Green revolution: a mutant gibberellin-synthesis gene in rice

The chronic food shortage that was feared after the rapid expansion of the world population in the 1960s was averted largely by the development of a high-yielding semi-dwarf variety of rice known as IR8, the so-called rice 'green revolution'. The short stature of IR8 is due to a mutation in the plant's sd1 gene, and here we identify this gene as encoding an oxidase enzyme involved in the biosynthesis of gibberellin, a plant growth hormone. Gibberellin is also implicated in green-revolution varieties of wheat, but the reduced height of those crops is conferred by defects in the hormone's signalling pathway.

Evidence for insulating behavior in the electric conduction of (NH(3))K(3)C(60) systems

Microwave study using the cavity perturbation technique revealed that the conductivity of the antiferromagnet (NH(3))K(3-x)Rb(x)C(60) at 200 K is already 3-4 orders of magnitude smaller than those of superconductors, K(3)C(60) and (NH(3))(x)NaRb(2)C(60), and that the antiferromagnetic compounds are insulators below 250 K without metal-insulator transitions. The striking difference in the magnitude of the conductivity between these materials strongly suggests that the Mott-Hubbard transition in the ammoniated alkali fullerides is driven by a reduction of lattice symmetry from face-centered-cubic to face-centered-orthorhombic, rather than by the magnetic ordering.

A gene network inference method from continuous-value gene expression data of wild-type and mutants

In this paper we introduce a new inference method of a gene regulatory network from steady-state gene expression data. Our method determines a regulatory structure consistent with an observed set of steady-state expression profiles, each generated from wild-type and single deletion mutant of the target network. Our method derives the regulatory relationships in the network using a graph theoretic approach. The advantage of our method is to be able to deal with continuous values of steady-state data, while most of the methods proposed in past use a Boolean network model with binary data. Performance of our method is evaluated on simulated networks with varying the size of networks, indegree of each gene, and the data characteristics (continuous-value/binary), and is compared with that of predictor method proposed by Ideker et al. As a result, we show the superiority of using continuous values to binary values, and the performance of our method is much better than that of the predictor method.

The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology

Researchers in computational biology today make use of a large number of different software packages for modeling, analysis, and data manipulation and visualization. In this paper, we describe the ERATO Systems Biology Workbench (SBW), a software framework that allows these heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' data and algorithmic capabilities. Our goal is to create a simple, open-source software infrastructure which is effective, easy to implement and easy to understand. SBW uses a broker-based architecture and enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol. The interfaces to the system are encapsulated in client-side libraries that we provide for different programming languages. We describe the SBW architecture and the current set of modules, as well as alternative implementation technologies.

Endoscopic thyroid resection using cutaneous elevation in lieu of insufflation

BACKGROUND

Laparoscopic surgery to resect cervical masses has gained increasing acceptance during the past decade. This report describes the authors' technique and experience using total video endoscopic surgery to resect thyroid masses.

METHODS

The video camera is introduced through a 12-mm trocar inserted via a 10-mm infraclavicular incision in the sternal line. This incision will be hidden by the patient's undergarments postoperatively. An incision for a 12-mm trocar is made in each axilla, with additional incisions in the anterior chest made as necessary for the endoscope and instruments. Excellent exposure is produced by elevating the skin with hooks rather than by using carbon dioxide insufflation. This method reduces the incidence of subcutaneous emphysema and pneumomediastinum.

RESULTS

Twenty-two thyroid lesions were resected using total video endoscopic surgery (adenoma, 13; cancer, 5; benign cyst, 3; and Graves' disease, 1). Procedures included thyroidectomy (12), thyroidectomy and isthmusectomy (4), and subtotal thyroidectomy (2). Subtotal cervical adenectomy was performed in 3 patients with papillary carcinoma. Cosmetic results were excellent.

CONCLUSION

Endoscopic surgery of the neck is safe, minimally invasive, and produces excellent cosmetic results. However, it is in an early stage of development. Techniques have yet to be standardized, and specialized instruments are not available. The field is likely to mature as surgeons gain more experience.

