Genome-Wide Association Study of Early Vigour-Related Traits for a Rice (Oryza sativa L.) japonica Diversity Set Grown in Aerobic Conditions

Aerobic rice production is a relatively new system in which rice is direct-seeded and grown in non-flooded but well-watered conditions to improve water productivity. Early vigour-related traits are likely to be important in aerobic conditions. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with early vigour-related traits in aerobic conditions using a japonica rice diversity set. Field experiments and glasshouse experiments conducted under aerobic conditions revealed significant genotypic variation in early vigour-related traits. Genome-wide association analysis identified 32 QTL associated with early vigour-related traits. Notably, two QTL, qAEV1.5 and qAEV8, associated with both early vigour score and mesocotyl length, explained up to 22.1% of the phenotypic variance. In total, 23 candidate genes related to plant growth development and abiotic stress response were identified in the two regions. This study provides novel insights into the genetic basis of early vigour under aerobic conditions. Validation of identified QTL and candidate genes in different genetic backgrounds is crucial for future studies. Moreover, testing the effect of QTL on yield under different environments would be valuable. After validation, these QTL and genes can be considered for developing markers in marker-assisted selection for aerobic rice production.

Low canopy temperature and high stomatal conductance contribute to high grain yield of contrasting japonica rice under aerobic conditions

Water limitation is a major concern in rice production. It has been suggested that with adapted genotypes, aerobic rice production offers the maintenance of grain yield while saving water. However, there has been limited exploration of japonica germplasm adapted for high-yield aerobic environments. Therefore, three aerobic field experiments with different levels of relatively high-water availability were conducted across two seasons to explore genetic variation in grain yield and physiological traits that contributed to high yield. In the first season, a japonica rice diversity set was explored under well-watered (WW20) conditions. While in the second season, a well-watered (WW21) experiment and an intermittent water deficit (IWD21) experiment were conducted to examine the performance of a subset of 38 genotypes selected for low (mean of -6.01°C) and high (mean of -8.22°C) canopy temperature depression (CTD). In WW20, CTD explained 19% of the variation in grain yield which was similar to the variation explained by plant height, lodging, and leaf death response to heat. In WW21, a relatively high average grain yield (9.09 t ha^-1) was achieved, while a 31% reduction was achieved in IWD21. Compared with the low CTD group, the high CTD group had 21% and 28% higher stomatal conductance, 32% and 66% higher photosynthetic rate, and 17% and 29% higher grain yield in the WW21 and IWD21, respectively. This work demonstrated the advantage of higher stomatal conductance and cooler canopy temperature which resulted in higher photosynthetic rate and higher grain yield. Two promising genotypes with high grain yield, cooler canopy temperature, and high stomatal conductance were identified as donor genotypes for use by the rice breeding program when aerobic rice production is a target. Field screening for cooler canopies within a breeding program with high-throughput phenotyping tools would be of value for genotype selection for aerobic adaption.

Quantitative trait loci (QTL) for low temperature tolerance at the young microspore stage in rice (Oryza sativa L.) in Australian breeding material

Low temperatures at the young microspore stage (YMS) decreases spikelet fertility and is a major limiting factor to rice production in temperate Australia. Low temperature tolerance is a difficult trait to phenotype, hence there is a strong desire for the identification of quantitative trait loci (QTL) for their use in marker-assisted selection (MAS). Association mapping was used in several breeding populations with a known source of low temperature tolerance, Norin PL8, to identify QTL for low temperature tolerance. A novel QTL for spikelet fertility was identified on chromosome 6, qYMCT6.1, in which the Australian variety, Kyeema, was the donor for increased fertility. Additional five genomics regions were identified that co-located with previously reported QTL, two of which have been previously cloned. Additionally, for the first time a QTL for spikelet fertility qYMCT10.1, has been shown to co-locate with the number of dehisced anthers qYMCTF10.1 which increases the shedding of pollen from the anthers. This study revealed one new QTL for low temperature tolerance at YMS in temperate japonica germplasm and identified an additional five previously reported. These QTL will be utilised for MAS in the Australian rice breeding program and may have merit for temperate breeding programs globally.

Genomic Regions and Floral Traits Contributing to Low Temperature Tolerance at Young Microspore Stage in a Rice (Oryza sativa L.) Recombinant Inbred Line Population of Sherpa/IRAT109

Aerobic rice production (AP) consumes less water compared to flooded systems. Developing genotypes and identifying genomic regions associated with low temperature (LT) tolerance at the young microspore stage (YMS) is imperative for AP, particularly for temperate regions. Using a recombinant inbred line population derived from the Australian LT tolerant variety Sherpa, experiments were conducted to map and dissect quantitative trait loci (QTL) associated with spikelet sterility (SS) after exposure to LT and to investigate floral traits contributing to the development of lower SS. Significant genotypic variation for SS was observed in the population after exposure to LT at YMS. Three genomic regions associated with SS, qYMCT3, qYMCT4, and qYMCT8.1 were identified in chromosomes 3, 4, and 8 respectively, using multiple QTL models explaining 22.4% of the genotypic variation. Introgression of the favorable allele from qYMCT3 was estimated to reduce SS by up to 15.4%. A co-locating genomic region with qYMCT3, qDTHW3.1 was identified as the major QTL affecting days to heading and explained as much as 44.7% of the genotypic variation. Whole-genome sequence and bioinformatic analyses demonstrated OsMADS50 as the candidate gene for qYMCT3/qDTHW3.1 and to our knowledge, this was the first attempt in connecting the role of OsMADS50 in both LT and flowering in rice. Differential sets selected for extreme SS showed LT tolerant genotype group produced higher total pollen per spikelet resulting in a higher number of dehisced anthers and pollen on stigma and eventually, lower SS than THE sensitive group. The relationship between these key floral traits with SS was induced only after exposure to LT and was not observed in warm ideal temperature conditions. Identification of elite germplasm with favorable QTL allele and combinations, gene cloning, and pyramiding with additional high-value QTL for key traits should empower breeders to develop AP adapted genotypes for temperate growing regions, and ultimately produce climate-resilient rice.

