Genome-wide association study of leaf photosynthesis using a high-throughput gas exchange system in rice

Enhancing leaf photosynthetic capacity is essential for improving the yield of rice (Oryza sativa L.). Although the exploitation of natural genetic resources is considered a promising approach to enhance photosynthetic capacity, genomic factors related to the genetic diversity of leaf photosynthetic capacity have yet to be fully elucidated due to the limitation of measurement efficiency. In this study, we aimed to identify novel genomic regions for the net CO2 assimilation rate (A) by combining genome-wide association study (GWAS) and the newly developed rapid closed gas exchange system MIC-100. Using three MIC-100 systems in the field at the vegetative stage, we measured A of 168 temperate japonica rice varieties with six replicates for three years. We found that the modern varieties exhibited higher A than the landraces, while there was no significant relationship between the release year and A among the modern varieties. Our GWAS scan revealed two major peaks located on chromosomes 4 and 8, which were repeatedly detected in the different experiments and in the generalized linear modelling approach. We suggest that high-throughput gas exchange measurements combined with GWAS is a reliable approach for understanding the genetic mechanisms underlying photosynthetic diversities in crop species.

Metabolomic analysis of rice brittle culm mutants reveals each mutant- specific metabolic pattern in each organ

INTRODUCTION

Plant cell walls play an important role in providing physical strength and defence against abiotic stress. Rice brittle culm (bc) mutants are a strength-decreased mutant because of abnormal cell walls, and it has been reported that the causative genes of bc mutants affect cell wall composition. However, the metabolic alterations in each organ of bc mutants have remained unknown.

OBJECTIVES

To evaluate the metabolic changes in rice bc mutants, comparative analysis of the primary metabolites was conducted.

METHODS

The primary metabolites in leaves, internodes, and nodes of rice bc mutants and wild-type control were measured using CE- and LC-MS/MS. Multivariate analyses using metabolomic data was performed.

RESULTS

We found that mutations in each bc mutant had different effects on metabolism. For example, higher oxalate content was observed in bc3 and bc1 bc3 mutants, suggesting that surplus carbon that was not used for cell wall components might be used for oxalate synthesis. In addition, common metabolic alterations such as a decrease of sugar nucleotides in nodes were found in bc1 and Bc6, in which the causative genes are involved in cellulose accumulation.

CONCLUSION

These results suggest that metabolic analysis of the bc mutants could elucidate the functions of causative gene and improve the cell wall components for livestock feed or bioethanol production.

Evolution of rhizobial symbiosis islands through insertion sequence-mediated deletion and duplication

Symbiosis between organisms influences their evolution via adaptive changes in genome architectures. Immunity of soybean carrying the Rj2 allele is triggered by NopP (type III secretion system [T3SS]-dependent effector), encoded by symbiosis island A (SymA) in B. diazoefficiens USDA122. This immunity was overcome by many mutants with large SymA deletions that encompassed T3SS (rhc) and N2 fixation (nif) genes and were bounded by insertion sequence (IS) copies in direct orientation, indicating homologous recombination between ISs. Similar deletion events were observed in B. diazoefficiens USDA110 and B. japonicum J5. When we cultured a USDA122 strain with a marker gene sacB inserted into the rhc gene cluster, most sucrose-resistant mutants had deletions in nif/rhc gene clusters, similar to the mutants above. Some deletion mutants were unique to the sacB system and showed lower competitive nodulation capability, indicating that IS-mediated deletions occurred during free-living growth and the host plants selected the mutants. Among 63 natural bradyrhizobial isolates, 2 possessed long duplications (261-357 kb) harboring nif/rhc gene clusters between IS copies in direct orientation via homologous recombination. Therefore, the structures of symbiosis islands are in a state of flux via IS-mediated duplications and deletions during rhizobial saprophytic growth, and host plants select mutualistic variants from the resultant pools of rhizobial populations. Our results demonstrate that homologous recombination between direct IS copies provides a natural mechanism generating deletions and duplications on symbiosis islands.

Genomic Basis of Transcriptome Dynamics in Rice under Field Conditions

How genetic variations affect gene expression dynamics of field-grown plants remains unclear. Expression quantitative trait loci (eQTL) analysis is frequently used to find genomic regions underlying gene expression polymorphisms. This approach requires transcriptome data for the complete set of the QTL mapping population under the given conditions. Therefore, only a limited range of environmental conditions is covered by a conventional eQTL analysis. We sampled sparse time series of field-grown rice from chromosome segment substitution lines (CSSLs) and conducted RNA sequencing (RNA-Seq). Then, by using statistical analysis integrating meteorological data and the RNA-Seq data, we identified 1,675 eQTLs leading to polymorphisms in expression dynamics under field conditions. A genomic region on chromosome 11 influences the expression of several defense-related genes in a time-of-day- and scaled-age-dependent manner. This includes the eQTLs that possibly influence the time-of-day- and scaled-age-dependent differences in the innate immunity between Koshihikari and Takanari. Based on the eQTL and meteorological data, we successfully predicted gene expression under environments different from training environments and in rice cultivars with more complex genotypes than the CSSLs. Our novel approach of eQTL identification facilitated the understanding of the genetic architecture of expression dynamics under field conditions, which is difficult to assess by conventional eQTL studies. The prediction of expression based on eQTLs and environmental information could contribute to the understanding of plant traits under diverse field conditions.

Maintaining higher leaf photosynthesis after heading stage could promote biomass accumulation in rice

Leaf photosynthetic rate changes across the growing season as crop plants age. Most studies of leaf photosynthesis focus on a specific growth stage, leaving the question of which pattern of photosynthetic dynamics maximizes crop productivity unanswered. Here we obtained high-frequency data of canopy leaf CO2 assimilation rate (A) of two elite rice (Oryza sativa) cultivars and 76 inbred lines across the whole growing season. The integrated A value after heading was positively associated with crop growth rate (CGR) from heading to harvest, but that before heading was not. A curve-smoothing analysis of A after heading showed that accumulated A at > 80% of its maximum (A80) was positively correlated with CGR in analyses of all lines mixed and of lines grouped by genetic background, while the maximum A and accumulated A at ≤ 80% were less strongly correlated with CGR. We also found a genomic region (~ 12.2 Mb) that may enhance both A80 and aboveground biomass at harvest. We propose that maintaining a high A after heading, rather than having high maximum A, is a potential target for enhancing rice biomass accumulation.

