A 300 kilobase interval genetic map of rice including 883 expressed sequences.

We have constructed a high resolution rice genetic map containing 1,383 DNA markers at an average interval of 300 kilobases (kb). The markers, distributed along 1,575 cM on 12 linkage groups, comprise 883 cDNAs, 265 genomic DNAs, 147 randomly amplified polymorphic DNAs (RAPD) and 88 other DNAs. cDNAs were derived from rice root and callus, analysed by single-run sequencing and searched for similarities with known proteins. Nearly 260 rice genes are newly identified and mapped, and genomic DNA and cloned RAPD fragments were also sequenced to generate STSs. Our map is the first significant gene expression map in plants. It is also the densest genetic map available in plants and the first to be backed up comprehensively by clone sequence data.

Successful Blood Transfusion Management of a Living Donor Liver Transplant Recipient in the Presence of Anti-Jra: A Case Report.

A 48-year-old Japanese woman was diagnosed with Budd-Chiari syndrome and transferred for possible living donor liver transplantation (LDLT). Examinations before LDLT revealed that the recipient had anti-Jra and preformed donor-specific anti-human leukocyte antigen (HLA) antibodies (DSA). Rituximab was administrated at 16 days prior to the patient's scheduled LDLT for the prophylaxis of antibody-mediated rejection by DSA. The clinical significance of anti-Jra has not been clearly established because of the rarity of this antibody, so we discussed blood transfusion strategy with the Department of Blood Transfusion Service and prepared for Jra-negative packed red blood cells (RBCs). Intraoperative blood salvage was used during LDLT procedures to reduce the use of packed RBCs. Although post-transplantation graft function was excellent, a total of 44 U of Jra-negative RBCs were transfused during the entire perioperative period. Because sufficient amounts of Jra-negative packed RBCs were supplied, Jra mismatched blood transfusion was avoided. The patient was discharged from our hospital on postoperative day 102 without clinical evidence of any blood transfusion-related adverse events. Although there are some controversies of blood transfusion related to anti-Jra antibodies, the current strategies of blood transfusion for liver transplantation with anti-Jra are as follows: (1) sufficient supply and transfusion of Jra-negative matched packed RBCs and (2) application of intraoperative blood salvage to reduce the total amount of rare blood type RBCs. These strategies may be changed when the mechanism of anti-Jra alloimmunization is fully understood in the future.

Evaluation of the effects of hydrophilic organic solvents on CYP3A-mediated drug-drug interaction in vitro.

This study evaluated the effects of the commonly used hydrophilic organic solvents, acetonitrile, methanol, ethanol, 1-propanol, dimethyl sulfoxide (DMSO), N,N-dimethylformamide, polyethylene glycol and propylene glycol, on CYP3A in pooled human liver microsomes, using testosterone and midazolam as substrates. Furthermore, we examined the modulation effect of organic solvents on CYP3A inhibition by ketoconazole. Testosterone 6beta-hydroxylation activity was potently inhibited in the presence of DMSO and 1-propanol in a concentration-dependent manner. Midazolam 1'-hydroxylation activity, however, was weakly inhibited only by 1% of DMSO, the highest concentration used in this study. Moreover, the potency of ketoconazole to inhibit CYP3A activities was variable, depending on the organic solvent used as a dissolving solvent for ketoconazole. Our data indicate that each organic solvent had an effect on CYP3A4 activity, evaluated by both substrates with different magnitudes. Furthermore, it was shown that the effects of organic solvents on CYP3A activity are substrate-dependent. The present study also shows that methanol had little effect on either substrate.

Eu-doped CsBr phosphor as a new optically-stimulable phosphor material for medical X-ray imaging sensor.

CsBr phosphor ceramics doped with different luminescence centres such as In2O3, Eu2O3, EuCl3, SmCl3, TbCl3, GdCl3 or NdCl3 as the candidate for a new optically-stimulable phosphor for medical X-ray imaging sensor were prepared using a conventional ceramic fabrication process. It was found that X-ray-irradiated Eu-doped CsBr (CsBr:Eu) exhibited intense optically stimulated luminescence (OSL). The peak wavelength of the OSL emission and stimulation spectra of CsBr:Eu phosphor ceramic sample were 450 and 690 nm, respectively. The dependence of OSL properties on the conditions of preparation of phosphor ceramic samples, such as Eu concentration, sintering temperature and sintering time, were studied. The optimum preparation conditions were also studied. It was found that the OSL intensity of CsBr:Eu phosphor ceramics fabricated under optimum preparation conditions is higher than that of commercially available imaging plates using BaFBr:Eu.