Effects of Variety, Early Harvest and Germination on Pasting Properties and Cooked Grain Texture of Brown Rice

Brown rice is superior to white rice in nutritional value and in prevention of chronic diseases. However, it is not the preference of consumers and the relative consumption of brown rice is limited due to a number of factors including chewiness and perceived hard texture after cooking. While both early harvested brown rice and germinated brown rice have been shown to contain superior nutritional components, there is limited knowledge on textural properties of these types of brown rice relative to standard brown rice, and how varieties may affect such properties. Thus, the present study examined the effect of variety, early harvest and germination on those properties of 8 rice varieties with contrasting amylose content and known texture in terms of milled rice. Early harvest and germination decreased pasting viscosities and cooked grain hardness. However, their effect on the characteristics of flour and whole grains differed, in which germination had greater effect on pasting properties, while early harvest on texture of cooked grains. Softer texture of brown rice, about 32% lower could be achieved by germination, and 46% by harvesting early. There was a good relationship between pasting characteristics particularly setback and hardness among different varieties in brown rice, germinated brown rice and also in early harvest brown rice. This is the first time the comparison of texture between the 3 brown rice types has been reported. The results also provide new options for selection of desired characteristics for food processing and brown rice consumption. This article is protected by copyright. All rights reserved.

QTL Validation and Development of SNP-Based High Throughput Molecular Markers Targeting a Genomic Region Conferring Narrow Root Cone Angle in Aerobic Rice Production Systems

Aerobic rice production (AP) provides potential solutions to the global water crisis by consuming less water than traditional permanent water culture. Narrow root cone angle (RCA), development of deeper rooting and associated genomic regions are key for AP adaptation. However, their usefulness depends on validation across genetic backgrounds and development of linked markers. Using three F2 populations derived from IRAT109, qRCA4 was shown to be effective in multiple backgrounds, explaining 9.3-17.3% of the genotypic variation and introgression of the favourable allele resulted in 11.7-15.1° narrower RCA. Novel kompetitive allele specific PCR (KASP) markers were developed targeting narrow RCA and revealed robust quality metrics. Candidate genes related with plant response to abiotic stress and root development were identified along with 178 potential donors across rice subpopulations. This study validated qRCA4's effect in multiple genetic backgrounds further strengthening its value in rice improvement for AP adaptation. Furthermore, the development of novel KASP markers ensured the opportunity for its seamless introgression across pertinent breeding programs. This work provides the tools and opportunity to accelerate development of genotypes with narrow RCA through marker assisted selection in breeding programs targeting AP, which may ultimately contribute to more sustainable rice production where water availability is limited.

Genotypic variation in intrinsic transpiration efficiency correlates with sugarcane yield under rainfed and irrigated field conditions

Intrinsic transpiration efficiency (_i TE), the ratio of photosynthesis (A) to stomatal conductance (g_s ), is considered a useful trait for improving productivity; however, higher _i TE with high A is more desirable than that with low g_s . This study dissects _i TE of 20 sugarcane genotypes to understand its relationship with total dry matter (TDM) and cane yield (TCH) under irrigated and rainfed conditions. Water stress reduced mean A and g_s by 56 and 61%, and mean TDM and TCH by 55 and 59%, respectively; however, genotype × irrigation treatment interaction was smaller than genotype variance. Mean _i TE increased from 117.4 μmol mol^-1 in the irrigated treatment to 130.6 μmol mol^-1 in the rainfed treatment. In irrigated conditions, _i TE had high heritability (H² _b  = 0.67) and significant genetic correlation with TDM (r_g  = 0.58) and TCH (r_g  = 0.72). Under water stress, at g_s below 0.1 mol m^-2  s^-1 , non-stomatal limitation to A was evident and _i TE had low heritability (H² _b  = 0.2). Whereas in the g_s range of 0.1-0.4 mol m^-2  s^-1 , heritability of _i TE (H² _b  = 0.63) and its genetic correlation with TDM (r_g  = 0.78) and TCH (r_g  = 0.75) were maximised. There was significant genotypic variation in photosynthetic capacity (A_c ), and the differences were related to TDM and _i TE. Selecting genotypes with higher _i TE and A_c could offer potential for improving productivity without the unfavourable effect of low g_s .

Stable and Novel Quantitative Trait Loci (QTL) Confer Narrow Root Cone Angle in an Aerobic Rice (Oryza sativa L.) Production System

BACKGROUND

Aerobic rice production (AP) may be a solution to the looming water crisis by utilising less water compared to traditional flooded culture. As such, development of genotypes with narrow root cone angle (RCA) is considered a key AP adaptation trait as it could lead to deeper rooting and ensure water uptake at depth. Quantitative trait loci (QTL) and genes associated with rooting angle have been identified in rice, but usually in conventional transplanted systems or in upland and drought conditions. This study aimed to identify QTL associated with RCA in AP systems using a recombinant inbred line population derived from IRAT109.

RESULTS

Four experiments conducted in glasshouse and aerobic field conditions revealed significant genotypic variation existed for RCA in the population. Single and multiple QTL models identified the presence of eight QTL distributed in chromosomes 1, 2, 3, 4, and 11. Combined, these QTL explained 36.7-51.2% of the genotypic variance in RCA present in the population. Two QTL, qRCA1.1 and qRCA1.3, were novel and may be new targets for improvement of RCA. Genotypes with higher number of favourable QTL alleles tended to have narrower RCA. qRCA4 was shown to be a major and stable QTL explaining up to 24.3% of the genotypic variation, and the presence of the target allele resulted in as much as 8.6° narrower RCA. Several genes related to abiotic stress stimulus response were found in the qRCA4 region.