Objective assessment of tumor regression in post-neoadjuvant therapy resections for pancreatic ductal adenocarcinoma: comparison of multiple tumor regression grading systems

Neoadjuvant therapy is increasingly used to control local tumor spread and micrometastasis of pancreatic ductal adenocarcinoma (PDAC). Pathology assessments of treatment effects might predict patient outcomes after surgery. However, there are conflicting reports regarding the reproducibility and prognostic performance of commonly used tumor regression grading systems, namely College of American Pathologists (CAP) and Evans' grading system. Further, the M.D. Anderson Cancer Center group (MDA) and the Japan Pancreas Society (JPS) have introduced other grading systems, while we recently proposed a new, simple grading system based on the area of residual tumor (ART). Herein, we aimed to assess and compare the reproducibility and prognostic performance of the modified ART grading system with those of the four grading systems using a multicenter cohort. The study cohort consisted of 97 patients with PDAC who had undergone post-neoadjuvant pancreatectomy at four hospitals. All patients were treated with gemcitabine and S-1 (GS)-based chemotherapies with/without radiation. Two pathologists individually evaluated tumor regression in accordance with the CAP, Evans', JPS, MDA and ART grading systems, and interobserver concordance was compared between the five systems. The ART grading system was a 5-tiered system based on a number of 40× microscopic fields equivalent to the surface area of the largest ART. Furthermore, the final grades, which were either the concordant grades of the two observers or the majority grades, including those given by the third observer, were correlated with patient outcomes in each system. The interobserver concordance (kappa value) for Evans', CAP, MDA, JPS and ART grading systems were 0.34, 0.50, 0.65, 0.33, and 0.60, respectively. Univariate analysis showed that higher ART grades were significantly associated with shorter overall survival (p = 0.001) and recurrence-free survival (p = 0.005), while the other grading systems did not show significant association with patient outcomes. The present study revealed that the ART grading system that was designed to be simple and more objective has achieved high concordance and showed a prognostic value; thus it may be most practical for assessing tumor regression in post-neoadjuvant resections for PDAC.

Rice Cultivar Takanari Has Higher Photosynthetic Performance Under Fluctuating Light Than Koshihikari, Especially Under Limited Nitrogen Supply and Elevated CO2

Plants in the field experience dynamic changes of sunlight rather than steady-state irradiation. Therefore, increasing the photosynthetic rate of an individual leaf under fluctuating light is essential for improving crop productivity. The high-yielding indica rice (Oryza sativa L.) cultivar Takanari is considered a potential donor of photosynthesis genes because of its higher steady-state photosynthesis at both atmospheric and elevated CO₂ concentrations than those of several Japanese commercial cultivars, including Koshihikari. Photosynthetic induction after a sudden increase in light intensity is faster in Takanari than in Koshihikari, but whether the daily carbon gain of Takanari outperforms that of Koshihikari under fluctuating light in the field is unclear. Here we report that Takanari has higher non-steady-state photosynthesis, especially under low nitrogen (N) supply, than Koshihikari. In a pot experiment, Takanari had greater leaf carbon gain during the initial 10 min after a sudden increase in irradiation and higher daily CO₂ assimilation under simulated natural fluctuating light, at both atmospheric (400 ppm) and elevated (800 ppm) CO₂ concentrations. The electron transport rate during a day under field conditions with low N supply was also higher in Takanari than in Koshihikari. Although the advantages of Takanari were diminished under high N supply, photosynthetic N use efficiency was consistently higher in Takanari than in Koshihikari, under both low and high N supply. This study demonstrates that Takanari is a promising donor parent to use in breeding programs aimed at increasing CO₂ assimilation in a wide range of environments, including future higher CO₂ concentrations.

High-yielding rice Takanari has superior photosynthetic response to a commercial rice Koshihikari under fluctuating light

Leaves within crop canopies experience variable light over the course of a day, which greatly affects photosynthesis and crop productivity. Little is known about the mechanisms of the photosynthetic response to fluctuating light and their genetic control. Here, we examined gas exchange, metabolite levels, and chlorophyll fluorescence during the photosynthetic induction response in an Oryza sativa indica cultivar with high yield (Takanari) and a japonica cultivar with lower yield (Koshihikari). Takanari had a faster induction response to sudden increases in light intensity than Koshihikari, as demonstrated by faster increases in net CO2 assimilation rate, stomatal conductance, and electron transport rate. In a simulated light regime that mimicked a typical summer day, the faster induction response in Takanari increased daily CO2 assimilation by 10%. The faster response of Takanari was explained in part by its maintenance of a larger pool of Calvin-Benson cycle metabolites. Together, the rapid responses of electron transport rate, metabolic flux, and stomatal conductance in Takanari contributed to the greater daily carbon gain under fluctuating light typical of natural environments.

A niche for cyanobacteria producing chlorophyll f within a microbial mat

Acquisition of additional photosynthetic pigments enables photosynthetic organisms to survive in particular niches. To reveal the ecological significance of chlorophyll (Chl) f, we investigated the distribution of Chl and cyanobacteria within two microbial mats. In a 7-mm-thick microbial mat beneath the running water of the Nakabusa hot spring, Japan, Chl f was only distributed 4.0-6.5 mm below the surface, where the intensity of far-red light (FR) was higher than that of photosynthetically active radiation (PAR). In the same mat, two ecotypes of Synechococcus and two ecotypes of Chl f-producing Leptolyngbya were detected in the upper and deeper layers, respectively. Only the Leptolyngbya strains could grow when FR was the sole light source. These results suggest that the deeper layer of the microbial mat was a habitat for Chl f-producing cyanobacteria, and Chl f enabled them to survive in a habitat with little PAR.