Production of recombinant rat viruses as a method of oncogene isolation in coculture medium.

A simple oncogene isolation was proved using the SD1-T rat embryonic cell line. The SD1-T cell line, which releases endogenous rat leukemia virus, was cocultured with (a) normal rat kidney cells transformed by cloned v-mos DNA, (b) the rat mammary tumor cell line (63SP), or (c) normal rat kidney cells transformed by 63SP DNA. Within 1 mo, oncogenic viruses were recovered from all three coculture supernatants. During this period, increase of oncogenic transcripts was observed in the cocultured cells. The oncogenic viruses appeared to contain the mos gene in cocultures (a) and ras-related sequences in cocultures (b) and (c). The emergence of virus containing mos from mos DNA-mediated normal rat kidney transformants demonstrated "rescue" of the active cellular oncogene by the rat leukemia virus. This coculture system seems to facilitate "rescue" of oncogenes functioning in the tumor and transformed cells.

Altered pharmacokinetics of a novel anticancer drug, UCN-01, caused by specific high affinity binding to alpha1-acid glycoprotein in humans.

The large species difference in the pharmacokinetics/pharmacodynamics of 7-hydroxystaurosporine (UCN-01) can be partially explained by the high affinity binding of UCN-01 to human alpha1-acid glycoprotein (AGP) (Fuse et al, Cancer Res., 58: 3248-3253, 1998). To confirm whether its binding to human AGP actually changes the in vivo pharmacokinetics, we have studied the alteration in its pharmacokinetics after simultaneous administration of human AGP to rats: (a) the protein binding of UCN-01 was evaluated by chasing its dissociation from proteins using dextran-coated charcoal. The UCN-01 remaining 0.1 h after adding dextran-coated charcoal to human plasma or AGP was approximately 80%, although the values for other specimens, except monkey plasma (approximately 20%), were <1%, indicating that the dissociation from human AGP was specifically slower than from other proteins; and (b) the pharmacokinetics of UCN-01 simultaneously administered with human AGP has been determined. The plasma concentrations after i.v. administration of UCN-O1 with equimolar human AGP were much higher than those after administration of UCN-01 alone. The steady-state distribution volume and the systemic clearance were reduced to about 1/100 and 1/200, respectively. Human AGP thus reduced the distribution and elimination of UCN-01 substantially. On the other hand, dog AGP, which has a low binding affinity for UCN-01, did not change the pharmacokinetics of UCN-01 so much. Furthermore, human AGP markedly reduced the hepatic extraction ratio of UCN-01 from 0.510 to 0.0326. Also, human AGP (10 microM) completely inhibited the initial uptake of UCN-01 (1 microM) into isolated rat hepatocytes, whereas the uptake of UCN-01 was unchanged in the presence of human serum albumin (10 microM). In conclusion, the high degree of binding of UCN-01 to human AGP causes a reduction in the distribution and clearance, resulting in high plasma concentrations in humans.

Unpredicted clinical pharmacology of UCN-01 caused by specific binding to human alpha1-acid glycoprotein.

The pharmacokinetics of UCN-01 after administration as a 72- or 3-h infusion to cancer patients in initial Phase I trials displayed distinctive features that could not have been predicted from preclinical data. The distribution volumes (0.0796-0.158 liters/kg) and the systemic clearance (0.0407-0.252 ml/h/kg) were extremely low, in contrast to large distribution volume and rapid systemic clearance in experimental animals. The elimination half-lives (253-1660 h) were unusually long. In vitro protein binding experiments demonstrated that UCN-01 was strongly bound to human alpha1-acid glycoprotein. The results suggest that unusual pharmacokinetics of UCN-01 in humans could be due, at least in part, to its specifically high binding to alpha1-acid glycoprotein.

Changes in Muscle Strength and Six-Minute Walk Distance Before and After Living Donor Liver Transplantation.