CONCLUSION

Stable and novel genomic regions associated with RCA have been identified. Genotypes which had combinations of these QTL, resulted in a narrower RCA phenotype. Allele mining, gene cloning, and physiological dissection should aid in understanding the molecular function and mechanisms underlying RCA and these QTL. Ultimately, our work provides an opportunity for breeding programs to develop genotypes with narrow RCA and deep roots for improved adaptation in an AP system for sustainable rice production.

X-ray photoelectron spectroscopic analysis of rice kernels and flours: Measurement of surface chemical composition

The objectives of this study were to evaluate the ability of X-ray photoelectron spectroscopy (XPS) to differentiate rice macromolecules and to calculate the surface composition of rice kernels and flours. The uncooked kernels and flours surface composition of the two selected rice varieties, Thadokkham-11 (TDK11) and Doongara (DG) demonstrated an over-expression of lipids and proteins and an under-expression of starch compared to the bulk composition. The results of the study showed that XPS was able to differentiate rice polysaccharides (mainly starch), proteins and lipids in uncooked rice kernels and flours. Nevertheless, it was unable to distinguish components in cooked rice samples possibly due to complex interactions between gelatinized starch, denatured proteins and lipids. High resolution imaging methods (Scanning Electron Microscopy and Confocal Laser Scanning Microscopy) were employed to obtain complementary information about the properties and location of starch, proteins and lipids in rice kernels and flours.

Drought resistance and soil water extraction of a perennial C4 grass: contributions of root and rhizome traits

Previously, we showed that genotypic differences in soil water extraction were associated with drought response, but we did not study underground root and rhizome characteristics. In this study, we demonstrate a similar relationship between drought resistance and soil water extraction but investigate the role of underground organs. Eighteen bermudagrass genotypes (Cynodon spp.) from four climatic zones were assessed under continuous drought at two locations with contrasting soils and climates. The criterion for drought resistance was the duration required to reach 50% green cover (GC50) after water was withheld. GC50, physiological traits, rhizome dry matter (RhDM), root length density (RLD) and average root diameter (ARD) were determined in both locations; water extraction was measured in one location. Large genotypic variation for drought resistance was observed in both locations, with GC50 being 187-277 days in a clay soil and 15-27 days in a sandy soil. Drought-resistant genotypes had greater soil water extraction and a higher water uptake rate. GC50 was correlated with relative water content (r=0.76), canopy temperature differential (r=-0.94) and photosynthetic rate (r=0.87) measured during drought; RhDM (r=0.78 to ~0.93) before and after drought; and ARD after drought (r=0.82 to ~0.94); GC50 was not correlated with RLD. Ecotypes collected from the Australian Mediterranean zone had superior drought resistance and were characterised by a large rhizome network. This is the first comprehensive study with perennial C4 grasses describing the association between water extraction, root distribution, rhizomes and drought resistance.

Evaluation of reduced-tillering (tin) wheat lines in managed, terminal water deficit environments

Small or shrivelled wheat kernels (screenings) that reduce crop value are commonly produced in terminal drought environments. The aim of this study was to establish whether the incorporation of the tiller inhibition (tin) gene would contribute to maintenance of kernel weight and reductions in screenings under terminal water deficit. Five Silverstar near-isogenic lines contrasting in high and low tiller potential and their recurrent Silverstar parent were established at two plant densities under managed terminal water deficit (mild and severe) and irrigated conditions. With irrigation (grain yield of 5.6 t ha(-1)), kernels of all lines weighed ~31 mg, with restricted-tillering (R-tin) lines producing an average 15% lower grain yield. Under both mild and severe terminal water deficit (4.1 t ha(-1) and 2.8 t ha(-1)), free-tillering lines had relatively high screenings ranging from 11.9% to 16.2%. Compared with free-tillering lines, R-tin lines maintained large kernel weight (~29 mg kernel(-1)) and had 29% and 51% fewer screenings under the two stresses, and a significantly greater (+11%) grain yield under mild stress. Higher kernel weights in tin lines were realized even with the greater kernel number per spike. The higher kernel weight of the R-tin lines under stress conditions was associated with greater anthesis biomass and increased stem water-soluble carbohydrates, ensuring more assimilate for later translocation to filling grain. The incorporation of the tin gene into genetic material adapted to the target environments provides scope for improvement in both grain yield and kernel weight, and a reduction in screenings in terminal water deficit environments.

Temporal and spatial patterns of soil water extraction and drought resistance among genotypes of a perennial C4 grass

The objective of this study was to investigate patterns of soil water extraction and drought resistance among genotypes of bermudagrass (Cynodon spp.) a perennial C4 grass. Four wild Australian ecotypes (1-1, 25a1, 40-1, and 81-1) and four cultivars (CT2, Grand Prix, Legend, and Wintergreen) were examined in field experiments with rainfall excluded to monitor soil water extraction at 30-190cm depths. In the study we defined drought resistance as the ability to maintain green canopy cover under drought. The most drought resistant genotypes (40-1 and 25a1) maintained more green cover (55-85% vs 5-10%) during water deficit and extracted more soil water (120-160mm vs 77-107mm) than drought sensitive genotypes, especially at depths from 50 to 110cm, though all genotypes extracted water to 190cm. The maintenance of green cover and higher soil water extraction were associated with higher stomatal conductance, photosynthetic rate and relative water content. For all genotypes, the pattern of water use as a percentage of total water use was similar across depth and time We propose the observed genetic variation was related to different root characteristics (root length density, hydraulic conductivity, root activity) although shoot sensitivity to drying soil cannot be ruled out.