Temperature change affected groundwater quality in a confined marine aquifer during long-term heating and cooling

Global warming and urbanization together with development of subsurface infrastructures (e.g. subways, shopping complexes, sewage systems, and Ground Source Heat Pump (GSHP) systems) will likely cause a rapid increase in the temperature of relatively shallow groundwater reservoirs (subsurface thermal pollution). However, potential effects of a subsurface temperature change on groundwater quality due to changed physical, chemical, and microbial processes have received little attention. We therefore investigated changes in 34 groundwater quality parameters during a 13-month enhanced-heating period, followed by 14 months of natural or enhanced cooling in a confined marine aquifer at around 17 m depth on the Saitama University campus, Japan. A full-scale GSHP test facility consisting of a 50 m deep U-tube for circulating the heat-carrying fluid and four monitoring wells at 1, 2, 5, and 10 m from the U-tube were installed, and groundwater quality was monitored every 1-2 weeks. Rapid changes in the groundwater level in the area, especially during the summer, prevented accurate analyses of temperature effects using a single-well time series. Instead, Dual-Well Analysis (DWA) was applied, comparing variations in subsurface temperature and groundwater chemical concentrations between the thermally-disturbed well and a non-affected reference well. Using the 1 m distant well (temperature increase up to 7 °C) and the 10 m distant well (non-temperature-affected), the DWA showed an approximately linear relationships for eight components (B, Si, Li, dissolved organic carbon (DOC), Mg(2+), NH4(+), Na(+), and K(+)) during the combined 27 months of heating and cooling, suggesting changes in concentration between 4% and 31% for a temperature change of 7 °C.

Application of a microbial sensor to the quality control of meat freshness

Samples of fresh meat stored at 5 degrees C were periodically removed from storage and washed with water for periods of up to 2 weeks. The amount of amino acids, polyamines and viable counts (number of bacteria) in the washed water were measured by using an HPLC system and a colony counting method. At the same time, the washed water was charged into a flow injection analysis (FIA) system combined a microbial sensor using yeast (Trichosporon cutaneum), which was developed in this work for monitoring the freshness of meat. A relationship between the sensor signals obtained by the FIA system and the amounts of polyamines and amino acids produced from the meat and the number of bacteria which had multiplied in the meat during the aging process was investigated. The sensor signal was found to correspond to increases in amino acid levels and viable counts in the meat with the storage time in the course of the first stage of aging. This is due to the fact that amino acids produced initially by enzymes in the meat serve as a source of nutrition for septic bacteria during the aging process, and as a result, the level of bacterial cells increases with increasing amounts of amino acids with the passage of days. A good correlation, with a correlation factor of 0.908, was obtained between the sensor signal and viable counts obtained by the colony counting method. The present sensor method was more sensitive than the colony counting method at the early stage of the aging process, where viable counts were in the vicinity of 10(4) g(-1).

Existence of an exotic torus configuration in high-spin excited states of 40Ca

We investigate the possibility of the existence of the exotic torus configuration in the high-spin excited states of (40)Ca. We here consider the spin alignments about the symmetry axis. To this end, we use a three-dimensional cranked Skyrme Hartree-Fock method and search for stable single-particle configurations. We find one stable state with the torus configuration at the total angular momentum J=60 ħ and an excitation energy of about 170 MeV in all calculations using various Skyrme interactions. The total angular momentum J=60 ħ consists of aligned 12 nucleons with the orbital angular momenta Λ=+4, +5, and +6 for spin-up or -down neutrons and protons. The obtained results strongly suggest that a macroscopic amount of circulating current breaking the time-reversal symmetry emerges in the high-spin excited state of (40)Ca.

Genetic diversity of symbiotic cyanobacteria in Cycas revoluta (Cycadaceae)

The diversity of cyanobacterial species within the coralloid roots of an individual and populations of Cycas revoluta was investigated based on 16S rRNA gene sequences. Sixty-six coralloid roots were collected from nine natural populations of cycads on Kyushu and the Ryukyu Islands, covering the entire distribution range of the species. Approximately 400 bp of the 5'-end of 16S rRNA genes was amplified, and each was identified by denaturing gradient gel electrophoresis. Most coralloid roots harbored only one cyanobiont, Nostoc, whereas some contained two or three, representing cyanobiont diversity within a single coralloid root isolated from a natural habitat. Genotypes of Nostoc within a natural population were occasionally highly diverged and lacked DNA sequence similarity, implying genetic divergence of Nostoc. On the other hand, Nostoc genotypes showed no phylogeographic structure across the distribution range, while host cycads exhibited distinct north-south differentiation. Cycads may exist in symbiosis with either single or multiple Nostoc strains in natural soil habitats.

Selective detection and phylogenetic diversity of Acaryochloris spp. that exist in association with didemnid ascidians and sponge

Acaryochloris spp. are unique cyanobacteria which contain chlorophyll d as the predominant pigment. The phylogenetic diversity of Acaryochloris spp. associated with 7 Prochloron- or Synechocystis-containing didemnid ascidians and 1 Synechococcus-containing sponge obtained from the coast of the Republic of Palau was analyzed; we established a PCR primer set designed to selectively amplify the partial 16S rRNA gene of Acaryochloris spp. even in DNA samples containing a large amount of other cyanobacterial and algal DNAs. Polymerase chain reaction-denaturing gradient gel electrophoresis with this primer set enabled detection of the phyogenetic diversity of Acaryochloris spp. All the ascidian and sponge samples contained Acaryochloris spp. Fourteen phylotypes that were highly homologous (98–100%) with A. marina MBIC11017 were detected, while only 2 phylotypes were detected with our previously developed method for detecting cyanobacteria. The results also revealed that many uncultured phylotypes of Acaryochloris spp. were associated with those didemnid ascidians, since a clonal culture of only 1 phylotype has been established thus far. No specific relationship was found among the Acaryochloris phylotypes and the genera of the ascidians even when sample localities were identical; therefore, these invertebrates may provide a favorable habitat for Acaryochloris spp. rather than hosts showing any specific symbiotic relationships.