Cortical and subcortical vestibular response to caloric stimulation detected by functional magnetic resonance imaging

The posterior insula, central sulcus, and inferior parietal lobule including the intraparietal sulcus have been considered the vestibular cortex based on functional brain mapping in humans as well as experiments in lower primates. The same regions receive optokinetic, visual, and proprioceptive projections. We examined the cortical and subcortical projection of vestibular activity with visual and proprioceptive input eliminated during caloric stimulation (CS), using functional magnetic resonance imaging (fMRI). Single-shot gradient-echo echoplanar image (EPI) volumes were sensitive to BOLD contrast in oblique orientation. We adopted a pharmacokinetic model for analysis of imaging data from 10 subjects as a group. The insular gyrus, intraparietal sulcus, superior temporal gyrus, hippocampus, cingulate gyrus, and thalamus showed activation by CS. Cortical and subcortical activation during CS in the present study was observed within regions less precisely delineated by other methods. As intraparietal sulcus activation showed right hemispheric dominance, this region may have an oculomotor projection as well as the vestibular input.

Cyst fluid levels of carcinoembryonic antigen, carbohydrate antigen 19-9, squamous cell carcinoma antigen, and amylase in thyroglossal duct and branchial cleft cysts

Cyst fluid was aspirated from five thyroglossal duct cysts (TDCs) and four branchial cleft cysts (BCCs). The cyst fluid levels of carcinoembryonic antigen (CEA), carbohydrate antigen (CA) 19-9, squamous cell carcinoma antigen (SCC), and amylase were measured and compared between the two types of cyst. The enzyme immunoassay technique was used for CEA and CA19-9, while SCC and amylase levels were measured by the immunoradiometric assay and nitrophenol method, respectively. Immunostaining for CEA, CA19-9, and amylase was also performed. The serum levels of these markers in both groups of patients were within the normal ranges. In contrast, their cyst fluid levels were extremely high. There was no significant difference in the cyst fluid levels of CEA and SCC between the two types of cyst; however, the cyst fluid from the TDCs showed significantly higher levels of CA19-9 and significantly lower levels of amylase compared with that from the BCCs. Immunostaining revealed expression of CA 19-9 in nearly half the columnar epithelial cells in the TDCs, but not in the squamous epithelial cells in the BCCs. CEA and amylase were not found in the epithelial cells of either type of cyst. These findings seem to reflect the difference in etiology between TDCs and BCCs.

[Two cases of effective weekly paclitaxel administration for metastatic breast cancer]

We report two cases of effective weekly paclitaxel (TXL) administration for metastatic breast cancer. TXL (80 mg/m2) was infused over 1 hour after short premedication on an outpatient basis. Administration was continued for 3 weeks followed by 1 week rest. Case 1: A 66-year-old woman was treated with adriamycin, cyclophosphamide, doxifluridine (5'-DFUR), fadrozole, medroxyprogesterone acetate (MPA) and pamidronate for pleural, mediastinal and supraclavicular lymph nodes and skull metastases. She complained of hoarseness and supraclavicular and mediastinal lymph nodes had developed, for which she received weekly TXL administration. Metastatic lymph nodes had disappeared 3 months after administration. Case 2: A 61-year-old woman was treated with CMF therapy, 5'-DFUR, tamoxifen, MPA fadrozole and pamidronate for bone metastasis and local recurrence. She received weekly TXL administration for an axillary recurrence and contralateral supraclavicular lymph node metastases. Metastatic and recurrent lesions had disappeared 3 months after administration. The toxic events were leukopenia (grade 1) and peripheral neuropathy (grade 1). No major adverse effects were observed in either case.

Performance assessment of O-18 water purifier

In the synthesis of 18F-FDG by the nucleophilic substitution method, 18O-H2O is usually used as target water. The target water should be recovered after synthesis and reused, because it is expensive, but recovered water contains impurities such as organic substances, and it must be purified before reuse. For this reason Sumitomo Heavy Industries, Ltd. developed an O-18 water purifier for elimination of organic substances in recovered water. This instrument consists of a UV irradiation unit and low-temperature distillation unit. Our institution had an opportunity to test use this instrument and evaluated its performance. The concentrations of organic substances after UV irradiation was greatly reduced, and recovery efficiency after distillation by the low-temperature distillation unit was very satisfactory at 99.3 +/- 0.5%. Furthermore, the yield of 18F-FDG from 18O-H20 purified with this instrument was sufficient for the clinical use.

Clinical outcome of laryngotracheal separation for intractable aspiration pneumonia

OBJECTIVES

To confirm that laryngotracheal separation (LTS) is a satisfactory treatment for patients with intractable aspiration pneumonia, even though it does not require tracheoesophageal anastomosis.

STUDY DESIGN

Retrospective.

METHODS

Nine patients with intractable aspiration pneumonia underwent LTS at our institution from 1996 to 1999. Two patients underwent postoperative barium swallow radiography.

RESULTS

Neither halitosis nor stimulation of the cough reflex occurred due to pooled secretions in the blind pouch of the proximal tracheal segment. Barium swallow radiography confirmed that the secretions drained within 40 min by swallowing or a change in patient position.

