No abstract

Although many studies have addressed the prognostic value of programmed cell death-ligand 1 (PD-L1) expression in lung cancer, the results remain controversial. A systematic search of the PubMed, EMBASE, and Cochrane Library databases was performed to identify the correlation between PD-L1 expression and driver mutations and overall survival (OS). This meta-analysis enrolled a total of 11,444 patients for 47 studies, and the pooled results showed that increased PD-L1 expression was associated with poor prognosis (HR = 1.40, 95% CI: 1.19–1.65, P < 0.001). In subgroup analysis stratified according to histology types, the pooled results demonstrated that increased PD-L1 expression was an unfavorable prognostic factor for non-small cell lung cancer (NSCLC) (HR = 1.26, 95% CI: 1.05–1.52, P = 0.01) and pulmonary lymphoepithelioma-like carcinoma (LELC) (HR = 3.04, 95% CI: 1.19–7.77, P = 0.02), rather than small cell lung cancer (SCLC) (HR = 0.62, 95% CI: 0.27–1.39, P = 0.24). The pooled ORs indicated that PD-L1 expression was associated with gender, smoking status, histology, differentiation, tumour size, lymph nodal metastasis, TNM stage and EGFR mutation. However, PD-L1 expression was not correlated with ALK rearrangement and KRAS mutations.

The recently discovered aging-dependent large accumulation of point mutations in the human fibroblast mtDNA control region raised the question of their occurrence in postmitotic tissues. In the present work, analysis of biopsied or autopsied human skeletal muscle revealed the absence or only minimal presence of those mutations. By contrast, surprisingly, most of 26 individuals 53 to 92 years old, without a known history of neuromuscular disease, exhibited at mtDNA replication control sites in muscle an accumulation of two new point mutations, i.e., A189G and T408A, which were absent or marginally present in 19 individuals younger than 34 years. These two mutations were not found in fibroblasts from 22 subjects 64 to 101 years of age (T408A), or were present only in three subjects in very low amounts (A189G). Furthermore, in several older individuals exhibiting an accumulation in muscle of one or both of these mutations, they were nearly absent in other tissues, whereas the most frequent fibroblast-specific mutation (T414G) was present in skin, but not in muscle. Among eight additional individuals exhibiting partial denervation of their biopsied muscle, four subjects >80 years old had accumulated the two muscle-specific point mutations, which were, conversely, present at only very low levels in four subjects <40 years old. The striking tissue specificity of the muscle mtDNA mutations detected here and their mapping at critical sites for mtDNA replication strongly point to the involvement of a specific mutagenic machinery and to the functional relevance of these mutations. R ecently, the discovery of an aging-dependent large accumulation of point mutations in the control region for mtDNA replication of human skin fibroblasts has been reported (1). Particularly striking was the demonstration, in a generally high proportion of molecules (up to 50%), of a T to G transversion at position 414 in the original Cambridge sequence (2), within the promoter for the synthesis of the RNA primer of mtDNA heavy (H)-strand synthesis (3) and for light (L)-strand transcription (4). This mutation was present in more than 50% of the individuals above 65 years of age and absent in younger individuals. In the present work, to investigate the occurrence of these aging-dependent mutations in other cell types, in particular, in postmitotic cells, a screening was carried out for the detection in human muscle of aging-related specific point mutations in the DLP4 and DLP6 segments of the main mtDNA control region, which were the segments previously found to carry the fibroblast mtDNA mutations (1). These two mtDNA segments correspond to one of the hypervariable portions of the main control region (5), and were chosen, for the purpose of analysis, as containing each a uniform melting domain (Y.M., unpublished data). They carry critical sequences for mtDNA replication (Fig. 1A). In particular, DLP4 contains the primary origin of H-strand mtDNA synthesis (O H1 ) (3), whereas DLP6 contains the promoter and start site for H-strand replication RNA...

Development of core collections is an effective tool to extensively characterize large germplasm collections, and the use of a mini-core subsampling strategy further increases the effectiveness of genetic diversity analysis at detailed phenotype and molecular levels. We report the formation of a mini-core subset containing 217 entries derived from 1794 core entries representing the genetic diversity found in more than 18,000 accessions of the USDA-ARS rice (Oryza sativa L.) germplasm collection. The mini-core was developed with PowerCore software on the basis of 26 phenotypic traits and 70 molecular markers. The 217 entries in the mini-core had a similar distribution over 15 geographical regions, with 1794 entries in the original core collection. The resultant mini-core had 6.3% of mean difference (MD%), 16.5% of variance difference (VD%), 102.7% of variable rate (VR%), and 97.5% of coincidence rate (CR%) with the core collection, which brought about full coverage of 26 traits. All 962 alleles identifi ed by the 70 markers in the core collection were captured in the mini-core, which maximized allelic richness up to 100% and resulted in an average genetic diversity (Nei index) of 0.76, ranging from 0.37 to 0.97 among the markers. In conclusion, the mini-core presented in this study is a highly suitable and representative subset of the USDA rice core collection as well as the entire USDA-ARS rice germplasm holdings.