Linear chain structure of four-α clusters in 16O

We investigate the linear chain configurations of four-α clusters in 16O using a Skyrme cranked Hartree-Fock method and discuss the relationship between the stability of such states and angular momentum. We show the existence of a region of angular momentum (13-18ℏ) where the linear chain configuration is stabilized. For the first time we demonstrate that stable exotic states with a large moment of inertia (ℏ2/2Θ∼0.06-0.08  MeV) can exist.

Evidence of global chlorophyll d

Although analyses of chlorophyll d (Chl d)-dominated oxygenic photosystems have been conducted since their discovery 12 years ago, Chl d distribution in the environment and quantitative importance for aquatic photosynthesis remain to be investigated. We analyzed the pigment compositions of surface sediments and detected Chl d and its derivatives from diverse aquatic environments. Our data show that the viable habitat for Chl d-producing phototrophs extends across salinities of 0 to 50 practical salinity units and temperatures of 1 degrees to 40 degrees C, suggesting that Chl d production can be ubiquitously observed in aquatic environments that receive near-infrared light. The relative abundances of Chl d derivatives over that of Chl a derivatives in the studied samples are up to 4%, further suggesting that Chl d-based photosynthesis plays a quantitatively important role in the aquatic photosynthesis.

Molecular detection of epiphytic Acaryochloris spp. on marine macroalgae

A molecular method for detecting the epiphyte community on marine macroalgae was developed by using PCR-denaturing gradient gel electrophoresis. Selective amplification of 16S rRNA gene fragments from either cyanobacteria or algal plastids improved the detection of minor epiphytes. Two phylotypes of Acaryochloris, a chlorophyll d-containing cyanobacterium, were found not only on red macroalgae but also on green and brown macroalgae.

Anatomical variations of the ten triangles around the cavernous sinus

The dimensions of the 10 triangles around the cavernous sinus were measured to define the anatomical characteristics of the triangles and to compare their consistency in shape and area. Twelve tissue blocks containing the bilateral cavernous sinuses and medial two-thirds of the middle cranial fossae were obtained from Japanese adults at autopsy, fixed to a stereotactic frame, and examined with an operative microscope. The dimensions of each triangle were measured with calipers and compared, based on the same point and border. The anteromedial triangle and the superolateral (Parkinson's) triangle were more consistent in shape than the paramedial and oculomotor triangles, but the oculomotor triangle was larger in area than these other triangles. The posteromedial (Kawase's) triangle was more consistent in shape and larger than the anterolateral, lateral, and the posterolateral (Glasscock's) triangles. The anteromedial and superolateral (Parkinson's) triangles are important for the combined epi- and subdural approach to cavernous sinus lesions. The posteromedial (Kawase's) triangle is important for gaining access to the posterior cranial fossa from the middle cranial fossa.

Luneburg lens approach to nuclear rainbow scattering

The physical interpretation of nuclear rainbow scattering within the frame of the optical model is critically investigated. Starting from the properties of the Luneburg lens, a gradient index device that displays refractive features similar to those of the nuclear potential, important differences between the mechanisms producing the nuclear and optical rainbows are pointed out.

Preparation of refractive index matching polymer film alternative to oil for use in a portable surface-plasmon resonance phenomenon-based chemical sensor method

In order to simplify the procedure for assembling a surface-plasmon resonance (SPR) sensor, a refractive index matching polymer film was prepared as an alternative to the conventionally used matching oil. The refractive index matching polymer film, the refractive index of which was nearly equal to the prism and sensor chip material (a cover glass) of the SPR sensor, was prepared by casting a tetrahydrofuran solution of poly (vinyl chloride) (PVC) containing equal weights of dioctyl phthalate and tricresyl phosphate. The refractive index matching polymer film was found to have a refractive index of 1.516, which is identical to that of the prism and the cover glass used for the present SPR sensor. The utility of the matching polymer film for the SPR sensor was confirmed by the detection of anti-human albumin, based on an antigen-antibody reaction.

Qualitatively different response of isolated rabbit aorta to methylene blue administered from intimal and adventitial surface

An isolated rabbit aortic preparation, on which administered drugs act selectively from intimal or adventitial surface, was made. Epinephrine (0.1 nM approximately 10 microM) produced concentration-dependent increase of intraluminal pressure, which is due to increase of contraction of the vascular smooth muscle. Sensitivity of contractile response to epinephrine administered from intimal surface was significantly higher than that administered from adventitial surface. The contractile response to epinephrine administered from intimal surface was reduced by removal of the endothelium. Cocaine (100 microM) potentiated the contractile response to epinephrine administered from adventitial surface. Cocaine also potentiated the contractile response to high concentration of epinephrine administered from intimal surface, while the drug reduced the contractile response to low concentration of epinephrine. Methylene blue (100 microM) administered from adventitial surface produced a marked contraction, while methylene blue administered from intimal surface produced a marked relaxation. The relaxing response to methylene blue administered from intimal surface was reduced by the removal of endothelium. Prazosin (1 microM) suppressed the contractile response to methylene blue administered from adventitial surface, indicating that methylene blue released norepinephrine from adrenergic nerve terminals. The contractile response to epinephrine administered from intimal surface was reduced by methylene blue administered from intimal surface. The present study clearly demonstrated variation in mechanical response of isolated rabbit aortic preparation with intimal or adventitial surface of drug entry.

