bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expressional and Biochemical Characterization of Rice Disease Resistance Gene Xa3/Xa26 Family
Authors: Xu Songjie , Cao Yinglong , Li Xianghua , Wang Shiping 
Published: June 2007

AbstractThe rice (Oryza sativa L.) Xa3/Xa26 gene, conferring race‐specific resistance to bacterial blight disease and encoding a leucine‐rich repeat (LRR) receptor kinase‐like protein, belongs to a multigene family consisting of tandem clustered homologous genes, colocalizing with several uncharacterized genes for resistance to bacterial blight or fungal blast. To provide more information on the expressional and biochemical characteristics of the Xa3/Xa26 family, we analyzed the family members. Four Xa3/Xa26 family members in the indica rice variety Teqing, which carries a bacterial blight resistance gene with a chromosomal location tightly linked to Xa3/Xa26, and five Xa3/Xa26 family members in the japonica rice variety Nipponbare, which carries at least one uncharacterized blast resistance gene, were constitutively expressed in leaf tissue. The result suggests that some of the family members may be candidates of these uncharacterized resistance genes. At least five putative N‐glycosylation sites in the LRR domain of XA3/XA26 protein are not glycosylated. The XA3/XA26 and its family members MRKa and MRKc all possess the consensus sequences of paired cysteines, which putatively function in dimerization of the receptor proteins for signal transduction, immediately before the first LRR and immediately after the last LRR. However, no homo‐dimer between the XA3/XA26 molecules or hetero‐dimer between XA3/XA26 and MRKa or MRKc were formed, indicating that XA3/XA26 protein might function either as a monomer or a hetero‐dimer formed with other protein outside of the XA3/XA26 family. These results provide valuable information for further extensive investigation into this multiple protein family.
Development of Oryza rufipogon and O. sativa Introgression Lines and Assessment for Yield‐related Quantitative Trait Loci
Authors: Tan Lubin , Liu Fengxia , Xue Wei , Wang Guijuan , Ye Sheng , Zhu Zuofeng , Fu Yongcai , Wang Xiangkun , Sun Chuanqing 
Published: June 2007

AbstractIntrogression lines population was effectively used in mapping quantitative trait loci (QTLs), identifying favorable genes, discovering hidden genetic variation, evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research. In this study, an advanced backcross and consecutive selfing strategy was used to develop introgression lines (ILs), which derived from an accession of Oryza rufipogon Griff. collected from Yuanjiang County, Yunnan Province of China, as the donor, and an elite indica cultivar Teqing (O. sativa L.), as the recipient. Introgression segments from O. rufipogon were screened using 179 polymorphic simple sequence repeats (SSR) markers in the genome of each IL. Introgressed segments carried by the introgression lines population contained 120 ILs covering the whole O. rufipogon genome. The mean number of homozygous O. rufipogon segments per introgression line was about 3.88. The average length of introgressed segments was approximate 25.5 cM, and about 20.8% of these segments had sizes less than 10 cM. The genome of each IL harbored the chromosomal fragments of O. rufipogon ranging from 0.54% to 23.7%, with an overall average of 5.79%. At each locus, the ratio of substitution of O. rufipogon alleles had a range of 1.67‐9.33, with an average of 5.50. A wide range of alterations in morphological and yield‐related traits were also found in the introgression lines population. Using single‐point analysis, a total of 37 putative QTLs for yield and yield components were detected at two sites with 7%‐20% explaining the phenotypic variance. Nineteen QTLs (51.4%) were detected at both sites, and the alleles from O. rufipogon at fifteen loci (40.5%) improved the yield and yield components in the Teging background. These O. rufipogon ‐O. sativa introgression lines will serve as genetic materials for identifying and using favorable genes from common wild rice.
Genome‐wide Analysis of Kelch Repeat‐containing F‐box Family
Authors: Sun Yujin , Zhou Xiaofan , Ma Hong 
Published: June 2007