Field phenotyping strategies and breeding for adaptation of rice to drought

This paper is a section of the book "Drought phenotyping in crops: from theory to practice" (Monneveux Philippe and Ribaut Jean-Marcel eds, published by CGIAR Generation Challenge Programme. Texcoco, Mexico). The section describes recent experience in drought phenotyping in rice which is one of the most drought-susceptible crops. The section contains genetic and genomic resources for drought adaptation and methods for selection of drought-resistant varieties in rice. In appendix, there is experience from Thailand on integration of direct selection for grain yield and physiological traits to confer drought resistance.

Water use, water use efficiency and drought resistance among warm-season turfgrasses in shallow soil profiles

As the available water supply for urban turfgrass management is becoming limited in Australia, it will be crucial to identify drought-resistant turfgrass species and water-saving management strategies. Eight (pre-)commercial turfgrasses grown in Australia, two each of four species including the bermudagrasses (Cynodon dactylon L.), the Queensland blue couches (Digitaria didactyla Willd), the seashore paspalums (Paspalum vaginatum Swartz.) and St Augustinegrasses (Stenotaphrum secundatum (Walt.) Kuntze) were evaluated in two lysimeter experiments. Shallow lysimeters (28 and 40cm) were used to represent shallow soil profiles typical of urban environments. We measured gravimetric water use for the eight cultivars and calculated water use efficiency (WUE, clipping yield to water use ratio) and WUEr (ratio of WUE under drought to that under irrigated conditions). WUEr measured in both experiments correlated strongly with survival period and this relationship was not affected by soil type or cutting height. Using survival period as the criterion for drought resistance, the best were the bermudagrasses and the worst were the seashore paspalums and Queensland blue couches. The bermudagrass genotypes had the lowest water use, highest WUE and WUEr and the Queensland blue couches and seashore paspalums had the greatest water use, lowest WUE and WUEr. The possible mechanisms of drought resistance included lower water use and lower stomatal conductance as indicated by higher canopy temperature in the early stage of water deficit.

Measurement of summer dormancy in temperate perennial pasture grasses

The search to improve drought survival in temperate perennial grasses has led to a renewed interest in summer dormancy and how to quantify it. This endogenously controlled trait, found in some temperate perennial grasses, is associated with drought that normally occurs in summer. While cessation of leaf growth and senescence of herbage occurs in all grasses in response to drought, it is under summer irrigation that these same responses are observed only in summer-dormant germplasm and hence the trait can be identified in germplasm. Across the spectrum from completely summer-dormant to non-dormant, there is a range of expression. Our objective here is to highlight differences in characteristics of indices which measure summer dormancy and to identify aspects for incorporation into a superior index for use in measuring this trait. The experimental program comprised three field trials that compared 6 cultivars and a fourth that assessed a larger group of 12 cultivars of the same three species, cocksfoot (Dactylis glomerata L.), tall fescue (Festuca arundinacea Schreb.), and phalaris (Phalaris aquatica L.). Seasonal herbage yield and foliage senescence were measured under three summer watering regimes: complete drought, mid-summer storm, and full irrigation at Mauguio, France. Different indices were calculated to compare against the approach which evaluates senescence under drought. The key outcomes are as follows. (1) The assessment of summer dormancy needs to be viewed as the plant response to a period of non-limiting water supply over summer. It makes little difference whether this is produced by full summer irrigation or a mid-summer simulated storm after a drought. Assessment of this trait under conditions of unbroken drought is discouraged because it can result in false scores. (2) The determination of summer dormancy intensity under full summer irrigation is most appropriate for the intensive study of the dynamics of dormancy expression over the entire summer. A simulated mid-summer storm within a drought gives an instantaneous view of dormancy intensity at a specific observation date and may be well adapted to the requirements of plant breeding. These methods are complementary. (3) Summer dormancy intensity can be assessed either by measuring herbage production or by a visual assessment of the level of herbage senescence. (4) An index of summer dormancy based on comparing irrigated summer herbage yield of any cultivar with that of a high, summer-yielding, non-dormant control cultivar was able to provide a reliable score of dormancy intensity. This index functions across a range of cultivars and species of perennial grasses. Further refinement of the index is needed to identify ‘standard’ high and low summer-dormant populations.

The significant influence of smoking status and gender on the clinical outcome in the patients with non-small cell lung cancer: The large cohort based study

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Background: To determine retrospectively whether smoking status and gender affect the treatment outcome and survival for the Japanese patients with non-small cell lung cancer. Methods: Using the database from the lung cancer registry of the National Hospital Study Group for Lung Cancer between 1987 and 2002, detailed demographic and survival information were obtained. A total of 18,346 (70%) documented smokers including the former and the current and 7,755 (30%) documented never smokers with non-small cell lung cancer were studied. A minimal follow-up period was two years. Among them, the 2,546 patients with stage IV lung adenocarcinoma were studied to examine the relationship between the smoking status or the gender and the chemotherapy effect. Multivariate analysis was performed using the Cox regression method. Results: There was an increased percentage of female subjects (72%) in the never smokers, and an increased percentage of male subjects (90%) in the smokers. The never smokers had lower performance status (PS) and lower clinical stage than the smokers (p<0.001). There was an increased percentage of adenocarcinoma (83%) in the never smokers. Multivariate analysis for all the patients demonstrated that the lower clinical stage, the lower PS, younger age, female and never smoking was an independent good prognostic factor The hazard ratio (HR) and its 95% CI was 3.73 (3.58–3.88), 2.69 (2.59–2.79), 1.21 (1.17–1.25), 1.15 (1.09–1.20), and 1.08 (1.04–1.14), respectively. Multivariate analysis for the stage IV adenocarcinoma also showed that the lower PS, female and never smoking was an independent good prognostic factor. The HR and its 95% CI was 2.37 (2.15–2.61), 1.35 (1.19–1.52) and 1.17 (1.04–1.32) respectively. In the treatment of chemotherapy for the stage IV adenocarcinoma patients, the never smokers had higher disease control rates (CR+PR+SD) than the smokers (p=0.08) and the females had higher response rates (CR+PR) than the males (p=0.02). Conclusions: The never smokers and females with non-small cell lung cancer were found to have a distinct and improved clinical outcome.