Substrate phage as a tool to identify novel substrate sequences of proteases

Combinatorial phage peptide libraries have been used to identify the ligands for specific target molecules. These libraries are also useful for identification of the specific substrates of various proteases. A substrate phage library has a random peptide sequence at the N-terminus of the phage coat protein and an additional tag sequence that enables attachment of the phage to an immobile phase. When these libraries are incubated with a specific enzyme, such as a protease, the uncleaved phage is excluded from the solution with tag-binding macromolecules. This provides a novel approach to define substrate specificity. The aim of this review is to summarize recent progress on the application of the substrate phage technique to identify specific substrates of proteolytic enzymes. As an example, some of our own experimental data on the selection and characterization of substrate sequences for thrombin, a serine protease, and membrane type-1 matrix metalloproteinase (MT1-MMP) will be presented. Using this approach, the canonical consensus substrate sequence for thrombin was deduced from the selected clones. As expected from the collagenolytic activity of MT1-MMP, a collagen-like sequence was identified in the case of MT1-MMP. A more selective substrate sequence for MT1-MMP was identified during a substrate phage screen. The delineation of the substrate specificity of proteases will help to elucidate the enzymatic properties and the physiological roles of these enzymes. Comprehensive screening of very large numbers of potential substrate sequences is possible with substrate phage libraries. Thus, this approach allows novel substrate sequences and previously unknown target molecules to be defined.

A novel secreted tumor antigen with a glycosylphosphatidylinositol-anchored structure ubiquitously expressed in human cancers

In a search for novel genes expressed in human cancers, we identified one gene from an assembled expressed sequence tag database. Northern blot analysis revealed that the gene, termed alcan, was expressed in various types of human cancer cell lines and in the fetus, but not in normal tissues. The alcan gene is located on chromosome 6 and is encoded on a 246-amino-acid protein with weak homology to classical major histocompatibility complex class I. Its gene product, ALCAN, had hydrophobic amino acid clusters at both the N- and C-terminal regions and was predicted to be a glycosylphosphatidylinositol (GPI)-anchored membrane protein. Flow cytometric analysis revealed that ALCAN was detected on the surface of human cancer cells and on alcan-transfected CHO-K1 cells. ALCAN was also secreted from these cells, suggesting that some portion of the molecules was secreted by enzymatic cleavage by, for example, phospholipases. Mutational analysis of ALCAN suggested that the GPI-anchored position was the Ser(216) residue. These findings indicate that ALCAN may be a potential target for cancer diagnosis or therapy.

Beta,gamma-methylene ATP-induced cAMP formation in C6Bu-1 cells: involvement of local metabolism and subsequent stimulation of adenosine A2B receptor

The mechanism underlying beta,gamma-methylene ATP (beta,gamma-MeATP)-induced cAMP elevation was investigated in rat glioma C6Bu-1 cells. Beta,gamma-MeATP increased forskolin-stimulated cAMP formation in a manner sensitive to both the P1 antagonist xanthine amine congener (XAC) and the P2 antagonist pyridoxalphosphate-6-azophenyl-2',4'-disulfonic acid (PPADS). Adenosine deaminase (ADA; 1 U/mL), which abolished the adenosine-induced response, did not eliminate the beta,gamma-MeATP-induced response. However, combination of ADA with alpha,beta-methylene ADP (alpha,beta-MeADP), an ecto-5'-nucleotidase inhibitor, blocked the beta,gamma-MeATP-induced response. AMP, the substrate for ecto-5'-nucleotidase, also induced cAMP formation in a manner sensitive to XAC and alpha,beta-MeADP inhibition. However, the AMP-induced response was not blocked by PPADS. HPLC analyses revealed that adenosine was generated from beta,gamma-MeATP and AMP. In addition, alpha,beta-MeADP inhibited the conversion of beta,gamma-MeATP and AMP to adenosine, whereas PPADS blocked adenosine formation from beta,gamma-MeATP but not from AMP. [3H]Adenosine generated from [3H]AMP was preserved on the cell surface environment even in the presence of ADA. The mRNAs for ecto-phosphodiesterase/pyrophosphatase 1 (EC 3.1.4.1), ecto-5'-nucleotidase (EC 3.1.3.5) and adenosine A2B receptor were detected by RT-PCR. These results suggest that C6Bu-1 cells possess ecto-enzymes converting beta,gamma-MeATP to adenosine, and the locally accumulated adenosine in this mechanism efficiently stimulates A2B receptors in a manner resistant to exogenous ADA.

Correlation between adenine nucleotide-induced cyclic AMP elevation and extracellular adenosine formation in NG108-15 cells

We previously demonstrated that extracellular adenine nucleotides induced cyclic AMP elevation in NG108-15 cells. This response was resistant to adenosine deaminase (ADA) and the ecto-5'-nucleotidase (CD73) inhibitor alpha,beta-methylene ADP (alpha,beta-MeADP), but was inhibited by both P1- and P2-receptor antagonists. In the present study, we investigated the relationship between adenine nucleotide-induced cyclic AMP elevation and extracellular adenosine formation. ATP, AMP and beta,gamma-methylene ATP (beta,gamma-MeATP) were time-dependently metabolized to adenosine in NG108-15 cells. Adenosine formations from ATP, AMP and beta,gamma-MeATP were not affected by alpha,beta-MeADP, but suppressed by the P2-receptor antagonist pyridoxalphosphate-6-azophenyl-2',4'-disulphonic acid (PPADS). A close correlation between extracellular adenosine formation and cyclic AMP increasing effects were obtained with several adenine nucleotide agonists in NG108-15 cells as well as their parent cell line C6Bu-1 and N18TG-2 cells, all of which possess functional adenosine A2 receptors. When NG108-15 cells were incubated with [3H]ATP or [3H]AMP in the presence of ADA, [3H]adenosine was found to distribute dominantly on the cell surface. NG108-15 cells expressed mRNA for the ecto-ATPase and nucleotide pyrophosphatase, but not for CD73. These results suggest that local adenosine formation by an ecto-enzyme distinct from CD73 is involved in adenine nucleotide-induced cyclic AMP formation in NG108-15 cells.