BACKGROUND: Impaired exercise capacity and muscle weakness are important characteristics of liver transplantation recipients. Perioperative rehabilitation has been introduced to promote early mobilization of patients and to prevent postoperative pulmonary complications. However, it is unknown how physical status recovers during the hospital stay after a liver transplant. The purpose of this study was to evaluate the changes in clinical indicators that represent the functional exercise capacity and muscle strength before and after living donor liver transplantation (LDLT). METHODS: We retrospectively reviewed 21 consecutive patients who underwent LDLT with perioperative rehabilitation from April 2014 to December 2015. Twelve patients who were tested for 6-minute walk distance, hand-grip strength, and isometric knee extensor muscle strength before and 4 weeks after LDLT were enrolled. RESULTS: At the preoperative baseline, the 6-minute walk distance significantly correlated with the Model for End-stage Liver Disease score and pulmonary functions (vital capacity, forced vital capacity, and forced expiratory volume in 1 second of predictive values). Comparisons between the preoperative and postoperative values revealed significant decreases in weight, Barthel Index, hand-grip strength, and isometric knee extensor muscle strength. Changes in hand-grip strength and isometric knee extensor muscle strength after LDLT correlated with the preoperative Model for End-stage Liver Disease score. CONCLUSIONS: Physical functional status had not been fully recovered 4 weeks after LDLT. Further investigation regarding developing a strategy for prevention of muscle atrophy before LDLT and recovery of physical fitness after LDLT would be helpful.

Expression of novel homeobox genes in early embryogenesis in rice.

We isolated four novel cDNA clones of rice (Oryza sativa L.), which encode predicted proteins with a KN1-like homeodomain. In situ hybridization and RT-PCR analysis with solid cDNA libraries as templates showed that these genes are expressed in distinct patterns during the early stages of rice embryogenesis.

A genome-wide survey of reproductive barriers in an intraspecific hybrid.

Genetic study of the reproductive barriers between related species plays an essential role in understanding the process of speciation. We developed a new method for mapping all possible factors causing deviations from expected Mendelian segregation ratios in F(2) progeny, which substantially contribute to reproductive isolation. A multiresponse nonlinear regression analysis of the allele frequencies of the markers covering an entire genome in the F(2) population was performed to estimate the map position and intensity of the reproductive barriers on each chromosome. In F(2) plants from a cross between a Japonica variety of rice, Nipponbare, and an Indica variety, Kasalath, the deviations of allele frequencies were well explained by 33 reproductive barriers. Of these, 15 reproductive barriers affected the allele transmission rate through the gametophyte and in 9 of these 15 cases, an Indica allele was transmitted at a higher frequency than a Japonica allele. The other 18 reproductive barriers altered the viability of the zygote via its genotype. Two zygotic reproductive barriers showed overdominance and 5 showed underdominance. The most pronounced reproductive barrier, mapped at 62.3 +/- 0.4 cM on chromosome 3, transmitted the Indica allele by 94% through the male gametophyte. The accuracy of the barrier position in the regression analysis was confirmed by progeny analysis. The regression analysis proved to be a powerful tool for detecting and characterizing every reproductive barrier, irrespective of whether it acted on the male or female gametophyte or the zygote.

Detailed comparative mapping of cereal chromosome regions corresponding to the Ph1 locus in wheat.

Detailed physical mapping of markers from rice chromosome 9, and from syntenous (at the genetic level) regions of other cereal genomes, has resulted in rice yeast artificial chromosome (YAC) contigs spanning parts of rice 9. This physical mapping, together with comparative genetic mapping, has demonstrated that synteny has been largely maintained between the genomes of several cereals at the level of contiged YACs. Markers located in one region of rice chromosome 9 encompassed by the YAC contigs have exhibited restriction fragment length polymorphism (RFLP) using deletion lines for the Ph1 locus. This has allowed demarcation of the region of rice chromosome 9 syntenous with the ph1b and ph1c deletions in wheat chromosome 5B. A group of probes located in wheat homoeologous group 5 and barley chromosome 5H, however, have synteny with rice chromosomes other than 9. This suggests that the usefulness of comparative trait analysis and of the rice genome as a tool to facilitate gene isolation will differ from one region to the next, and implies that the rice genome is more ancestral in structure than those of the Triticeae.

Physical mapping of duplicated genomic regions of two chromosome ends in rice.