No significant financial relationships to disclose.

Phase II study of docetaxel and S-1 combination therapy in patients with previously treated non-small cell lung cancer

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Background: Docetaxel is active against chemotherapy-pretreated non-small-cell lung cancer (NSCLC). S-1 is a novel oral fluoropyrimidine, composed of tegafur, 5-chloro-2,4-dihydroxypyridine (dihydropyrimidinedehydrogenase inhibitor), and potassium oxonate (orotate phosphoribosyl transferase inhibitor). It has been commercially available and used for NSCLC in Japan. We conducted this study to evaluate the efficacy and safety of docetaxel combined with S-1 in NSCLC patients (pts) who were previously treated with one or more regimens. Methods: Eligible pts were required to have histologically or cytologically confirmed measurable or evaluable stage IIIB or IV NSCLC, age= 20 years, one or more previous chemotherapy, a performance status (PS) 0–1, and adequate organ function and bone marrow reserve. In this study, pts received S-1 (80 mg/m2 orally on days 1–14) and docetaxel (40mg/m2 IV on days 1). Treatment was repeated every 3 weeks. Results: Between January 2005 and May 2006, 30 pts were enrolled on this study. 29 pts were eligible and evaluable. Median age was 67 (48–79), male/female (23/6), PS 0/1 (9/20), stage IIIB/IV (7/22), and prior chemotherapy regimen 1/2/3 (23/4/2). 28 pts received a platinum-based chemotherapy. Response: PR=7(24%), SD=13, PD=7, NE=2. Median survival time was 10.2 months. Grade 3/4 toxicities (% of pts) were as follows: leukocytes 6/0 (20.6%), neutrophils 7/3 (34.4%), platelets 0/0, infection 0/1 (3.4%), fever 2/0 (6.9%), diarrhea 1/0 (3.4%), neurology 0/1 (3.4%), and mucositis 1/0 (3.4%). There were no treatment-related deaths. Conclusions: The combination of docetaxel and S-1 was effective with acceptable toxicity in pts with previously treated NSCLC. These results warrant further investigations of this regimen a randomized controlled trial as a second-line treatment for NSCLC.

No significant financial relationships to disclose.

[Extraabdominal desmoid tumor of the chest wall]

We report a rare case of desmoid tumor of the chest wall. A 75-year-old female visited our hospital due to a feeling of oppression in the left chest. A chest X-ray, computed tomography (CT) and magnetic resonance imaging (MRI) revealed a large mass in the left thorax. Surgical resection of the tumor was performed under the left standard thoracotomy. The tumor was 90 x 80 x 75 mm in size and diagnosed pathologically as desmoid tumor which showed proliferation of spindle shape cells and collagen fibers. Immunohistochemistry revealed that the tumor cells were positive for vimentin, alpha-smooth muscle actin and negative for CD34. The patient has been well without recurrence for 2 years and 2 months after surgery.

Phase II study of UFT, vinorelbine and gemcitabine as first-line treatment in advanced non-small-cell lung cancer

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Background: Vinorelbine (VNR)/gemcitabine (GEM) is active and well tolerated chemotherapy regimens for the treatment of patients (pts) with advanced non-small-cell lung cancer (NSCLC). UFT is composed of uracil and tegafur in a molar ratio of 4:1, and tegafur is a prodrug of 5-FU. Sequential exposure to 5-FU followed by GEM has been reported to give additive effects in vitro. For these reasons, we conducted a phase II study of triple treatment with these 3 drugs for advanced NSCLC. The objectives were to determine the tumor response rate, survival, safety and toxicity of this combination chemotherapy. Methods: Eligible pts were required to have histologically or cytologically comfirmed measurable or evaluable stage IIIB or IV NSCLC, age <75 years, no previous chemotherapy, a Karnofsky performance status (PS) 0–1, and adequate organ function and bone marrow reserve. In this study, pts received UFT (300 mg/m2 orally on days 1-5, 8–12) plus VNR (25 mg/m2 IV on days 6 and 13) and GEM (1000 mg/m2 IV on days 6 and 13). Treatment was repeated every 3 weeks. Results: Between September 2002 and November 2004, 32 pts were enrolled on this study. Characteristics of this study were as follows: male/female = 20/12; median age = 65 years (range 46–74); PS 0/1 = 11/21; stage IIIB/IV = 5/27. Median # of cycles = 2 (range 1–10). Response: PR = 7 (21.9%), SD = 14, PD = 10, NE = 1. Median survival time was 13.9 mos. 1-year survival rate was 56.7% (95% confidence interval, 38.9–74.4%). Gr 3/4 toxicity (% of pts) was as follows: leukocytes 40.6%, neutrophils 56.3%, platelets 3.1%, infection 9.4%, hypoxia 6.3%, dyspnea 3.1% and ALT/AST 3.1%. There were no treatment-related deaths. Conclusions: The combination of UFT, VNR and GEM appears effective with acceptable toxicity.

No significant financial relationships to disclose.