Identification and functional characterization of a novel subtype of neuromedin U receptor

Neuromedin U is a bioactive peptide isolated originally from the porcine spinal cord. We recently identified neuromedin U as the cognate ligand for the orphan G protein-coupled receptor FM-3. In this study, we isolated cDNA coding for a novel G protein-coupled receptor, TGR-1, which was highly homologous with FM-3. We found that neuromedin U specifically and clearly elevated the extracellular acidification rates, arachidonic acid metabolite release, and intracellular Ca(2+) mobilization in Chinese hamster ovary cells expressing TGR-1. Radiolabeled neuromedin U specifically bound with high affinity to membrane fractions prepared from these cells. These results show that TGR-1, like FM-3, is a specific and functional receptor for neuromedin U. We analyzed TGR-1 mRNA tissue distribution in rats using quantitative reverse transcription-polymerase chain reaction and found it to considerably differ from that of FM-3 mRNA. TGR-1 mRNA was primarily expressed in the uterus, suggesting that TGR-1 mediates the contractile activity of neuromedin U in this tissue. The identification of specific and functional receptor subtypes for neuromedin U will facilitate the study of their physiological roles and the search for their specific agonists and antagonists.

Purification and characterization of cytokine-inducing protein of seed extract from Aeginetia indica L., a parasitic plant

We have isolated 55 kDa protein from the seed extract of Aeginetia indica L. (AIL), a parasitic plant, by an affinity chromatography on N-hydroxysuccinimide (NHS)-activated Sepharose High Performance column bound F3 monoclonal antibody which neutralizes cytokine-inducing and antitumor effect of AIL. In in vitro model using human peripheral blood mononuclear cells (PBMC), the 55 kDa protein (AILb-A) induced multiple cytokines, such as IFN-gamma, tumor necrosis factor (TNF)-alpha, granulocyte macrophage-colony stimulating factor (GM-CSF), IL-2, IL-6, IL-10, IL-12 and IL-18, and also accelerated killer cell activities of PBMC. When compared with a commonly used immunotherapeutic agent OK-432, AILb-A induced Th1 cytokines are greater than OK-432. Of the Th2 cytokines, the amounts of IL-6 and IL-10 induced by AILb-A were lower than those by OK-432. No significant induction of IL-4 and IL-13 was observed in AILb-A-stimulated PBMC. TNF family including TNF-alpha, TNF-beta, Fas ligand (FasL) and TNF-related apoptosis-inducing ligand (TRAIL) were suggested to be important for AILb-A-induced killing activity of PBMC by reverse transcription-polymerase chain reaction (RT-PCR) analysis. Furthermore, the neutralizing test using cytokine-specific antibodies demonstrated that IL-18 plays a most significant role for IFN-gamma- and killer cell-inducing ability of AILb-A among the cytokines tested. These findings clearly indicated that AILb-A, a 55 kDa protein of AIL, is a potent Th1 cytokine inducer and may be a useful immunotherapeutic agent for the patients with malignancies.

Barrier-wave-internal-wave interference and airy minima in 16O16+O elastic scattering

Taking 16O+16O elastic scattering at 124 MeV as an example, we show that a barrier-wave-internal-wave decomposition of the elastic scattering amplitude provides valuable information on the light heavy-ion interaction and complements the more conventional nearside-farside decomposition. In particular, we show that the Airy minima present in the angular distributions are due to a barrier-wave-internal-wave interference mechanism, which sheds additional light on the exceptional transparency displayed by some light heavy-ion scattering systems. Extension of these ideas to other fields, like atomic and molecular collision physics, could prove rewarding.

Purification and DNA-binding properties of the cro-type regulatory repressor protein cng encoded by the Lactobacillus plantarum phage phi g1e

The putative repressor protein Cng (10kDa on an SDS gel) for the lytic pathway of Lactobacillus plantarum phage φg1e was purified using the Escherichia coli Pt7 system, and its DNA-binding ability for the seven operator-like sequences, the GATAC-boxes (Gb1 to Gb7), was investigated in vitro. In gel-shift assays, Cng selectively bound to the DNA fragments containing the GATAC-box(es). In addition, DNase I footprinting analysis with supercoiled DNA demonstrated that Cng can specifically cover about a 25bp region centered around each of the GATAC-boxes, although two boxes, Gb4 and Gb6, were only partially protected. Moreover, protein crosslinking experiments using glutaraldehyde suggested that Cng most likely functions as a dimer. On the other hand, the binding ability of Cpg for the GATAC-boxes in supercoiled DNA was also examined under the same conditions as in Cng; unlike Cng, Cpg covered Gb4 and Gb6 completely sufficiently as well as the other five boxes. Thus, the present and previous [Kakikawa et al., Gene 215 (1998) 371-379; 242 (2000) 155-166] results indicate a possibility that the two proteins Cng and Cpg selectively bind to the GATAC-boxes that act as operators, and can decide between the lytic or lysogenic pathways through repression of the promoter activity of P(R) as well as P(L).

Effects of AMP derivatives on cyclic AMP levels in NG108-15 cells

1. In NG108-15 neuroblastomaxglioma hybrid cells, ATP stimulates intracellular cyclic AMP formation, which is inhibited by both adenosine (P(1)) and P2 receptor antagonists. In the present study, we examined the effects of several AMP derivatives in NG108-15 cells and mouse neuroblastoma N18TG-2 cells. 2. Adenosine 2'-monophosphate (A2P), adenosine 3'-monophosphate (A3P) and adenosine 5'-phosphosulphate (A5PS) increased cyclic AMP levels with similar concentration-dependencies in NG108-15 cells. 3. Increases in cyclic AMP by AMP derivatives were inhibited by the P2 receptor antagonist PPADS, but not by suramin. Effects of AMP derivatives were also inhibited by P(1) receptor antagonists ZM241385, XAC, DPCPX and partially by alloxazine. The ecto-nucleotidase inhibitor alpha, beta-methyleneADP was without effect. 4. In contrast, AMP derivatives did not change cyclic AMP levels in N18TG-2 cells. Accumulation of cyclic AMP in N18TG-2 cells was stimulated by adenosine A(2) receptor agonists CGS21680 and NECA, but not by ATP or beta, gamma-methyleneATP, agonists for cyclic AMP production in NG108-15 cells. 5. Reverse transcription-coupled polymerase chain reaction (RT - PCR) analyses revealed that N18TG-2 cells express both A(2A) and A(2B) receptors, while NG108-15 cells express mainly A(2A) receptors. 6. AMP derivatives did not affect the P2X and P2Y receptors expressed in NG108-15 cells. 7. These results suggest that A2P, A3P and A5PS act as agonists for cyclic AMP production and that these compounds are valuable tools for determinating the mechanism of ATP-stimulated cyclic AMP response in NG108-15 cells.