CONCLUSION

LTS is a satisfactory solution to the problem of chronic aspiration. Neither pooled secretions in the proximal tracheal segment nor fistula formation were significant postoperative problems.

Neuronal expression of mint1 and mint2, novel multimodular proteins, in adult murine brain

Mints are multimodular adapter proteins in functioning membrane transport and organization. Mint1 and mint2 are neuron-specific. We localized these isoforms in mouse brain. By in situ hybridization, mRNA encoding mint1 or mint2 was expressed in neurons throughout the brain. Mint1 mRNA expression was greatest in the limbic system including cingulate cortex, hippocampus, anterior thalamic nuclei, medial habenular nucleus, and mammillary body. Mint2 mRNA was rich in cerebral cortex, entorhinal cortex, and hippocampus, but less prominent in other limbic structures. Mint1 mRNA and mint2 mRNA were distributed among hippocampal pyramidal neurons, while mint2 mRNA was especially abundant in CA3. Mint1, but not Mint2 mRNA was abundant in the substantia nigra pars compacta. Immunohistochemistry visualized mint proteins in axon terminals and neuronal somata, generally following mRNA distribution. In the hippocampus, mint1 was rich in the entorhinal projections and mossy fibers of the dentate gyrus, while mint2 was rich in commisural fibers from the contralateral hippocampus and in CA1. Mint1 intensely stained catecholamine-containing neurons such as the substantia nigra pars compacta, ventral tegmental area, and locus ceruleus. Mint2 protein was ubiquitous in these regions. Mint1 and mint2 distribution also differed elsewhere in the brainstem and in the cerebellum. Central nervous system neurons, then, predominantly express either mint1 or mint2. Mints may be involved in synaptic vesicle transport toward the active zone, also participating in transport of certain membrane proteins toward the postsynaptic density. Mint1 and mint2 may divide roles either regionally or depending on neuronal functional characteristics.

Cloning and functional analysis of two gibberellin 3 beta -hydroxylase genes that are differently expressed during the growth of rice

We have cloned two gibberellin (GA) 3 beta-hydroxylase genes, OsGA3ox1 and OsGA3ox2, from rice by screening a genomic library with a DNA fragment obtained by PCR using degenerate primers. We have used full-scan GC-MS and Kovats retention indices to show function for the two encoded recombinant fusion proteins. Both proteins show 3 beta-hydroxylase activity for the steps GA(20) to GA(1), GA(5) to GA(3), GA(44) to GA(38), and GA(9) to GA(4). In addition, indirect evidence suggests that the OsGA3ox1 protein also has 2,3-desaturase activity, which catalyzes the steps GA(9) to 2,3-dehydro-GA(9) and GA(20) to GA(5) (2,3-dehydro GA(20)), and 2 beta-hydroxylase activity, which catalyzes the steps GA(1) to GA(8) and GA(4) to GA(34). Molecular and linkage analysis maps the OsGA3ox1 gene to the distal end of the short arm of chromosome 5; the OsGA3ox2 gene maps to the distal end of the short arm of chromosome 1 that corresponds to the D18 locus. The association of the OsGA3ox2 gene with the d18 locus is confirmed by sequence and complementation analysis of three d18 alleles. Complementation of the d18-AD allele with the OxGA3ox2 gene results in transgenic plants with a normal phenotype. Although both genes show transient expression, the highest level for OsGA3ox1 is from unopened flower. The highest level for OsGA3ox2 is from elongating leaves.

Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm

A mechanism for generating circadian rhythms has been of major interest in recent years. After the discovery of per and tim, a model with a simple feedback loop involving per and tim has been proposed. However, it is recognized that the simple feedback model cannot account for phenotypes generated by various mutants. A recent report by Glossop, Lyons & Hardin [Science286, 766 (1999)] on Drosophila suggests involvement of another feedback loop by dClk that is interlocked with per-tim feedback loop. In order to examine whether interlocked feedback loops can be a basic mechanism for circadian rhythms, a mathematical model was created and examined. Through extensive simulation and mathematical analysis, it was revealed that the interlocked feedback model accounts for the observations that are not explained by the simple feedback model. Moreover, the interlocked feedback model has robust properties in oscillations.

slender rice, a constitutive gibberellin response mutant, is caused by a null mutation of the SLR1 gene, an ortholog of the height-regulating gene GAI/RGA/RHT/D8