With the aim of identifying rice (Oryza spp.) germplasm having enhanced grain nutritional value, the mineral nutrient and trace element concentrations (or ionome) of whole (unmilled) grains from a set of 1763 rice accessions of diverse geographic and genetic origin were evaluated. Seed for analysis of p, Mg, K, S, Ca, As, Cd, Co, Cu, Fe, Mn, Mo, Ni, rb, Sr, and Zn concentrations by inductively coupled plasma mass spectrometry was produced over 2 yr in Beaumont, TX, under both flooded and unflooded watering regimes. The distributions of all element concentrations analyzed were skewed toward higher concentration. A significant portion of this ionomic variation has a genetic basis (broad sense heritabilities 0.14-0.75), indicating an ability to breed for improved grain concentration of all elements except possibly Ni. Variation in grain elemental concentrations was not strongly associated with plant height, heading time, or grain shape, suggesting these physiological factors are not of primary importance in controlling ionomic variation in rice grain. Accessions high in specific elements were sometimes found to have similar genetic or geographic origins, suggesting they share a heritable mechanism underlying their enhanced ionomes. For example, accessions with high Ca, Mg, or K were more common in the indica than in the japonica subgroup; low As was most common among temperate japonica accessions; and several lines high in Mo originated in Malaysia or adjacent Brunei.

Field experiments in 1988 and 1989 identified rice accessions from the USDA-ARS rice germplasm collection for allelopathic effects to ducksalad [Heteranthera limosa (Sw.) Willd.]. About 10000 accessions were evaluated; 347 accessions had apparent allelopathic activity. Accessions that had demonstrated allelopathic activity to ducksalad in 1988 or 1989 were evaluated further for allelopathic activity in 1990 (67 accessions) and 1991 (47 accessions). In 1990, 12 accessions had a radius of activity of 0.18-0.20 m and 80-90% weed control within the area of activity. In 1991, 12 different accessions had a radius of activity of 0.13-0.18 m and 50-85% weed control in the area of activity.

The exact cause of straighthead is unknown, but independent studies have shown that straighthead is in-Straighthead disease is a physiological disorder of rice (Oryza sacreased by consistent flood (Wells and Gilmour, 1977; tiva L.) characterized by sterility of the florets leading to reduced Wilson et al., 2001), sandy to silt loam textured soils grain yield. Knowledge of the straighthead response of new cultivars (Collier, 1912;Adair et al., 1973), low soil pH and low is important for producer control of this disease, and identification of resistant germplasm is essential for breeding improved cultivars. free iron (Baba and Harada, 1954), rich organic matter The objectives of this study were to characterize U.S. cultivar reactions in soil (Jones et al., 1938, p. 28), and high arsenic (As) to straighthead and search for resistant germplasm. Twelve lines, inlevel in the soil (Wells and Gilmour, 1977; Horton et al., cluding 10 U.S. cultivars, a Chinese and Japanese cultivar, were tested 1983). Straighthead has been frequently observed when for straighthead reaction induced by monosodium methanearsonate rice is grown on land where As has accumulated from (MSMA) at 0, 6.7, and 9.0 kg ha Ϫ1 under nitrogen fertilizer of 0, 67, previous applications of herbicides with an As base such 134, and 269 kg N ha Ϫ1 in 1999 and 2000. Straighthead delayed heading as monosodium methanearsonate (MSMA) (Gilmour date, shortened plant height, and dramatically reduced grain yield. and Wells, 1980). Cocodrie, Mars, Kaybonnet, and Bengal were highly susceptible to MSMA is a popular herbicide in cotton (Gossypium straighthead with ratings from 7.2 to 8.0 and grain yield reductions spp.) production in the USA; therefore, rice fields with from 80 to 96%. Wells, LaGrue, Drew, Cypress, and Japan 92.09.31 were a cotton growing history usually have residual As (Gilsusceptible with ratings from 5.9 to 6.7 and yield reductions from 49 mour and Wells, 1980). Residual As chemicals in the soil to 73%. Priscilla and Jefferson were tolerant with ratings of 4.9 and have been shown to cause injuries in rice that are similar 5.3, and yield reductions of 24 and 36%, respectively. The Chinese indica cultivar Zhe 733 was essentially immune to straighthead, show-to straighthead (Baker et al., 1976; Schweizer, 1967; Wells ing neither symptoms nor detectable yield reduction. A total of 124 and Gilmour, 1977; Gilmour and Wells, 1980). Wells and Chinese cultivars including 109 indica and 15 japonica were evaluated Gilmour (1977) noted that cultivars showing tolerance for straighthead resistance in 2001. Nineteen cultivars, 18 indica and to MSMA also appeared to be resistant to straighthead. 1 japonica, were identified as straighthead resistant. Grain yields of On the basis of this observation, a straighthead testing the resistant cultivars were not significantly reduced by their straightarea based on the application of MSMA has been estabhead ratings of 1 to 3. Variation in yield, plant height, maturity, and lished at the University of Arkansas, Rice Research...

A valuable core collection that is a subset of a whole germplasm collection should capture most of the variation present in the whole collection, while allowing for more efficient evaluation and management due to smaller size. The United States Department of Agriculture (USDA) rice (Oryza sativa L.) core subset (RCS), assembled by stratified random sampling, consists of 1790 entries from 114 countries and represents approximately 10% of the 18412 accessions in the rice whole collection (RWC). Data for this study were obtained from the USDA germplasm system at http://www.ars-grin.gov for the RWC and from an evaluation conducted in 2002 for the RCS. Comparative analysis for frequency distributions of 14 descriptors demonstrated that the RCS was highly correlated with the RWC (r = 0.94, P < 0.0001). Thus, information drawn from the RCS could be effectively used to assess the RWC with 88% certainty. Correlation coefficients between the RCS and the RWC for eight descriptors were ≥ 0.9, indicating that the RCS was highly representative of the RWC. Correlation coefficients for the other six descriptors were lower (0.65–0.88), but still significant.