Minimising cold damage during reproductive development among temperate rice genotypes. II. Genotypic variation and flowering traits related to cold tolerance screening

Low temperature during microspore development increases spikelet sterility and reduces grain yield in rice (Oryza sativa L.). The objectives of this study were to determine genotypic variation in spikelet sterility in the field in response to low temperature and then to examine the use of physio-morphological traits at flowering to screen for cold tolerance. Multiple-sown field experiments were conducted over 4 consecutive years in the rice-growing region of Australia to increase the likelihood of encountering low temperature during microspore development. More than 50 cultivars of various origins were evaluated, with 7 cultivars common to all 4 years. The average minimum temperature for 9 days during microspore development was used as a covariate in the analysis to compare cultivars at a similar temperature. The low-temperature conditions in Year 4 identified cold-tolerant cultivars such as Hayayuki and HSC55 and susceptible cultivars such as Sasanishiki and Doongara. After low temperature conditions, spikelet sterility was negatively correlated with the number of engorged pollen grains, anther length, anther area, anther width, and stigma area. The number of engorged pollen grains and anther length were found to be facultative traits as their relationships with spikelet sterility were identified only after cold water exposure and did not exist under non-stressed conditions.

Minimising cold damage during reproductive development among temperate rice genotypes. I. Avoiding low temperature with the use of appropriate sowing time and photoperiod-sensitive varieties

Multiple-sown field trials in 4 consecutive years in the Riverina region of south-eastern Australia provided 24 different combinations of temperature and day length, which enabled the development of crop phenology models. A crop model was developed for 7 cultivars from diverse origins to identify if photoperiod sensitivity is involved in determining phenological development, and if that is advantageous in avoiding low-temperature damage. Cultivars that were mildly photoperiod-sensitive were identified from sowing to flowering and from panicle initiation to flowering. The crop models were run for 47 years of temperature data to quantify the risk of encountering low temperature during the critical young microspore stage for 5 different sowing dates. Cultivars that were mildly photoperiod-sensitive, such as Amaroo, had a reduced likelihood of encountering low temperature for a wider range of sowing dates compared with photoperiod-insensitive cultivars. The benefits of increased photoperiod sensitivity include greater sowing flexibility and reduced water use as growth duration is shortened when sowing is delayed. Determining the optimal sowing date also requires other considerations, e.g. the risk of cold damage at other sensitive stages such as flowering and the response of yield to a delay in flowering under non-limiting conditions. It was concluded that appropriate sowing time and the use of photoperiod-sensitive cultivars can be advantageous in the Riverina region in avoiding low temperature damage during reproductive development.

The interaction of nitrogen application and temperature during reproductive stage on spikelet sterility in field-grown rice

Increased grain yield in response to high rates of application of nitrogen (N) fertiliser is often limited by increased spikelet sterility, particularly under low temperature conditions in the New South Wales (NSW) rice industry. In 3 field experiments, different N rates were applied for different sowing dates to investigate the interaction between N rate and temperature during microspore development on spikelet sterility and grain yield. In one experiment the effect of water depth on spikelet sterility was also investigated. Engorged pollen production, spikelet sterility, and yield and its components were recorded. Application of N affected a few different processes that lead into spikelet sterility. Application of N at both pre-flood (PF) and panicle initiation (PI) significantly reduced the number of engorged pollen grains per anther, which was negatively correlated with spikelet sterility. Application of N and low temperature during microspore development with the absence of deep water also decreased pollen engorgement efficiency (the percentage of pollen grains that were engorged). Application of N further increased spikelet density, which, in turn, increased both spikelet sterility and grain yield. The combined effect of spikelet density and low temperature during microspore development explained the 44% of variation in the number of engorged pollen grains per anther. Grain yield was decreased by low temperature during microspore development in the shallow water when N was applied. Spikelet sterility as a result of late sowing was strongly correlated with minimum temperature during flowering. It is concluded that N application reduced pollen number per anther as a result of increased spikelet density, and this made the spikelets more susceptible to low temperature, causing increased spikelet sterility.

[An operative approach of extrapleural pneumonectomy]

We present a case of breast cancer with pleural metastasis and empyema treated with extrapleural pneumonectomy. We showed the some of technically important points for this operation. The careful preparation was needed to prevent hemorrhage from such as great vessels, bronchial arteries and intercostal arteries. Especially in this surgical procedure, we should select the best approach method to have enough surgical field for complete tumor resection. We suggest that we should make additional thoracotomy and skin incision immediately when we feel the surgical field is not wide enough during the operation. The extrapleural pneumonectomy is one of the most highly invasive operation in general thoracic surgery, so careful perioperative managements should be required.

Low temperature induced spikelet sterility in rice. I. Nitrogen fertilisation and sensitive reproductive period

Low temperature during panicle development in rice increases spikelet sterility. This effect is exacerbated by high rates of nitrogen (N) application in the field. Spikelet sterility induced by low temperature and N fertilisation was examined in glasshouse experiments to clarify the mechanisms involved. In two glasshouse experiments, 12-h periods of low (18/13�C) and high (28/23�C) day/night temperatures were imposed over periods of 5–7 days during panicle development, to determine the effects of low temperature and N fertilisation on spikelet sterility. In one experiment, 50% sunlight was imposed together with low temperature to investigate the additive effects of reduced solar radiation and low temperature. The effect of increased tillering due to N fertilisation was examined by a tiller removal treatment in the same experiment. Pollen grain number and spikelet sterility were recorded at heading and harvest, respectively. Although there was no significant effect of low temperature on spikelet sterility in the absence of applied N, low temperature greatly increased spikelet sterility as a result of a reduction in the number of engorged pollen grains per anther in the presence of applied N. Spikelet sterility was strongly correlated with the number of engorged pollen grains per anther. Low temperature during very early (late stage of spikelet differentiation–pollen mother cell stage) and peak (second meiotic division stage–early stage of extine formation) microspore development caused a severe reduction in engorged pollen production mainly as a result of reduced total pollen production. Unlike low temperature, the effect of shading was rather small. The increased tillering due to application of high rates of N, increased both spikelet number per plant and spikelet sterility under low temperature conditions. The removal of tillers as they appeared reduced the number of total spikelets per plant and maintained a large number of engorged pollen grains per anther which, in turn, reduced spikelet sterility. The number of engorged pollen grains per anther determined the numbers of intercepted and germinated pollen grains on the stigma. It is concluded that N increased tillering and spikelet number per plant and this, in turn, reduced the number of engorged pollen grains per anther, leading into increased spikelet sterility under low temperature condition.