AbstractThe ubiquitin‐dependent protein degradation pathway plays diverse roles in eukaryotes. Previous studies indicate that both F‐box and Kelch motifs are common in a variety of organisms. F‐box proteins are subunits of E3 ubiquitin ligase complexes called SCFs (SKP1, Cullin1, F‐box protein, and Rbx1); they have an N‐terminal F‐box motif that binds to SKP1 (S‐phase kinase associated protein), and often have C‐terminal protein‐protein interaction domains, which specify the protein substrates for degradation via the ubiquitin pathway. One of the most frequently found protein interaction domains in F‐box proteins is the Kelch repeat domain. Although both the F‐box and Kelch repeats are ancient motifs, Kelch repeats‐containing F‐box proteins (KFB) have only been reported for human and Arabidopsis previously. The recent sequencing of the rice genome and other plant genomes provides an opportunity to examine the possible evolution history of KFB. We carried out extensive BLAST searches to identify putative KFBs in selected organisms, and analyzed their relationships phylogenetically. We also carried out the analysis of both gene duplication and gene expression of the KFBs in rice and Arabidopsis. Our study indicates that the origin of KFBs occurs before the divergence of animals and plants, and plant KFBs underwent rapid gene duplications.
Micro RNAs and Short‐interfering RNAs in Plants
Authors: Sunkar Ramanjulu , Zhu Jian‐Kang 
Published: June 2007

AbstractGene silencing can occur either at the transcriptional level or post‐transcriptional level or both. Many instances of sequence‐specific silencing requires small RNAs that can be divided into two major classes: microRNAs (miRNAs) and short‐interfering RNAs (siRNAs). miRNAs function in post‐transcriptional gene silencing by guiding mRNA degradation or translational repression. Endogenous siRNAs are more diverse in plants than in animals and can direct post‐transcriptional gene silencing through mRNA degradation or transcriptional gene silencing by triggering DNA methylation and histone modifications. This review discusses recent advances in the field of small RNA‐guided gene silencing in plants including rice.
A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants: Case Analyses of Arabidopsis and Oryza
Authors: Fan Chuanzhu , Vibranovski Maria D. , Chen Ying , Long Manyuan 
Published: June 2007

AbstractTo systematically estimate the gene duplication events in closely related species, we have to use comparative genomic approaches, either through genomic sequence comparison or comparative genomic hybridization (CGH). Given the scarcity of complete genomic sequences of plant species, in the present study we adopted an array based CGH to investigate gene duplications in the genus Arabidopsis. Fragment genomic DNA from four species, namely Arabidopsis thaliana, A. lyrata subsp. lyrata, A. lyrata subsp. petraea, and A. halleri, was hybridized to Affymetrix (Santa Clara, CA, USA) tiling arrays that are designed from the genomic sequences of A. thaliana. Pairwise comparisons of signal intensity were made to infer the potential duplicated candidates along each phylo‐genetic branch. Ninety‐four potential candidates of gene duplication along the genus were identified. Among them, the majority (69 of 94) were A. thaliana lineage specific. This result indicates that the array based CGH approach may be used to identify candidates of duplication in other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. sativa and A. thaliana and found a strikingly higher number of chimera retroposed genes in rice. The higher rate of gene duplication through retroposition and other mechanisms may indicate that the grass species is able to adapt to more diverse environments.
Evolutionary Genomics of Weedy Rice in the USA
Authors: Olsen Kenneth M. , Caicedo Ana L. , Jia Yulin 
Published: June 2007

AbstractRed rice is an interfertile, weedy form of cultivated rice (Oryza sativa L.) that competes aggressively with the crop in the southern US, reducing yields and contaminating harvests. No wild Oryza species occur in North America and the weed has been proposed to have evolved through multiple mechanisms, including “de‐domestication” of US crop cultivars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedy Oryza strains. The phenotype of US red rice ranges from “crop mimics”, which share some domestication traits with the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity have indicated that many weed strains are closely related to Asian taxa (including indica and aus rice varieties, which have never been cultivated in the US, and the Asian crop progenitor O. rufipogon), whereas others show genetic similarity to the tropical japonica varieties cultivated in the southern US. Herein, we review what is known about the evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to further characterize the evolutionary genomics of this aggressive weed.
Molecular Population Genetics of Rice Domestication
Authors: Tang Tian , Shi Suhua 
Published: June 2007

