1, TAC and BAC clones. The entire top arm of chromosome 3, except for the centromeric and telomeric regions, was covered by a single contig 13.3 Mb long. This fine physical map will facilitate gene isolation by map-based cloning experiments as well as genome sequencing of the top arm of chromosome 3. The map and end-sequence information are available on the web site KAOS (Kazusa Arabidopsis data Opening Site) at [http://www.kazusa.or.jp/arabi/].

Establishment of framework P1 clones for map-based cloning and genome sequencing: direct RFLP mapping of large clones

Large insert capacity, clone stability and convenient propagation in Escherichia coli have made bacterial artificial chromosome and phage P1 vector-based libraries the first choice for large-scale sequencing projects, and these libraries have also proven useful for chromosome walking. The application of these libraries for either purpose is greatly facilitated by the establishment of a set of framework clones distributed across the genome. Using a P1-based library of Arabidopsis thaliana with genomic inserts of 70-90kb (Liu, Y.-G., Mitsukawa, N., Vazquez-Tello, A., Whittier, R.F., 1995. Generation of a high-quality P1 library of Arabidopsis suitable for chromosome walking. Plant J. 7, 351-358), we have now established such a set of framework clones. To date, such clones have usually been identified by hybridization to smaller, previously mapped clones that detect restriction fragment length polymorphisms (RFLPs). In order to establish framework clones more efficiently, we refined protocols for P1 clone DNA isolation and RFLP detection in order to employ whole P1 clones directly as probes. This strategy enabled a very high rate of RFLP detection, and obviated the need to screen the P1 library with smaller RFLP probes. Altogether 95 clones were mapped providing a framework into which further clones can be integrated by physical overlap.

[Polymorphism of HLA-DQA1,-DQB1 genes in Uygur and Kazak ethnic groups and comprehensive analysis of 25 related populations]

HLA-DQA1 and -DQB1 genes were investigated in two Chinese minor natinalities, Uygur and Kazak using PCR-RFLP genotyping method. Of the 8 DQA1 alleles, DQA1 *0301 was the most common in Uygurs and Kazaks. DQA1 *0401 and *0601 were the rarest alleles in Uygurs and *0601 in Kazaks. Of the 16 DQB1 alleles tested, DQB1 *0201 and *0301 were the most frequent alleles in Uygurs and Kazaks. DQB1 *0502, *05032 and *0504 in Uygurs, *05032, *0504 and *0605 in Kazaks were absent. Neither DQA1 nor DQB1 difference was found between the two populations. From the phylogenetic tree based on the gene frequencies of HLA-DQA1 and -DQB1 in Uygur, Kazak and other 25 related ethnic groups, we suggest that Uygurs and Kazaks have a closer relationship, and they are closer to Mongoloid, not Caucasoid.

Selective induction of apoptosis of NB4 cells from G2+M phase by sodium arsenite at lower doses

Apoptosis of NB4 cells induced by sodium arsenite and arsenate was studied using flow cytometry and DNA gel electrophoresis in order to investigate their effects on cell cycle and determine the relationship between apoptosis and cell cycle. In this study, we found that: 1) at low doses, sodium arsenite selectively induced apoptosis of NB4 cells in G2+M phase of cell cycle after its being arrested in G2 phase. With increment of the cells blocked in G2 phase, dUTP-specifically labeling cells in G2+M phase increased without concomitant increment of dUTP-labeling cells in other two phases of cell cycle; 2) at high doses, extensive apoptosis was induced in NB4 cells from all phases of cell cycle without cell cycle preference and cell cycle blockade; 3) sodium arsenite-induced apoptosis of NB4 cells occurred in the presence of bcl-2 expression as the unapoptotic cells; 4) sodium arsenite with As3+ induced apoptosis of NB4 cells more strongly than sodium arsenate with As5+ did although both of them affected NB4 cells in the same pattern. These results not only suggested that both arsenite and arsenate induced apoptosis of NB4 cells through 2 different mechanisms--at low doses, arsenical might directly induce apoptosis through regulation of cell cycle checkpoint, while at high doses they might directly induce it, but also indicated that bcl-2 might not play an important role in arsenite or arsenate-induced apoptosis of NB4 cells, whereas chemical valence of As in a compound might be related to efficiency in arsenical induction of apoptosis.

