Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within-and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence-absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding.Asian cultivated rice is grown worldwide and comprises the staple food for half of the global population. It is envisaged that by the year 2035 1 feeding this growing population will necessitate that an additional 112 million metric tons of rice be produced on a smaller area of land, using less water and under more fluctuating climatic conditions, which will require that future rice cultivars be higher yielding and resilient to multiple abiotic and biotic stresses. The foundation of the continued improvement of rice cultivars is the rich genetic diversity within domesticated populations and wild relatives [2][3][4] . For over 2,000 years, two major types of O. sativa-O. sativa Xian group (here referred to as Xian/Indica (XI) and also known as , Hsien or Indica) and O. sativa Geng Group (here referred to as Geng/Japonica (GJ) and also known as , Keng or Japonica)-have historically been recognized [5][6][7] . Varied degrees of post-reproductive barriers exist between XI and GJ rice accessions 8 ; this differentiation between XI and GJ rice types and the presence of different varietal groups are well-documented at isozyme and DNA levels 6,9 . Two other distinct groups have also been recognized using molecular markers 10 ; one of these encompasses the Aus, Boro and Rayada ecotypes from Bangladesh and India (which we term the circum-Aus group (cA)) and the other comprises the famous Basmati and Sadri aromatic varieties (which we term the circum-Basmati group (cB)).Approximately 780,000 rice accessions are available in gene banks worldwide 11 . To enable the more efficient use of these accessions in future rice improvement, the Chinese Academy of Agricultural Sciences, BGI-Shenzhen and International Rice Research Institute sequenced over 3,000 rice genomes (3K-RG) as part of the 3,000 Rice Genomes Project 12. Here we present analyses of genetic variation in the 3K-RG that focus on important aspects of O. sativa diversity, single nucleotide polymorphisms (SNPs) and structural variation (deletions, duplications, inversions and translocations). We also construct a species pangenome consisting of 'core...

Palladium (Pd) nanoparticles were deposited on the surface of halloysite nanotubes (HNTs) modified with γ-aminopropyltriethoxysilane (APTES) to produce Pd/NH2-HNTs nanocomposites. The results indicated that Pd nanoparticles were densely immobilized onto NH2-HNTs with an average diameter of ~ 3 nm. The Pd distribution on the surface of silanized HNTs showed much more uniform, and the Pd nanoparticle size became smaller compared with those directly deposited onto HNTs without silanization. Systematic characterization demonstrated that APTES were chemically bonded onto HNTs, and further confirmed the bond formation between Pd and -NH2 groups, which could ensure the firm deposit of Pd nanoparticles on the surface of silanized HNTs. The as-synthesized Pd/NH2-HNTs exhibited an excellent catalytic activity in the liquid-phase hydrogenation of styrene to ethylbenzene with full conversion within 30 min. The mechanism of the deposit of Pd nanoparticles on silanized HNTs was also investigated.

Purpose: Chemokine receptors are implicated in metastasis of several malignant tumors. This study was done to evaluate the contribution of chemokine receptors CXCR4 and CCR7 to metastasis of human nasopharyngeal carcinoma. Experimental Design: Reverse transcription-PCR, immunohistochemistry, and flow cytometry were used to evaluate mRNA and protein expression of CXCR4 and CCR7 in nasopharyngeal carcinoma tumor tissues and cell lines. Chemotaxis assays were used to evaluate the function of CXCR4 in nasopharyngeal carcinoma cells. Antisense CXCR4 was used to inhibit receptor expression and to block metastasis of human nasopharyngeal carcinoma cells in vivo in athymic mice. Results: CXCR4 protein was detected in tumor cells in 31of 40 primary human nasopharyngeal carcinoma and in 13 of 15 lymph node metastases. CXCR4 transcripts were detected in eight CXCR4 protein^positive primary nasopharyngeal carcinoma tissues and seven nasopharyngeal carcinoma cell lines tested. On the other hand, the transcripts for CCR7 were detected only in four primary nasopharyngeal carcinoma tissues and in none of the nasopharyngeal carcinoma cell lines. In functional experiments, metastatic nasopharyngeal carcinoma cell lines that expressed high levels of CXCR4 were found to migrate in response to the CXCR4 ligand SDF-1a. Transfection of antisense CXCR4 in metastatic nasopharyngeal carcinoma cells inhibited the expression of CXCR4 and SDF-1a-induced cell migration in vitro and reduced the capacity of the tumor cells to form metastasis in the lungs and lymph nodes when injected in athymic mice. Conclusion:The expression of functional CXCR4 but not CCR7 is correlated with the metastatic potential of human nasopharyngeal carcinoma cells. Therefore, CXCR4 may be considered as a potential target for the prevention of nasopharyngeal carcinoma metastasis.