Two genomic regions duplicated in distal ends of the short arms of chromosomes 11 and 12 in rice (Oryza sativa L.) were characterized by YAC ordering with 46 genetic markers. Physical maps covering most of the duplicated regions were generated. Thirty-five markers, including 21 rice cDNA clones, showed the duplicated loci arrayed strictly in the same order along the two specific genomic regions. Regardless of their different genetic distances, the two duplicated segments may have a similar and minimum physical size with an expected length of about 2.5 Mb. However, differences of RFLP frequency for the duplicated DNA copies and recombination frequency for a given homoeologous area between the two regions were observed, indicating that these changes in genome organization occurred after the duplication. Our results establish a good model system for resolving the relationships between gene duplication, expression of duplicated genes, and the frequency of meiotic recombination in small chromosomal regions.

A high-density rice genetic linkage map with 2275 markers using a single F2 population.

A 2275-marker genetic map of rice (Oryza sativa L.) covering 1521.6 cM in the Kosambi function has been constructed using 186 F2 plants from a single cross between the japonica variety Nipponbare and the indica variety Kasalath. The map provides the most detailed and informative genetic map of any plant. Centromere locations on 12 linkage groups were determined by dosage analysis of secondary and telotrisomics using > 130 DNA markers located on respective chromosome arms. A limited influence on meiotic recombination inhibition by the centromere in the genetic map was discussed. The main sources of the markers in this map were expressed sequence tag (EST) clones from Nipponbare callus, root, and shoot libraries. We mapped 1455 loci using ESTs; 615 of these loci showed significant similarities to known genes, including single-copy genes, family genes, and isozyme genes. The high-resolution genetic map permitted us to characterize meiotic recombinations in the whole genome. Positive interference of meiotic recombination was detected both by the distribution of recombination number per each chromosome and by the distribution of double crossover interval lengths.

Mutations in the v-mos gene abolish its ability to induce differentiation but not transformation.

The v-mos oncogene product has the ability to induce differentiation in human monocytic leukemia U937 cells, thereby arresting cell proliferation, and also exhibits transforming activity in mouse NIH3T3 cells. Mutation in the v-mos gene consisting of one or two amino acid substitutions in the putative ATP-binding domain impaired its differentiation-inducing activity although mutant proteins showed rather higher levels of autophosphorylation in vitro. Macrophage-specific characteristics such as their morphology, expression of C3b receptor and Fc receptor, and production of interleukin-1 beta and tumor necrosis factor alpha, were equally diminished in cells transfected with mutant mos genes when compared to those with intact v-mos. The ability of the gene to arrest the proliferation of U937 cells was likewise diminished, while the transforming efficiency of the intact and mutant mos genes were essentially the same. These results suggest that the mos product functions differently in cell differentiation and transformation.

Cloning and mapping of telomere-associated sequences from rice.

We have isolated three telomere-associated sequences from rice using cassette-ligation-mediated polymerase chain reaction (PCR). Each of the obtained clones hybridized to the terminal of one or several rice chromosome arms. The telomeres recognized by the clones displayed a high level of polymorphism between two rice varieties, Nipponbare (a japonica variety) and Kasalath (an indica variety). Variability in the chromosome termini was also detected among individual F2 progeny plants, which were derived from a cross between the two rice varieties. One clone containing telomere-associated sequences was located to one end of chromosome 5, and another clone to one end of chromosome 11. For another clone, non-allelic segregation of polymorphic hybridization bands was observed between japonica and indica rice; this clone was mapped to one end of chromosome 12 in japonica and to one end of chromosome 11 in indica rice. This indicates an exchange of termini between nonhomologous chromosomes.

Yeast artificial chromosome clones of rice chromosome 2 ordered using DNA markers.

Yeast artificial chromosome (YAC) clones were ordered for the physical mapping of rice chromosome 2, the last of the 12 rice chromosomes to be assigned YACs by the Rice Genome Research Program. A total of 128 restriction fragment length polymorphism markers and 4 sequence-tagged site (STS) markers located on our high-density genetic map were used for YAC clone landing. By colony/Southern hybridization and polymerase chain reaction screening, a total of 239 individual YACs were selected from our YAC library of 6934 clones covering six genome equivalents. The YACs located on the corresponding marker positions in the linkage map formed 43 contigs and islands and were estimated to encompass about 50% of the length of rice chromosome 2.

Construction of YAC contigs on rice chromosome 5.