A physical map of Arabidopsis thaliana chromosome 3 represented by two contigs of CIC YAC, P1, TAC and BAC clones

We have constructed a physical map of Arabidopsis thaliana chromosome 3 by ordering the clones from CIC YAC, P1, TAC and BAC libraries using the sequences of a variety of genetic and EST markers and terminal sequences of clones. The markers used were 112 DNA markers, 145 YAC end sequences, and 156 end sequences of P1, TAC and BAC clones. The entire genome of chromosome 3, except for the centromeric and telomeric regions, was covered by two large contigs, 13.6 Mb and 9.2 Mb long. This physical map will facilitate map-based cloning experiments as well as genome sequencing of chromosome 3. The map and end sequence information are available on the KAOS (Kazusa Arabidopsis data Opening Site) web site at http://www.kazusa.or.jp/arabi/.

Benign cystic teratoma of unilateral fallopian tube associated with intrauterine pregnancy: a case report

Primary teratomas of the fallopian tube are extremely uncommon. To date, only about 50 cases have been reported in the literature. Six of them are reported to have been in conjunction with tubal ectopic pregnancies. Herein we present the first case of benign cystic teratoma of the unilateral fallopian tube associated with an intrauterine term pregnancy, reported in Taiwan.

Differential effects of aneugens and clastogens on incidences of multinucleated cells and of micronucleate cells in Chinese hamster lung (V79) cell line in vitro

Two aneugens, vinblastine (0.025-0.4 microgram/ml) and colchicine (0.05-0.4 microgram/ml), and two clastogens, mitomycin C (0.05-0.4 microgram/ml) and cyclophosphamide (1-16 micrograms/ml) were applied respectively to the micronucleus test in Chinese hamster lung (V79) cells in vitro, and the frequency of multinucleated cells (Fmu) and that of micronucleate cells (Fmi) in each group were observed. The results showed that at relatively high concentrations, all four agents increased both Fmu and Fmi, but the ratios of Fmu to Fmi in groups of the two aneugens (average of 2.2, 2.8, respectively) were much (10-30 folds) higher than that in groups of the two clastogens (0.09, 0.20). The difference between aneugens and clastogens in the above ratio was much more remarkable than that in areas of micronuclei (only 1.6-2.5 folds for the latter). At relatively low concentrations, the two clastogens increased only Fmi (but not Fmu), while the two aneugens increased only Fmu (but not Fmi). This indicates that the induction of multinuclei by aneugens may be more sensitive than by clastogens, and the induction of micronuclei by clastogens may be more sensitive than by aneugens. So, it is possible for the ratio of Fmu to Fmi to become a simple and sensitive (though indirect) index for distinguishing aneugens from clastogens. Further studies with other mutagens and (or) other cell types will be needed to confirm the deduction. As no difference in frequency of polyploid cells was observed between control group and each treatment, the multinucleation does not seem related to endoreduplication of chromosomes.

A fine physical map of Arabidopsis thaliana chromosome 5: construction of a sequence-ready contig map

A fine physical map of Arabidopsis thaliana chromosome 5 was constructed by ordering the clones from YAC, P1, TAC and BAC libraries of the genome using the sequences of a variety of genetic and EST markers and terminal sequences of clones. The markers used were 88 genetic markers, 13 EST markers, 87 YAC end probes, 100 YAC subclone end probes, and 390 end probes of P1, TAC and BAC clones. The entire genome of chromosome 5, except for the centromeric and telomeric regions, was covered by two large contigs 11.6 Mb and 14.2 Mb long separated by the centromeric region. The minimum tiling path of the chromosome was constituted by a total of 430 P1, TAC and BAC clones. The map information is available at the Web site http://www.kazusa.or.jp/arabi/.

Targeted damage effects of high intensity focused ultrasound (HIFU) on liver tissues of Guizhou Province miniswine

HIFU can pass through tissues and accurately damage target tissues inside organisms. This article reports on the oriented damage effects of HIFU upon miniswine internal and external liver tissues, and suggests a new conception of the 'biological focal field'. The results revealed that: (1) HIFU can be used to damage accurately liver tissues under the guide of a B-modal ultrasound device; (2) the scope of the injury is connected with sound intensity and irradiation time; and (3) the different layers of tissue through which the ultrasound has passed remain undamaged.

Characterization and mapping of Ds-GUS-T-DNA lines for targeted insertional mutagenesis

The transposition patterns of the Ds-GUS transposon T-DNA in 23 independent single-copy lines have been characterized and the map positions of 10 of them on three of the five Arabidopsis chromosomes are reported. Using overexpressed Activator (Ac) elements as a transposase source, it was found that the primary determinant of transposition frequency is the insertion site of the Ac-T-DNA. Neither the structure of the transposon T-DNA nor, in most cases, its insertion site have a significant effect on transposition frequency. Both the frequency and timing of transposition are influenced by the parent through which the transposon and transposase T-DNAs are transmitted. Overall, nearly 75% of plants in which excision has occurred bear a reinserted element and very short-range transpositions predominate, underlining the advantage of using mapped transposons for insertional mutagenesis.

