X.L. Wang

A draft sequence of the rice genome (Oryza sativa L. ssp indica)

The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole-genome shotgun sequencing. The assembled sequence covers 93% of the 420-megabase genome. Gene predictions on the assembled sequence suggest that the genome contains 32,000 to 50,000 genes. Homologs of 98% of the known maize, wheat, and barley proteins are found in rice. Synteny and gene homology between rice and the other cereal genomes are extensive, whereas synteny with Arabidopsis is limited. Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops.

Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis

The genetic diversity of Yersinia pestis, the etiologic agent of plague, is extremely limited because of its recent origin coupled with a slow clock rate. Here we identified 2,326 SNPs from 133 genomes of Y. pestis strains that were isolated in China and elsewhere. These SNPs define the genealogy of Y. pestis since its most recent common ancestor. All but 28 of these SNPs represented mutations that happened only once within the genealogy, and they were distributed essentially at random among individual genes. Only seven genes contained a significant excess of nonsynonymous SNP, suggesting that the fixation of SNPs mainly arises via neutral processes, such as genetic drift, rather than Darwinian selection. However, the rate of fixation varies dramatically over the genealogy: the number of SNPs accumulated by different lineages was highly variable and the genealogy contains multiple polytomies, one of which resulted in four branches near the time of the Black Death. We suggest that demographic changes can affect the speed of evolution in epidemic pathogens even in the absence of natural selection, and hypothesize that neutral SNPs are fixed rapidly during intermittent epidemics and outbreaks.

An atlas of DNA methylomes in porcine adipose and muscle tissues

It is evident that epigenetic factors, especially DNA methylation, have essential roles in obesity development. Here, using pig as a model, we investigate the systematic association between DNA methylation and obesity. We sample eight variant adipose and two distinct skeletal muscle tissues from three pig breeds living within comparable environments but displaying distinct fat level. We generate 1,381 Gb of sequence data from 180 methylated DNA immunoprecipitation libraries, and provide a genome-wide DNA methylation map as well as a gene expression map for adipose and muscle studies. The analysis shows global similarity and difference among breeds, sexes and anatomic locations, and identifies the differentially methylated regions. The differentially methylated regions in promoters are highly associated with obesity development via expression repression of both known obesity-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of adipose deposition and muscle growth.

Search for ferromagnetism in SnO2 doped with transition metals (V, Mn, Fe, and Co)

Based on first-principles calculations, we have investigated electronic structures and magnetic properties of SnO2 doped with V, Mn, Fe, and Co. Our results show that ferromagnetism is the ground state and that the Curie temperatures are expected to have high values for Fe-?and Co-doped SnO2, which is in good agreement with the experimental observations (Ogale et al 2003 Phys. Rev. Lett. 91 077205; Coey et al 2004 Appl. Phys. Lett. 84 1332). However, in V-?and Mn-doped SnO2, paramagnetism is more stable than ferromagnetism. In addition, we also probe the effect of an oxygen vacancy. The results exhibit that an oxygen vacancy strongly influences the magnetic properties of these doped systems, and an oxygen vacancy strongly attracts Fe and Co ions. As a result, transition metal?oxygen vacancy?transition metal groups will be common in Fe-?and Co-doped SnO2, but this tendency does not exist in the cases of V?and Mn doping. In V-doped SnO2, ferromagnetism becomes more stable than antiferromagnetism after inducing additional n-type carriers and the Curie temperature increases with increasing density of n-type carriers. Hence, raising the density of n-type carriers is a practical way to realize high Curie temperatures in V-doped SnO2.

A draft sequence of the rice (Oryza sativa ssp.indica) genome

The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a “whole genome shotgun” approach, we have produced a draft rice genome sequence ofOryza sativa ssp.indica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from anindica variant cultivar93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEMBLER, a custom-designed software package used for the initial assembly, were verified rigorously by comparisons against finished BAC clone sequences from bothindica andjapanica strains, available from the public databases. Over all, 96.3% of full-length cDNAs, 96.4% of STS, STR, RFLP markers, 94.0% of ESTs and 94.9% unigene clusters were identified from the draft sequence. Our preliminary analysis on the data set shows that our rice draft sequence is consistent with the comman standard accepted by the genome sequencing community. The unconditional release of the draft to the public also undoubtedly provides a fundamental resource to the international scientific communities to facilitate genomic and genetic studies on rice biology.