Low temperature induced spikelet sterility in rice. II. Effects of panicle and root temperatures

Low temperatures impose restrictions on rice (Oryza sativa L.) production at high latitudes. This study is related to low temperature damage that can arise mid-season during the panicle development phase. The objective of this study was to determine whether low temperature experienced by the root, panicle, or foliage is responsible for increased spikelet sterility. In temperature-controlled glasshouse experiments, water depth, and water and air temperatures, were changed independently to investigate the effects of low temperature in the root, panicle, and foliage during microspore development on spikelet sterility. The total number of pollen and number of engorged pollen grains per anther, and the number of intercepted and germinated pollen grains per stigma, were measured. Spikelet sterility was then analysed in relation to the total number of pollen grains per spikelet and the efficiency with which these pollen grains became engorged, were intercepted by the stigma, germinated, and were involved in fertilisation. There was a significant combined effect of average minimum panicle and root temperatures on spikelet sterility that accounted for 86% of the variation in spikelet sterility. Total number of pollen grains per anther was reduced by low panicle temperature, but not by low root temperature. Whereas engorgement efficiency (the percentage of pollen grains that were engorged) was determined by both root and panicle temperature, germination efficiency (the percentage of germinated pollen grains relative to the number of engorged pollen grains intercepted by the stigma) was determined only by root temperature. Interception efficiency (i.e. percentage of engorged pollen grains intercepted by the stigma), however, was not affected by either root or panicle temperature. Engorgement efficiency was the dominant factor explaining the variation in spikelet sterility. It is concluded that both panicle and root temperature affect spikelet sterility in rice when the plant encounters low temperatures during the microspore development stage.

Crystal structure of human AUH protein, a single-stranded RNA binding homolog of enoyl-CoA hydratase

BACKGROUND

The AU binding homolog of enoyl-CoA hydratase (AUH) is a bifunctional protein that has two distinct activities: AUH binds to RNA and weakly catalyzes the hydration of 2-trans-enoyl-coenzyme A (enoyl-CoA). AUH has no sequence similarity with other known RNA binding proteins, but it has considerable sequence similarity with enoyl-CoA hydratase. A segment of AUH, named the R peptide, binds to RNA. However, the mechanism of the RNA binding activity of AUH remains to be elucidated.

RESULTS

We determined the crystal structure of human AUH at 2.2 A resolution. AUH adopts the typical fold of the enoyl-CoA hydratase/isomerase superfamily and forms a hexamer as a dimer of trimers. Interestingly, the surface of the AUH hexamer is positively charged, in striking contrast to the negatively charged surfaces of the other members of the superfamily. Furthermore, wide clefts are uniquely formed between the two trimers of AUH and are highly positively charged with the Lys residues in alpha helix H1, which is located on the edge of the cleft and contains the majority of the R peptide. A mutational analysis showed that the lysine residues in alpha helix H1 are essential to the RNA binding activity of AUH.

CONCLUSIONS

Alpha helix H1 exposes a row of Lys residues on the solvent-accessible surface. These characteristic Lys residues are named the "lysine comb." The distances between these Lys residues are similar to those between the RNA phosphate groups, suggesting that the lysine comb may continuously bind to a single-stranded RNA. The clefts between the trimers may provide spaces sufficient to accommodate the RNA bases.

[Examination of eye position after strabismus surgery in Kawasaki Medical School Hospital]

PURPOSE

To examine the factors which affect changes in the position of the eyes following the strabismus surgery.

METHODS

The postoperative position of 240 eyes with concomitant strabismus was examined. The factors which seemed to have an effect on the position of the eyes were enumerated, and a logistic regression analysis of the results was done.

RESULTS

In comparison with esotropia, in exotropia the eyes showed a tendency to return gradually to a normal position. There was no remarkable improvement in stereoscopic vision following strabismus surgery. Based on the standards of the Japanese Association of Strabismus and Amblyopia [the cure standard for strabismus], the results of strabismus surgery were as follows: Grade 1(cosmetically satisfactory) was mainly observed for esotropia, and Grade 3(good) for exotropia. The factors which had a significant effect on the postoperative position of the eyes were as follows: esotropia amblyopia, muscle movement, and operative methods; exotropia: retinal correspondence, operative methods, and the necessity of inferior oblique muscle surgery.

CONCLUSIONS

There was little correction of the position of the eyes. In individual cases, the factors which affect position of eyes were examined, and it was considered necessary to increase the amount of correction. Age is a factor which has an effect, but the effect on esotropia and exotropia is small.

Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase

Valyl-tRNA synthetase (ValRS) strictly discriminates the cognate L-valine from the larger L-isoleucine and the isosteric L-threonine by the tRNA-dependent "double sieve" mechanism. In this study, we determined the 2.9 A crystal structure of a complex of Thermus thermophilus ValRS, tRNA(Val), and an analog of the Val-adenylate intermediate. The analog is bound in a pocket, where Pro(41) allows accommodation of the Val and Thr moieties but precludes the Ile moiety (the first sieve), on the aminoacylation domain. The editing domain, which hydrolyzes incorrectly synthesized Thr-tRNA(Val), is bound to the 3' adenosine of tRNA(Val). A contiguous pocket was found to accommodate the Thr moiety, but not the Val moiety (the second sieve). Furthermore, another Thr binding pocket for Thr-adenylate hydrolysis was suggested on the editing domain.