Isolation and mapping of a new set of 129 RFLP markers in Arabidopsis thaliana using recombinant inbred lines

A new collection of 129 Arabidopsis thaliana RFLP markers has been established based upon DNA fragments cloned in the pUC119 plasmid vector and insert end sequences of P1 clones. Dominant/null alleles affecting low-copy number sequences account for nine of the mapped polymorphisms, suggesting that deletions are not rare in A. thaliana. Recombinant inbred (RI) lines were used for mapping these marker loci. RI line-based mapping allows integration of this set of markers with markers previously reported as well as with any markers mapped in the future using this replenishable mapping resource. These markers are useful for map-based gene isolation and genome physical mapping in A. thaliana as well as studies of chromosome colinearity (synteny) with related species.

Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR

Thermal asymmetric interlaced (TAIL-) PCR is an efficient technique for amplifying insert ends from yeast artificial chromosome (YAC) and P1 clones. Highly specific amplification is achieved without resort to complex manipulations before or after PCR. The adaptation of this method for recovery and mapping of genomic sequences flanking T-DNA insertions in Arabidopsis thaliana is described. Insertion-specific products were amplified from 183 of 190 tested T-DNA insertion lines. Reconstruction experiments indicate that the technique can recover single-copy sequences from genomes as complex as common wheat (1.5 x 10(10) bp). RFLPs were screened using 122 unique flanking sequence probes, and the insertion sites of 26 T-DNA transgenic lines were determined on an RFLP map. These lines, whose mapped T-DNA insertions confer hygromycin resistance, can be used for fine-scale mapping of linked phenotypic loci.

Study of gastric and gallbladder kinetics with real-time ultrasonography in cases of functional dyspepsia

Gastric and gallbladder emptying in 113 patients with functional dyspepsia (FD) were evaluated by real-time ultrasonography (RUS) after a liquid-fat meal by the patients, and compared with 15 healthy volunteers. The results showed that in FD group 69 patients (61.06%) had delayed gastric emptying, and 28 patients (24.77%) had gallbladder hypokinesia. Among them both delayed gastric emptying and gallbladder hypokinesia were found in 11 patients (9.7%), 44 patients (38.93%) had normal gastric emptying and 85 patients (75.22%) had normal gallbladder emptying.

Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking

Isolation of DNA segments adjacent to known sequences is a tedious task in genome-related research. We have developed an efficient PCR strategy that overcomes the shortcomings of existing methods and can be automated. This strategy, thermal asymmetric interlaced (TAIL)-PCR, utilizes nested sequence-specific primers together with a shorter arbitrary degenerate primer so that the relative amplification efficiencies of specific and nonspecific products can be thermally controlled. One low-stringency PCR cycle is carried out to create annealing site(s) adapted for the arbitrary primer within the unknown target sequence bordering the known segment. This sequence is then preferentially and geometrically amplified over nontarget ones by interspersion of high-stringency PCR cycles with reduced-stringency PCR cycles. We have exploited the efficiency of this method to expedite amplification and sequencing of insert end segments from P1 and YAC clones for chromosome walking. In this study we present protocols that are amenable to automation of amplification and sequencing of insert end sequences directly from cells of P1 and YAC clones.

Wheat phylogeny determined by RFLP analysis of nuclear DNA. 2. Wild tetraploid wheats

Intra- and inter-specific variations in the nuclear DNA of Triticum dicoccoides Körn. (2n = 28, genome constitution AABB) and T. araraticum Jakubz. (2n = 28, AAGG), wild species, respectively, of the Emmer and Timopheevi group, were studied by restriction fragment length polymorphism (RFLP) analysis. Total DNAs of 32 T. dicoccoides and 24 T. araraticum accessions, collected from throughout the distribution areas of these species, were treated with two 6-bp cutters and hybridized with 30 nuclear DNA clones as probes to detect RFLPs. A total of 167 hybrid bands were observed per accession. All the enzyme-probe combinations showed RFLPs between accessions. The average genetic distance between the T. dicoccoides accessions was 0.0135 ± 0.0031 and that between the T. araraticum accessions 0.0036 ± 0.0015, indicative of about a four-fold intraspecific variation in T. dicoccoides as compared to T. araraticum in terms of genetic distance. No significant genetic differentiation was found for the geographical populations of these species, the genetic distance between the two species being 0.0482 ± 0.0022. The interspecific divergence corrected for intraspecific divergence was 0.0395, about three times that for T. dicoccoides and 11 times that for T. araraticum. The results show that in the wild state the Emmer and Timopheevi groups are clearly differentiated and that T. dicoccoides has much greater variation than T. araraticum, suggesting a relatively recent origin for the latter and therefore a diphyletic origin for these species.