The genetic switch for the regulatory pathway of Lactobacillus plantarum phage (phi)g1e: characterization of the promoter P(L), the repressor gene cpg, and the cpg-encoded protein Cpg in Escherichia coli

The structural and functional features of the approximately 530 bp P(L)/Gb5-Gb6-cpg-Gb7 region (P(L) overlaps Gb5) for the lysogenic pathway of L. plantarum phage (phi)gle were investigated using the cat gene of E. coli plasmid pKK232-8 as a reporter. In E. coli XL1-Blue, a recombinant plasmid pKPL2 (cat under P(L)/Gb5-Gb6) exhibited distinct CAT activity, whereas the activity of pKPLCP1 (cat under P(L)/Gb5-Gb6-cpg) was only marginal. When pKPL2 was coexistent with a compatible derivative of plasmid pACYC177 carrying P(L)/Gb5-Gb6-cpg, the CAT activity was declined to the level of pKPLCP1. On the other hand, the cpg-encoded protein Cpg was overproduced in E. coli under P(T7). The molecular mass of the purified Cpg (14.5 kDa on a SDS gel) corresponded well with that (15.1 kDa) predicted from the DNA sequence. Gel-shift and footprinting assays demonstrated that Cpg selectively binds to about 25 bp bases centered around the GATAC-box (from 1 to 7). Moreover, protein crosslinking experiments using glutaraldehyde showed that Cpg most likely functions as a dimeric form. Thus, the present results indicate that Cpg probably represses P(L) through binding to the operator GATAC-box(es), and the P(L)/cpg region might participate in the lysogenic pathway.

Effects of P(1) and P2 receptor antagonists on beta, gamma-methyleneATP- and CGS21680-induced cyclic AMP formation in NG108-15 cells

1. We have previously shown that ATP increased cyclic AMP in NG108-15 cells, which was inhibited by P(1) receptor antagonist methylxanthines. In the present study, we examined the effects of P(1) and P2 receptor antagonists on cyclic AMP formation induced by beta,gamma-methyleneATP (beta,gamma-MeATP) and CGS21680, an A(2A) adenosine receptor agonist, in NG108-15 cells. 2. beta,gamma-MeATP and CGS21680 increased intracellular cyclic AMP with EC(50) values of 8. 0+/-0.98 microM (n=4) and 42+/-7.5 nM (n=4), respectively. 3. Several P(1) receptor antagonists inhibited both beta,gamma-MeATP- and CGS21680-induced cyclic AMP increase with a similar rank order of potency; ZM241385>CGS15943>XAC>DPCPX. However, the pK(i) values of these antagonists for beta,gamma-MeATP were larger than those for CGS21680. 4. Alloxazine, a P(1) receptor antagonist, and several P2 receptor antagonists (PPADS, iPPADS, reactive blue-2) inhibited beta, gamma-MeATP-induced response, while these antagonists little affected CGS21680-induced one. Suramin was effective only for beta, gamma-MeATP-induced response at 1 mM. 5. 2-chloroadenosine (2CADO) and 2-chloroATP (2ClATP) increased cyclic AMP with similar potencies. The effects of these agonists were both inhibited by ZM241385, but only 2ClATP-induced response was inhibited by PPADS. 6. ATP- and beta, gamma-MeATP-induced responses were little affected by alpha, beta-methyleneADP, a 5'-nucleotidase inhibitor. 7. These results clearly demonstrate that ATP-stimulated cyclic AMP formation can be distinguished from the A(2A) receptor agonist-induced one by using the several P(1) and P2 receptor antagonists.

Identification of substrate sequences for membrane type-1 matrix metalloproteinase using bacteriophage peptide display library

Membrane type-1 matrix metalloproteinase (MT1-MMP) has been reported to mediate the activation of progelatinase A (proMMP-2) which is associated with tumor invasion and metastasis, and also known to have an ability to digest extracellular matrix components. To clarify substrate specificity of MT1-MMP, we have searched for amino acid sequences cleaved by this protease using the hexamer substrate phage library consisting of a large number of randomized amino acids sequences. The consensus substrate sequences for MT1-MMP were deduced from the selected clones and appeared to be P-X-G/P-L at the P3-P1' sites. Peptide cleavage assay revealed that MT1-MMP preferentially digested a synthetic substrate containing Pro of the P1 position compared to that being substituted with Gly. Our results may have an important implication to identifying new target proteins for MT1-MMP and leading to the design of its selective inhibitors suitable for cancer chemotherapy.

Comparison of maitotoxin with thromboxane A2 in rabbit platelet activation

Maitotoxin (MTX), a Ca2+ channel-activating marine toxin, caused shape change followed by aggregation in rabbit platelets, like U46619, a thromboxane A2 analogue. Although both drugs failed to cause aggregation in the absence of external Ca2+, U46619, but not maitotoxin, elicited shape change in the absence of external Ca2+. The observations of platelets with a scanning electron microscope showed that both drugs caused contraction of platelets and extension of pseudopodia (shape change) followed by aggregation with a clot in the presence of Ca2+. It is noteworthy that long term exposure to MTX caused the lysis of platelets in the presence of Ca2+. While U46619 transiently increased the internal Ca2+ concentration ([Ca2+]i), maitotoxin slowly but irreversibly increased [Ca2+]i in an external Ca2(+)-dependent manner. MTX-induced phosphoinositide hydrolysis was totally dependent on the presence of external Ca2+, but U46619-induced phosphoinositide hydrolysis was still observed in the absence of external Ca2+. MTX-induced phosphoinositide hydrolysis was partly inhibited by SK&F96365, a voltage-independent Ca2+ channel antagonist, or by genistein, a tyrosine kinase inhibitor. MTX caused phosphorylation of tyrosine residues of several proteins, like U46619. Thus, MTX is similar to U46619 in functions of Ca2+ mobilization, phosphoinositide hydrolysis and tyrosine phosphorylation, but MTX-induced actions are strictly dependent on the presence of external Ca2+.