A physical map of rice chromosome 5 was constructed with yeast artificial chromosome (YAC) clones along a high-resolution molecular linkage map carrying 118 DNA markers distributed over 123.7 cM of genomic DNA. YAC clones have been identified by colony and Southern hybridization for 105 restriction fragment length polymorphism (RFLP) markers and by polymerase chain reaction (PCR) screening for 8 sequence-tagged site (STS) markers and 5 randomly amplified polymorphic DNA (RAPD) markers. Of 458 YACs, 235 individual YACs with an average insert length of 350 kb were selected and ordered on chromosome 5 from the YAC library. Forty-eight contigs covering nearly 21 Mb were formed on the chromosome 5; the longest one was 6 cM and covered 1.5 Mb. The length covered with YAC clones corresponded to 62% of the total length, of chromosome 5. There were many multicopy sequences of expressed genes on chromosome 5. The distribution of many copies of these expressed gene sequences was determined by YAC Southern hybridization and is discussed. A physical map with these characteristics provides a powerful tool for elucidation of genome structure and extraction of useful genetic information in rice.

Ordered YAC clone contigs assigned to rice chromosomes 3 and 11.

Yeast artificial chromosome (YAC) clones were arranged on the positions of restriction fragment length polymorphism (RFLP) and sequence-tagged site (STS) markers already mapped on the high-resolution genetic maps of rice chromosomes 3 and 11. From a total of 416 and 242 YAC clones selected by colony/Southern hybridization and polymerase chain reaction (PCR) analysis, 238 and 135 YAC clones were located on chromosomes 3 and 11, respectively. For chromosomes 3 and 11, 24 YAC contigs and islands with total coverage of about 46% and 12 contigs and islands with coverage of about 40%, respectively, were assigned. Although many DNA fragments of multiple copy marker sequences could not be mapped to their original locations on the genetic map by Southern hybridization because of a lack of RFLP, the physical mapping of YAC clones could often assign specific locations of such multiple copy sequences on the genome. The information provided here on contig formation and similar sequence distribution revealed by ordering YAC clones will help to unravel the genome organization of rice as well as being useful in isolation of genes by map-based cloning.

Physical mapping of rice chromosomes 4 and 7 using YAC clones.

Physical maps of rice chromosomes 4 and 7 were constructed by landing yeast artificial chromosomes (YACs) along our high-density molecular linkage map. Using 114 DNA markers, 258 individual YACs were located on chromosome 4. Sixty-two out of 258 YACs carried two or more DNA marker positions and formed 16 contigs which covered a total length of 17.1 cM. The other YACs were arranged to 23 positions. On chromosome 7, 203 individual YACs were landed on 109 DNA markers. Sixty-four out of 203 YACs formed 15 contigs which covered a total length of 21.8 cM and 139 YACs were localized to 26 positions. Chromosomes 4 and 7 were covered with minimum tiling paths of 45 and 48 YACs, respectively. Taking the average size of YAC insert DNA to be 350 kb and the entire genome size to be 430 Mb, about 16-18 Mb of each chromosome or an estimated 50% of their total lengths have been covered with YACs. Physical maps of these 2 chromosomes should be of great help in identifying useful trait genes and unraveling genetic and biological characteristics in rice.

Physical mapping of rice chromosomes 8 and 9 with YAC clones.

First efforts for physical mapping of rice chromosomes 8 and 9 were carried out by ordering YAC clones of a rice genomic DNA library covering six genome equivalents with mapped DNA markers. A total of 79 and 74 markers from chromosomes 8 and 9, respectively, were analyzed by YAC colony and Southern hybridization using RFLP markers of cDNA and genomic clones, and by polymerase chain reaction (PCR) screening using PCR-derived and sequence-tagged site (STS) markers. As a result, 252 YAC clones were confirmed to contain the mapped DNA fragments on both chromosomes. A contig map was constructed by ordering these YAC clones and about 53% and 43% genome coverage was obtained for chromosomes 8 and 9, respectively, assuming a YAC clone size of 350 kb and overlap between neighboring YACs of 50%. A continuous array of YAC clones with minimum overlap gave a total size of 18.9 Mb for chromosome 8 and 15.6 Mb for chromosome 9, which are close to previous estimates. These contig maps may provide valuable information that can be useful in understanding chromosome structure and isolating specific genes by map-based cloning.