Rapid preparation of megabase plant DNA from nuclei in agarose plugs and microbeads

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Toxicity and toxicokinetics of MeISP in isolated rat hepatocytes

Toxicity and toxicokinetics of a new organophosphorus insecticide, MeISP, in isolated rat hepatocytes were studied. It was found that at the final concentration of 1.5 mmol/L, MeISP can (1) result in an increase of leakage of intracellular enzymes, alanine amino-transferase (ALT), lactate dehydrogenase (LDH), beta-glucuronidase (beta-GDase) and acid phosphatase (AcP) to the medium in a dose-dependent fashion; (2) give rise to obvious plasma membrane blebbing; (3) rapidly deplete the intracellular GSH and (4) almost completely inhibit the protein synthesis and gluconeogenesis from sodium pyruvate. The kinetics study showed that at the final concentration of 15 mumol/L, MeISP is rapidly metabolized and this process fits the one-compartment model. The metabolism of MeISP in the hepatocytes with phenobarbital-induced microsomal enzymes is accelerated. These results indicate that (1) MeISP has obvious toxicity to isolated rat hepatocytes and isolated hepatocytes provide a suitable system to examine the toxic effects of xenobiotics at the cellular level and (2) MeISP is metabolized mainly by microsomal enzymes.

[Clinical study of erythromycin action on gallbladder motility in patients with non-ulcer dyspepsia]

Thirty-two patients of non-ulcer dyspepsia (NUD) with gallbladder hypokinesia treated by oral erythromycin administration 0.125g three times daily for two weeks. Before and after oral erythromycin administration, gallbladder volumes were determined by ultrasound, and plasma motilin concentration were determined by radioimmunoassay. The results showed that before and after oral erythromycin administration, maximal percentage emptying of gallbladder were 48.24 +/- 8.30ml vs 69.74 +/- 10.78ml (P < 0.01), plasma motilin were 361.28 +/- 87.92ng/L vs 394.97 +/- 134.27ng/L (P > 0.05). It is indicated that erythromycin could reduce fasting and postprandial residual gallbladder volumes and increases maximal percentage emptying of gallbladder. It suggests that erythromycin might have an agonist action on the motilin receptor as an agonist action on the motilin receptor as an exogenously administrated motilin.

[Histochemical and ultrastructural study of myotonic dystrophy]

The pathological, histochemical and ultrastructural changes in the muscular biopsies from 9 patients with myotonic dystrophy were investigated. The major changes observed under light microscopy were degeneration of muscle fibers, increased number of nuclei, tendency of central nuclei to form chains, subsarcolemmal masses of cytoplasm and circularly arranged fibrils. The myosin ATPase and NADH-TR stain demonstrated histochemical selectivity of type I fiber atrophy in 7 of the 9 cases studied. The outstanding ultrastructural changes were extensive small disruptions of plasma membrane, destructions of Z bands and myofilaments, swelling of mitochondria, dilatational sarcoplasmic reticulum and regeneration of muscle fibers. Genetic fault of the surface membrane is a possible cause that leads to enzyme metabolic disorder, mitochondrial calcium overload, increased calcium content in sarcoplasm, resulting finally in mitochondrial metabolic disorder, myofilament destruction and muscle fiber necrosis.

[The effects of rapid entry into plateau on SODs and LPO levels in rats]

The activities of CuZn-SOD and Mn-SOD in rat plasma and liver dropped (P < 0.05 and P < 0.01, respectively) but LPO levels increased significantly (P < 0.01) after the rats were got into plateau from plain rapidly. The decrease of the activities of SODs was associated with the rise of LPO levels. The results suggested that the formation of free radicals in the body increased and the antioxidant ability lowered after their rapid entry into plateau from plain, and it was unfavourable to their acclimatization to plateau.

Rapid sequencing of unpurified PCR products by thermal asymmetric PCR cycle sequencing using unlabeled sequencing primers

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