Genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq.

BACKGROUND: Nucleotide-binding and leucine-rich repeat (NLR) genes have attracted wide attention due to their crucial role in protecting plants from pathogens. SMRT-RenSeq, combining PacBio sequencing after resistance gene enrichment sequencing (RenSeq), is a powerful method for selectively capturing and sequencing full-length NLRs. Haynaldia villosa, a wild grass species with a proven potential for wheat improvement, confers resistance to multiple diseases. So, genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq can facilitate disease resistance genes exploration. RESULTS: In this study, SMRT-RenSeq was performed to identify the genome-wide NLR complement of H. villosa. In total, 1320 NLRs were annotated in 1169 contigs, including 772 complete NLRs. All the complete NLRs were phylogenetically analyzed and 11 main clades with special characteristics were derived. NLRs could be captured with high efficiency when aligned with cloned R genes, and cluster expansion in some specific gene loci was observed. The physical location of NLRs to individual chromosomes in H. villosa showed a perfect homoeologous relationship with group 1, 2, 3, 5 and 6 of other Triticeae species, however, NLRs physically located on 4VL were largely in silico predicted to be located on the homoeologous group 7. Fifteen types of integrated domains (IDs) were integrated in 52 NLRs, and Kelch and B3 NLR-IDs were found to have expanded in H. villosa, while DUF948, NAM-associated and PRT_C were detected as unique integrated domains implying the new emergence of NLR-IDs after H. villosa diverged from other species. CONCLUSION: SMRT-RenSeq is a powerful tool to identify NLR genes from wild species using the baits of the evolutionary related species with reference sequences. The availability of the NLRs from H. villosa provide a valuable library for R gene mining and transfer of disease resistance into wheat.

Salicylic Acid Regulates Indole-3-Carbinol Biosynthesis Under Blue Light in Broccoli Sprouts (Brassica oleracea L.).

Indole-3-carbinol (I3C), an important secondary metabolite with strong anti-cancer ability, is widely found in cruciferous plants. Light and phytohormones are one of the most important external and internal signals, respectively, that control the growth, development, and secondary metabolism of the plant life cycle. However, there are few studies about the influence of the blue light and salicylic acid (SA) on the regulation of I3C accumulation. In this study, a negative correlation was found between the content of I3C and SA in different species. Among this, broccoli and Arabidopsis thaliana were chosen for further studies. We observed that blue light treatment increased the accumulation of I3C, and exogenous SA treatment significantly inhibited the accumulation of I3C in broccoli sprouts. Based on the RNA sequence, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that blue light promoted the enrichment of differentially expressed genes (DEGs) in plant hormone signal transduction pathways. More specifically, downregulated expression of genes related to SA biosynthesis and upregulated expression of I3C genes related to metabolic pathway were observed under blue light. Taken together, these results suggested that SA negatively regulates blue light-induced I3C accumulation in broccoli sprouts.

Pharmacogenetic and germline prognostic markers of lung cancer.

INTRODUCTION: Lung cancer is the leading global cause of cancer-related mortality. Interindividual variability in treatment response and cancer outcomes has focused attention on genetic polymorphisms as prognostic markers. We evaluated the overall contribution of candidate polymorphism association studies to our current understanding of the genetic predictors of lung cancer outcomes. METHODS: We examined the results of 90 studies that evaluated associations between genetic polymorphisms and lung cancer outcomes published between January 1990 and May 2009. RESULTS: A total of 170 genetic variations in 90 studies were identified. Overall survival was a primary outcome in 81% of the studies and toxicity in 19%. Candidate polymorphisms in the DNA repair/synthesis pathway were the most frequently studied. Strong evidence in large-scale confirmatory studies of any single polymorphism was lacking. Polymorphisms of EGFR, XRCC1, and ERCC1 were associated with pharmacogenetic outcomes, whereas polymorphisms of MDM2, p53, and GSTM1 were associated with prognostic outcomes. All remaining polymorphisms had results lacking or failing replication testing. Heterogeneity in study populations, incomplete reporting of important population or study characteristics, inadequate power, and inconsistencies in methodology were common. CONCLUSIONS: Although the quality of existing studies involving the candidate polymorphism approach is highly variable, a small set of candidate polymorphisms was identified as potential biomarkers of clinical or pharmacogenetic outcome and would benefit from further replication testing. Newer approaches including haplotype tagging, pathway, genome-wide association, and combination methods with validative approaches may facilitate a more accurate prediction of lung cancer outcomes by genetic variation.

Soluble mesothelin-related Peptide and osteopontin as markers of response in malignant mesothelioma.

PURPOSE: In malignant mesothelioma (MM), radiologic assessment of disease status is difficult. Both soluble mesothelin-related peptide (SMRP) and osteopontin (OP) have utility in distinguishing MM from benign pleural disease. We evaluated whether SMRP and OP also correlated with the disease course of MM. PATIENTS AND METHODS: Serial plasma samples from patients with MM were prospectively collected, and SMRP and OP levels were measured. Radiologic tests across time periods showing disease progression, stability, or shrinkage were compared with corresponding changes in SMRP/OP levels. RESULTS: From 41 patients, 165 samples were collected (range, 2 to 10; median 4). At study entry, 37 of 41 patients had measurable disease, of whom 92% (34 of 37) had elevated baseline SMRP levels; four of 41 patients had no evidence of recurrence and each had normal baseline SMRP levels. In 21 patients receiving systemic therapy, percentage change in SMRP more than 10% correlated with the radiologic assessment by a trained thoracic radiologist (P < .001), by formal Response Evaluation Criteria in Solid Tumors (RECIST; P = .008), or by modified RECIST (P < .001). All seven patients who underwent surgical resection with negative margins had elevated preoperative SMRP levels that fell to normal postoperatively. Rising SMRP was observed in all patients with radiologic disease progression. No associations were found with OP. CONCLUSION: Percentage changes in SMRP levels, but not changes in OP levels, are a potentially useful marker of disease course. These findings should be validated prospectively for a role as an objective adjunctive measure of disease course in both clinical trials and clinical practice.