[Effectiveness of docetaxel plus cisplatin in large cell lung cancer showing little response to prior chemotherapy with MVP]

The present patient was a 53-year-old male who had large cell lung cancer of c-T4N1M0. We administered multi-drug regimen including mitomycin C, vindesine and cisplatin (CDDP) because of cancer invasion into the great vessels seen on a chest CT. After 3 courses, the cancer showed no change in size. Therefore, we adopted chemotherapy of docetaxel (Taxotere: TXT) and CDDP. After 4 courses, the size of the mass had decreased (partial response). The only major toxic defect was grade 3 neutropenia. A good response to TXT and CDDP could lead to complete resection of lung cancer. It is suggested that TXT is effective in the treatment of large cell lung cancer.

[Preoperative evaluation of cardiac disease for patients with lung cancer: usefulness of treadmill exercise electrocardiogram]

118 patients with lung cancer who underwent treadmill exercise electrography (ECG) as part of their preoperative evaluation, were investigated for postoperative events. On the treadmill exercise ECG 27 patients were positive and 91 were negative. The more elderly patients tended to reveal ischemic findings in treadmill exercise ECG. Of the 71 patients with normal of result by ECG at rest, 15 patients (21.1%) had postoperative ischemic change on ECG. As a result, it was considered that this examination was insufficient to detect latent ischemic heart disease. The patients who had a discontinued at stage 2 or less of the Bruce protocol and had a negative result by treadmill exercise ECG, were classified as insufficient group and separated from the others. (27/118 patients). This group consisted of advanced age (p < 0.05) who tended to experience postoperative events. In the sufficient group, patients showed ischemic events predominantly on ECG at postoperative period (p < 0.01). We concluded that as preoperative screening of heart disease prior to lung cancer surgery ECG at rest was not adequate while treadmill exercise ECG was useful.

Grain nitrogen concentration differences among three sorghum hybrids with similar grain yield

The differences in grain nitrogen (N) concentration among 3 sorghum (Sorghum bicolor (L.) Moench) hybrids with similar grain yield were examined under N-limiting conditions in relation to the availability of assimilate and N to grain. Several manipulation treatments [N fertiliser application, lower leaves shading, thinning (reduced plant population), whole canopy shading, canopy opening, spikelet removal] were imposed to alter the relative N and assimilate availability to grain under full irrigation supply. Grain N concentration increased by either increased grain N availability or yield reduction while maintaining N uptake. Grain N concentration, however, did not decrease in the treatments where relative abundance of N compared with assimilate was intended to be reduced. The minimum levels of grain N concentration differed from 0.95% (ATx623/RTx430) to 1.14% (DK55plus) in these treatments. Regardless of the extent of variation in assimilate and N supply to grain, the ranking of hybrids on grain N concentration was consistent across the manipulation treatments. For the 3 hybrids examined, higher grain N concentration was associated with higher N uptake during grain filling and, to a lesser extent, with higher N mobilisation. Hybrids with larger grain N accumulation had a larger number of grains. There was no tradeoff between grain N concentration and yield, suggesting that grain protein concentration can be improved without sacrificing yield potential.

Enzyme structure with two catalytic sites for double-sieve selection of substrate

High-fidelity transfers of genetic information in the central dogma can be achieved by a reaction called editing. The crystal structure of an enzyme with editing activity in translation is presented here at 2.5 angstroms resolution. The enzyme, isoleucyl-transfer RNA synthetase, activates not only the cognate substrate L-isoleucine but also the minimally distinct L-valine in the first, aminoacylation step. Then, in a second, "editing" step, the synthetase itself rapidly hydrolyzes only the valylated products. For this two-step substrate selection, a "double-sieve" mechanism has already been proposed. The present crystal structures of the synthetase in complexes with L-isoleucine and L-valine demonstrate that the first sieve is on the aminoacylation domain containing the Rossmann fold, whereas the second, editing sieve exists on a globular beta-barrel domain that protrudes from the aminoacylation domain.

Barley yield and grain protein concentration as affected by assimilate and nitrogen availability

Two types of experiments were conducted with the malting barley cv. Grimmett to examine how assimilate and nitrogen (N) availability at different growth stages determined yield and grain protein concentration (GPC) in south-east Queensland. In one series of experiments, plants were sown in April, June, and August so that they would experience different growing conditions, and responses to N application rate were examined. Another experiment examined response of growth, yield, and GPC to variation of assimilate production pre and post anthesis, caused by the canopy manipulation treatments of opening, closure, and 50% shading at 3 different growth stages. Without N application all 3 sowings produced similar yields (1·9-2·3 t/ha), but when N was applied, yield was higher and responded more to applied N in the June sowing than in the other sowings.The different responses of grain yield to N application rate among the 3 sowing dates were not due to differences in N uptake but to the efficiency of N use; with favourable temperatures throughout crop growth, the crop sown in June utilised N most eciently to develop a large number of grainsand to produce sufficient as similates to fill these grains. When yield had a positive response to low N application rates, then there was generally no response of GPC, whereas when there was no response of grain yield to further rate of N application then GPC increased. The results of the second experiment show that N uptake depended on plant N demand at early stages of growth when N was still available in the soil, but total N content of tops at maturity was similar among canopy manipulation treatments. Canopy opening at any stage of growth tended to increase tiller number, leaf area index, and above-ground dry matter, but the effect was greater attillering stage which produced the highest yield because of the greatest number of heads. Shading reduced yield at all stages, but particularly at pre-anthesis. Shading and canopy closure during grain filling reduced grain yield, but with similar N uptake these treatments significantly increased GPC .These results indicate that GPC depends on both assimilate and N availability to grain, and GPC can increase sharply when grain yield is reduced with low assimilate availability as a result of adverse growing conditions. Responses of grain yield to applied N depended on environmental conditions, particularly the patterns of air temperature during growth, and the crop utilised N more efficiently to produce higher yield when it was not exposed to extreme temperatures during the latter stages of growth.