Human T lymphocytes, bearing T cell receptor (TCR) ␥␦, play an important role in anti-tumor/microbe immune responses. However, few tumor antigens recognized by TCR␥␦ have been defined so far. To investigate antigenic epitopes/proteins recognized by ␥␦T cells, we have established a new immunobiochemical strategy that uses complementarity-determining region 3 of TCR ␦ chain (CDR3␦) peptide-mediated epitope/protein-binding assays. CDR3␦ peptides synthesized using the CDR3 region in TCR V␦2 chain were validated for their binding specificity to target cells or tissues. These CDR3␦ peptides were then employed as probes to pan putative epitopes in a 12-mer random peptide phage-displayed library and to identify putative protein ligands within tumor protein extracts by affinity chromatography and liquid chromatography/electrospray ionizationtandem mass spectrometry analysis. As a result, we have identified nine peptides and two proteins for TCR␥␦, including human mutS homolog 2 (hMSH2) and heat shock protein (HSP) 60. All nine tested epitope peptides not only bind to ␥␦T cells but also functionally activate ␥␦T cells in vitro. Identification of HSP60 confirms the validity of this method as HSP60 is an identified ligand for TCR␥␦. We show that hMSH2 is expressed on the surface of SKOV3 tumor cells, and cytotoxicity of V␦2 ␥␦T cells to SKOV3 cells was blocked by anti-hMSH2 antibody, suggesting that hMSH2 may be a new ligand for TCR␥␦. Taken together, our findings provide a novel immunobiochemical strategy to identify epitopes/proteins recognized by ␥␦T cells. T lymphocytes are classified structurally into two types according to different T cell receptors (TCR)3 ␣␤ or ␥␦. TCR␣␤ specifically recognize antigenic peptides (epitopes) presented by MHC I/II molecules. Although many peptide ligands have been identified for TCR␣␤ (1), only a few ligands have been identified for TCR␥␦ so far (2, 3).Human ␥␦T cells account for ϳ5% of CD3 ϩ T cells in the peripheral blood, but constitute a major T cell subset in other anatomic locations, such as the intestine. In the peripheral blood of healthy individuals, TCR V␦2 chain pairing with one particular V␥9 chain is expressed on 50 -90% of the ␥␦T cells, whereas intestinal intraepithelial ␥␦T cells frequently express the V␦1 gene, which can associate with different V␥ elements (4). The antigen-binding site of TCR␥␦ is formed primarily from three complementarity-determining regions (CDRs) contributed by each V␥ and V␦ domain. CDR1 and CDR2 fragments are encoded by germ line V genes, whereas the CDR3 is formed by somatic rearrangement of V(D) and J fragments. Sequence diversity in antigen receptors is not evenly distributed among all six CDRs but is highly concentrated in one or two CDR3. It had been proposed that the principal antigen specificity of an immunoglobulin or TCR is derived from its most diverse CDR3 fragments (5).In addition to TCR diversity, structures of the TCR-CD3 complex, and tissue distribution, the pattern of antigenic recognition is another key difference between ␥␦T cel...

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