We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

No abstract

PD-L1 expression is a feature of Epstein-Barr virus (EBV) associated malignancies such as nasopharyngeal carcinoma (NPC). Here, we found that EBV-induced latent membrane protein 1 (LMP1) and IFN-γ pathways cooperate to regulate programmed cell death protein 1 ligand (PD-L1). Expression of PD-L1 was higher in EBV positive NPC cell lines compared with EBV negative cell lines. PD-L1 expression could be increased by exogenous and endogenous induction of LMP1 induced PD-L1. In agreement, expression of PD-L1 was suppressed by knocking down LMP1 in EBV positive cell lines. We further demonstrated that LMP1 up-regulated PD-L1 through STAT3, AP-1, and NF-κB pathways. Besides, IFN-γ was independent of but synergetic with LMP1 in up-regulating PD-L1 in NPC. Furthermore, we showed that PD-L1 was associated with worse disease-free survival in NPC patients. These results imply that blocking both the LMP1 oncogenic pathway and PD-1/PD-L1 checkpoints may be a promising therapeutic approach for EBV positive NPC patients.

Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica. Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059-2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.Oryza sativa | reference genomes | BAC-by-BAC strategy | transcriptome R ice is one of the most important food crops in the world and provides more than 20% of the caloric intake for one-half of the world's population. Asian cultivated rice can be divided into two subspecies-that is, Oryza sativa subsp. indica and O. sativa subsp. japonica-which are highly distinctive in geographical distribution, reproductively isolated, and have been shown to have extensive differentiation in genome structure and gene content (1). Indica rice accounts for more than 70% of world rice production (2) and is genetically much more diverse than japonica rice (3). Genomic studies have established that indica rice can be further subdivided into two major varietal groups, indica I and indica II, which have been independently bred and widely cultivated in China and Southeast Asia, respectively (4). Hybrids between these groups usually show strong heterosis, which provided the basis for the great success of hybrid rice in several countries, including China and the United States. For example, Zhenshan 97 (ZS97, indica I) and Minghui 63 (MH63, indica II) are the parents of the elite hybrid Shanyou 63 (SY63) (SI Appendix, Fig. S1 A and B), which exhibits superiority for a large array of agronomic traits including yield, resistance to multiple diseases, wide adaptability, and good eating quality, and thus has been the most widely cultivated hybrid in China over the past three decades (SI Appendix, Fig. S1C).Because of the importance of hybrid rice in helping to ensure a stable and secure food supply for generations, a series of attempts have been...

Patients with antiphospholipid antibodies (APLAs) are at increased risk for arterial and venous thrombosis. Many APLAs associated with these events react with ␤ 2 glycoprotein I (␤ 2 GPI), and endothelial cell reactive antibodies that activate endothelial cells in a ␤ 2 GPI-dependent manner occur commonly in these patients. We previously reported that ␤ 2 GPI binds with high affinity to annexin A2 on the endothelial surface, though the relevance of this interaction to APLA/anti-␤ 2 GPI antibodyinduced endothelial activation has not been determined. In this report, we confirm that anti-␤ 2 GPI antibodies activate endothelial cells in the presence of ␤ 2 GPI, and demonstrate that anti-annexin A2 antibodies directly cause endothelial cell activation of a similar magnitude and with a similar time course. Moreover, bivalent anti-annexin A2 F(ab) 2 fragments also caused endothelial cell activation, whereas monomeric Fab fragments not only did not cause activation, but blocked activation induced by anti-annexin A2 antibodies and F(ab) 2 fragments, as well as that caused by anti-␤ 2 GPI antibodies in the presence of ␤ 2 GPI. These observations suggest a novel pathway for endothelial activation induced by APLA/anti-␤ 2 GPI antibodies that is initiated by crosslinking or clustering of annexin A2 on the endothelial surface. (Blood. 2005;105: 1964-1969