The rice slender mutant (slr1-1) is caused by a single recessive mutation and results in a constitutive gibberellin (GA) response phenotype. The mutant elongates as if saturated with GAs. In this mutant, (1) elongation was unaffected by an inhibitor of GA biosynthesis, (2) GA-inducible alpha-amylase was produced by the aleurone layers without gibberellic acid application, and (3) endogenous GA content was lower than in the wild-type plant. These results indicate that the product of the SLR1 gene is an intermediate of the GA signal transduction pathway. SLR1 maps to OsGAI in rice and has significant homology with height-regulating genes, such as RHT-1Da in wheat, D8 in maize, and GAI and RGA in Arabidopsis. The GAI gene family is likely to encode transcriptional factors belonging to the GRAS gene superfamily. DNA sequence analysis revealed that the slr1-1 mutation is a single basepair deletion of the nuclear localization signal domain, resulting in a frameshift mutation that abolishes protein production. Furthermore, introduction of a 6-kb genomic DNA fragment containing the wild-type SLR1 gene into the slr1-1 mutant restored GA sensitivity to normal. These results indicate that the slr1-1 mutant is caused by a loss-of-function mutation of the SLR1 gene, which is an ortholog of GAI, RGA, RHT, and D8. We also succeeded in producing GA-insensitive dwarf rice by transforming wild-type rice with a modified SLR1 gene construct that has a 17-amino acid deletion affecting the DELLA region. Thus, we demonstrate opposite GA response phenotypes depending on the type of mutations in SLR1.

Non-optically probing near-field microscopy with illumination of total internal reflection

We have developed a non-optically probing near-field microscope with illumination of total internal reflection. Because the illumination light does not pass through the specimens, it is possible to observe thick specimens or highly absorptive materials. It reduces the background noise because the decay length of the evanescent wave is a few hundred nanometres. We found that although in the total internal reflection illumination system the light passed through the photosensitive film and illuminated the specimen, it did not affect the photosensitive film severely and did not limit the resolution. The imaging properties of reflection illumination and transmission illumination are analysed using a finite-differential time domain method.

Endotoxin clearance and its relation to hepatic and renal disturbances in rats with liver cirrhosis

BACKGROUND/AIMS

Little is known about endotoxin clearance and secretion of cytokines from macrophages in liver cirrhosis. The aims of this study were to investigate the relationship of endotoxin clearance and release of tumor necrosis factor alpha by various macrophages to hepatic and renal disturbances in liver cirrhosis.

METHODS

Male Sprague-Dawley rats were given 0.04% thioacetamide orally for 6 or 12 months. The organ distribution of infused [3H]-endotoxin (10 microg/kg b.w.) was analyzed at 30 min or at 24 h. Uptake of [3H]-endotoxin and secretion of tumor necrosis factor alpha by Kupffer cells, splenic macrophages and peripheral blood monocytes (1 x 10(4) cells/ml) from cirrhotic and control rats were determined.

RESULTS

In cirrhotic rats, more endotoxin was left in the body and more endotoxin accumulated in the spleen and kidney, and thus was related to elevation of serum total bilirubin, aspartate aminotransferase, alanine aminotransferase, blood urea nitrogen, creatinine and tumor necrosis factor alpha. Endotoxin uptake and tumor necrosis factor alpha release by the Kupffer cells were decreased and those by the splenic macrophages and peripheral blood monocytes were increased in cirrhotic rats.

CONCLUSIONS

In liver cirrhosis, impaired clearance of endotoxin together with increased secretion of tumor necrosis factor alpha by extrahepatic macrophages may play an important role in the progression of hepatic and renal disturbances.

Recognition of novel lipopolypeptides with many pendent sugar residues by lectin

A lipid-polypeptide conjugate (lipo-polypeptide) was obtained by the ring-opening polycondensation of N-epsilon-Z-L-lysine N-carboxyanhydride (NCA) using 3-aminopropyl dioctadecylamine as initiator and subsequent deprotection. Maltose lactone was coupled with the lipo-polypeptide to give novel amphiphiles which carried many maltoamide residues as pendent groups. The sugar group-carrying amphiphiles incorporated in phospholipid liposomes were recognized by a lectin from Canavalia ensiformis (Con A), which was proven by the increase in turbidity of the liposome suspension after mixing with the lectin. The recognition was largely affected by the degree of polymerization of lysine residues and the surface density of the amphiphile in the liposomes. The association constant (K(ass)) of Con A with maltoamide residues on the liposome was much larger than those for small molecular weight sugars due to the "cluster effect".