Hydrogen sensors based on AlGaN/AlN/GaN HEMT

Pt/AlGaN/AlN/GaN high electron mobility transistors (HEMT) were fabricated and characterized for hydrogen sensing. Pt and Ti/Al/Ni/Au metals were evaporated to form the Schottky contact and the ohmic contact, respectively. The sensors can be operated in either the field effect transistor (FET) mode or the Schottky diode mode. Current changes and time dependence of the sensors under the FET and diode modes were compared. When the sensor was operated in the FET mode, the sensor can have larger current change of 8mA, but its sensitivity is only about 0.2. In the diode mode, the current change was very small under the reverse bias but it increased greatly and gradually saturated at 0.8mA under the forward bias. The sensor had much higher sensitivity when operated in the diode mode than in the FET mode. The oxygen in the air could accelerate the desorption of the hydrogen and the recovery of the sensor.

The growth of high-Al-content InAlGaN quaternary alloys by RF-MBE

High-Al-content InxAlyGa1-x-yN (x = 1-10%, y = 34-45%) quaternary alloys were grown on sapphire by radio-frequency plasma-excited molecular beam epitaxy. Rutherford back-scattering spectrometry, high resolution x-ray diffraction and cathodoluminescence were used to characterize the InAlGaN alloys. The experimental results show that InAlGaN with an appropriate Al/In ratio (near 4.7, which is a lattice-match to the GaN under-layer) has better crystal and optical quality than the InAlGaN alloys whose Al/In ratios are far from 4.7. Some cracks and V-defects occur in high-Al/In-ratio InAlGaN alloys. In the CL image, the cracks and V-defect regions are the emission-enhanced regions.

Gene identification and expression analysis of 86,136 Expressed Sequence Tags (EST) from the rice genome.

Expressed Sequence Tag (EST) analysis has pioneered genome-wide gene discovery and expression profiling. In order to establish a gene expression index in the rice cultivar indica, we sequenced and analyzed 86,136 ESTs from nine rice cDNA libraries from the super hybrid cultivar LYP9 and its parental cultivars. We assembled these ESTs into 13,232 contigs and leave 8,976 singletons. Overall, 7,497 sequences were found similar to the existing sequences in GenBank and 14,711 are novel. These sequences are classified by molecular function, biological process and pathways according to the Gene Ontology. We compared our sequenced ESTs with the publicly available 95,000 ESTs from japonica, and found little sequence variation, despite the large difference between genome sequences. We then assembled the combined 173,000 rice ESTs for further analysis. Using the pooled ESTs, we compared gene expression in metabolism pathway between rice and Arabidopsis according to KEGG. We further profiled gene expression patterns in different tissues, developmental stages, and in a conditional sterile mutant, after checking the libraries are comparable by means of sequence coverage. We also identified some possible library specific genes and a number of enzymes and transcription factors that contribute to rice development.

Al compositional inhomogeneity of AlGaN epilayer with a high Al composition grown by metal–organic chemical vapour deposition

The Al compositional distribution of AlGaN is investigated by cathodoluminescence (CL). Monochromatic CL images and CL spectra reveal a lateral Al compositional inhomogeneity, which corresponds to surface hexagonal patterns. Cross-sectional CL images show a relatively uniform Al compositional distribution in the growth direction, indicating columnar growth mode of AlGaN films. In addition, a thin AlGaN layer with lower Al composition is grown on top of the buffer AlN layer near the bottom of the AlGaN epilayer because of the larger lateral mobility of Ga adatoms on the growth surface and their accumulation at the grain boundaries.

Structural properties and Raman measurement of AlN films grown on Si (111) by NH3-GSMBE

Epitaxial growth of AlN has been performed by molecular beam epitaxy (MBE) with ammonia. The structural properties of materials were studied by cross-sectional transmission electron microscopy (TEM), X-ray diffraction (XRD), and atomic force microscopy (AFM). XRD and TEM diffraction pattern confirm the AlN is single crystalline 2H-polytype with the epitaxial relationship of (0001)AlNparallel to(111)Si, [11 (2) over bar0](AlN)parallel to[110](Si), [10 (1) over bar0](AlN)parallel to[11 (2) over bar](Si). Micro-Raman scattering measurement shows that the E-2 (high) and A(1) (LO) phonon mode shift 9 cm(-1) toward the low frequency, which shows the existence of large tensile strain in the AlN films. Furthermore, the appearance of forbidden A, (TO) mode and its anomalous shift toward high frequency was found and explained