Effects of YT-146 [2-(1-octynyl) adenosine], an adenosine A2A receptor agonist, on cAMP production and noradrenaline release in PC12 cells

Effects of YT-146 [2-(1-octynyl) adenosine], an adenosine A2 receptor agonist, on cAMP production and noradrenaline (NA) release were investigated in PC12 cells. YT-146 caused a concentration-dependent cAMP accumulation (EC50: 1.2+/-0.9 nM). In [3H]NA-prelabeled cells, YT-146 increased the basal NA release and enhanced ATP-evoked NA release in a concentration-dependent manner (EC50: 0.23+/-0.15 nM). YT-146 augmented the maximal response to ATP without affecting the EC50 value of ATP. These effects of YT-146 were inhibited by several adenosine receptor antagonists with a characteristic of adenosine A2A receptor subtype. The effects of YT-146 were mimicked by forskolin, dibutylyl cAMP and Sp-cAMPS, and inhibited by H-89, a cAMP-dependent protein kinase inhibitor. YT-146 had little effect on ATP-induced increase in intracellular Ca2+ concentration. YT-146 enhanced the NA release induced by several different stimuli including Ca2+ ionophore A23187. The present results suggest that YT-146 is a potent agonist on adenosine A2A receptors in PC12 cells and causes a cAMP-dependent enhancement of NA release by affecting the exocytosis process at a point downstream of the intracellular Ca2+ increase.

Inhibition of ATP-induced cAMP formation by 5'-p-fluorosulfonylbenzoyladenosine in NG108-15 cells

ATP is known to increase intracellular cAMP levels in NG108-15 cells via a novel purinoceptor and this response is inhibited by the P1 purinoceptor antagonist methylxanthine. In the present study, we examined the effects of 5'-p-fluorosulfonylbenzoyladenosine (FSBA), an affinity ligand for ATP-binding proteins, on cAMP formation mediated by activation of adenylate cyclase (AC)-linked purinoceptors in NG108-15 cells. cAMP levels were determined by RIA using an anti-succinyl-cAMP antiserum. FSBA (100 microM) increased intracellular cAMP about 2.6-fold. However, FSBA-induced cAMP formation was abolished by pretreatment with adenosine deaminase, suggesting that adenosine, a breakdown product of FSBA, is involved in FSBA-induced cAMP formation. In contrast, pretreatment of cells with FSBA in the presence of adenosine deaminase inhibited cAMP formation induced by ATP and beta,gamma-methylene-ATP (beta,gamma-MeATP), without affecting the prostaglandin E1 (PGE1)-induced response. The inhibitory effect of FSBA on ATP-induced cAMP formation was concentration-dependent with a concentration required for half-maximal inhibition (IC50) of around 3 microM. The inhibitory effect of FSBA was not affected by pertussis toxin (PTX)-treatment. Pretreatment with FSBA (10 microM) depressed the maximal response to beta,gamma-MeATP by 60%, but did not affect the response to 5'-N-ethylcarboxamidoadenosine. The inhibitory effect of FSBA (100 microM) increased time-dependently during pretreatment and partly resisted wash-out. The inhibition by FSBA was protected by simultaneous addition of beta,gamma-MeATP during the FSBA pretreatment, indicating that both FSBA and the ATP analogue interacted with the same receptor site. The pretreatment with FSBA did not affect the increase in [Ca2+]i induced by ATP, UTP or benzoylbenzoic ATP. These results suggest that FSBA inhibits cAMP accumulation induced in NG108-15 cells by ATP or related agonists by selective modification of an AC-linked purinoceptor.

Construction of recombinant vaccinia virus expressing Rinderpest Virus nucleocapsid protein and its immunogenicity in mice

Recombinant vaccinia virus (rVV) was constructed by inserting Rinderpest Virus (RPV) nucleocapsid (N) protein gene. The rVV expressed RPV-N protein in the rVV-infected cells. The rVV was shown to produce RPV-N-specific antibody in mice.

Characteristic epiluminescent microscopic features of early malignant melanoma on glabrous skin. A videomicroscopic analysis

OBJECTIVE

To investigate the characteristic epiluminescent microscopic features of early lesions of malignant melanoma affecting glabrous skin, which is the most prevalent site of the neoplasm in nonwhite populations.

DESIGN

The epiluminescent microscopic features of various kinds of melanocytic lesions affecting glabrous skin were investigated using a videomicroscope. All the diagnoses were determined clinically and histopathologically using the standard criteria.

SETTING

A dermatology clinic at a university hospital.

PATIENTS

The following 130 melanocytic lesions consecutively diagnosed at our department were examined: 16 lesions of acral lentiginous melanoma, 6 lesions of malignant melanoma in situ, and 108 lesions of benign melanocytic nevus (acquired or congenital).

MAIN OUTCOME MEASURE

The incidence of each characteristic epiluminescent feature was compared among disease categories.

RESULTS

On epiluminescent microscopy, malignant melanoma in situ and the macular portions of invasive malignant melanoma showed accentuated pigmentation on the ridges of the skin markings, which are arranged in parallel patterns on glabrous skin. This "parallel ridge pattern" was found in 5 (83%) of 6 lesions of malignant melanoma in situ and in 15 (94%) of 16 lesions of malignant melanoma. The parallel ridge pattern was rarely found in the lesions of benign melanocytic nevus. Most benign melanocytic nevi showed 1 of the following 3 typical epiluminescent patterns: (1) a parallel furrow pattern exhibiting pigmentation on the parallel sulci of [he skin markings (54%), (2) a latticelike pattern (21%), and (3) a fibrillar pattern showing filamentous or meshlike pigmentation (15%). The remaining 11 benign nevi (10%) showed a nontypical pattern.

CONCLUSION

Because epiluminescent microscopic features of early malignant melanoma on glabrous skin are characteristic, we can effectively detect early lesions using this noninvasive method.