Endoscopic surgery for lateral cervical cysts. A report of three cases

Recently, endoscopic surgery has been applied to cervical exploration. We have developed new techniques for endoscopic neck surgery, and in this paper report our experience with three patients with lateral cervical cysts. A 5- or 10-mm midline trocar for the endoscope and two 5- or 10-mm lateral trocars were inserted from the anterior chest wall and/or both axillary fossae to avoid neck scars. There were no intraoperative complications. Slight subcutaneus emphysema was present postoperatively, but it was limited to the neck and disappeared in a few days. The incisions were completely covered by the patients' undergarments. This is the first report of endoscopic lateral cervical cystectomy.

Shoot organization genes regulate shoot apical meristem organization and the pattern of leaf primordium initiation in rice

The mechanism regulating the pattern of leaf initiation was analyzed by using shoot organization (sho) mutants derived from three loci (SHO1, SHO2, and SHO3). In the early vegetative phase, sho mutants show an increased rate of leaf production with random phyllotaxy. The resulting leaves are malformed, threadlike, or short and narrow. Their shoot apical meristems are relatively low and wide, that is, flat shaped, although their shape and size are highly variable among plants of the same genotype. Statistical analysis reveals that the shape of the shoot meristem rather than its size is closely correlated with the variations of plastochron and phyllotaxy. Rapid and random leaf production in sho mutants is correlated with the frequent and disorganized cell divisions in the shoot meristem and with a reduction of expression domain of a rice homeobox gene, OSH1. These changes in the organization and behavior of the shoot apical meristems suggest that sho mutants have fewer indeterminate cells and more determinate cells than wild type, with many cells acting as leaf founder cells. Thus, the SHO genes have an important role in maintaining the proper organization of the shoot apical meristem, which is essential for the normal initiation pattern of leaf primordia.

Direct observation of the washboard noise of a driven vortex lattice in a high-temperature superconductor, Bi2Sr2CaCu2O(y)

We studied the conduction noise spectrum in the vortex state of a high-temperature superconductor, Bi(2)Sr(2)CaCu(2)O(y), subject to a uniform driving force. Two characteristic features, a broad-band noise (BBN) and a narrow-band noise (NBN), were observed in the vortex-solid phase. The origin of the large BBN was determined to be plastic motion of the vortices, whereas the NBN was found to originate from the washboard modulation of the translational velocity of the driven vortices. We believe this to be the first observation of washboard noise of dc driven vortices in any superconductor.

Rice dwarf mutant d1, which is defective in the alpha subunit of the heterotrimeric G protein, affects gibberellin signal transduction

Previously, we reported that the rice dwarf mutant, d1, is defective in the alpha subunit of the heterotrimeric G protein (Galpha). In the present study, gibberellin (GA) signaling in d1 and the role of the Galpha protein in the GA-signaling pathway were investigated. Compared with the wild type, GA induction of alpha-amylase activity in aleurone cells of d1 was greatly reduced. Relative to the wild type, the GA(3)-treated aleurone layer of d1 had lower expression of Ramy1A, which encodes alpha-amylase, and OsGAMYB, which encodes a GA-inducible transcriptional factor, and no increase in expression of Ca(2 +)-ATPase. However, in the presence of high GA concentrations, alpha-amylase induction occurred even in d1. The GA sensitivity of second leaf sheath elongation in d1 was similar to that of the wild type in terms of dose responsiveness, but the response of internode elongation to GA was much lower in d1. Furthermore, Os20ox expression was up-regulated, and the GA content was elevated in the stunted internodes of d1. All these results suggest that d1 affects a part of the GA-signaling pathway, namely the induction of alpha-amylase in the aleurone layer and internode elongation. In addition, a double mutant between d1 and another GA-signaling mutant, slr, revealed that SLR is epistatic to the D1, supporting that the Galpha protein is involved in GA signaling. However, the data also provide evidence for the presence of an alternative GA-signaling pathway that does not involve the Galpha protein. It is proposed that GA signaling via the Galpha protein may be more sensitive than that of the alternative pathway, as indicated by the low GA responsiveness of this Galpha-independent pathway.

Endoscopic surgery for a parathyroid functioning adenoma resection with the neck region-lifting method

Recently, endoscopic surgery has been applied to cervical exploration. We have developed new techniques for endoscopic neck surgery. We reported on a 53-year-old Japanese man with functioning parathyroid adenoma resected by endoscopic surgery with a neck region-lifting method. A 10-mm midline trocar for the endoscope and two 5-mm lateral trocars were inserted from the anterior chest wall to avoid neck scars. There were no intraoperative complications. The incisions were completely covered by the patient's undergarments.