AbstractDomestication is a selection process that genetically modifies species to meet human needs. A most intriguing feature of domestication is the extreme phenotypic diversification among breeds. What could be the ultimate source of such genetic variations? Another notable outcome of artificial selection is the reduction in the fitness of domesticated species when they live in the wild without human assistance. The complete sequences of the two subspecies of rice cultivars provide an opportunity to address these questions. Between the two subspecies, we found much higher rates of non‐synonymous (N) than synonymous (S) substitutions and the N/S ratios are higher between cultivars than between wild species. Most interestingly, substitutions of highly dissimilar amino acids that are deleterious and uncommon between natural species are disproportionately common between the two subspecies of rice. We suggest strong selection in the absence of effective recombination may be the driving force, which we called the domestication‐associated Hill‐Robertson effect. These hitchhiking mutations may contribute to some fitness reduction in cultivars. Comparisons of the two genomes also reveal the existence of highly divergent regions in the genomes. Haplotypes in these regions often form highly polymorphic linkage blocks that are much older than speciation between wild species. Genes from such regions could contribute to the differences between indica and japonica and are likely to be involved in the diversifying selection under domestication. Their existence suggests that the amount of genetic variation within the single progenitor species Oryza rufipogon may be insufficient to account for the variation among rice cultivars, which may come from a more inclusive gene pool comprising most of the A‐genome wild species. Genes from the highly polymorphic regions also provide strong support for the independent domestication of the two subspecies. The genomic variation in rice has revealing implications for studying the genetic basis of indica‐japonica differentiation under rice domestication and subsequent improvement.
Identification of Chromosomes from Multiple Rice Genomes Using a Universal Molecular Cytogenetic Marker System
Authors: Tang Xiaomin , Bao Weidong , Zhang Wenli , Cheng Zhukuan 
Published: June 2007

AbstractTo develop reliable techniques for chromosome identification is critical for cytogenetic research, especially for genomes with a large number and smaller‐sized chromosomes. An efficient approach using bacterial artificial chromosome (BAC) clones as molecular cytological markers has been developed for many organisms. Herein, we present a set of chromosomal arm‐specific molecular cytological markers derived from the gene‐enriched regions of the sequenced rice genome. All these markers are able to generate very strong signals on the pachytene chromosomes of Oryza sativa L. (AA genome) when used as fluorescence in situ hybridization (FISH) probes. We further probed those markers to the pachytene chromosomes of O. punctata (BB genome) and O. officinalis (CC genome) and also got very strong signals on the relevant pachytene chromosomes. The signal position of each marker on the related chromosomes from the three different rice genomes was pretty much stable, which enabled us to identify different chromosomes among various rice genomes. We also constructed the karyotype for both O. punctata and O. officinalis with the BB and CC genomes, respectively, by analysis of 10 pachytene cells anchored by these chromosomal arm‐specific markers.
Genome‐Wide Comparative Analysis and Expression Pattern of TCP Gene Families in Arabidopsis thaliana and Oryza sativa
Authors: Yao Xuan , Ma Hong , Wang Jian , Zhang Dabing 
Published: June 2007

AbstractSeveral TCP genes have been reported to play important roles in plant development; the TCP homologs encode a plant‐specific family of putative transcription factors. To understand the evolutionary relationship of TCP genes of Arabidopsis thaliana and Oryza sativa L. (hereafter called rice), we have identified 23 and 22 TCP genes in the Arabidopsis and rice genomes, respectively. Using phylogenetic analysis, we grouped these TCP genes into three classes. In addition, the motifs outside the TCP domain further support the evolutionary relationships among these genes. The genome distribution of the TCP genes strongly supports the hypothesis that genome‐wide and tandem duplication contributed to the expansion of the TCP gene family. The expression pattern of the TCP genes was analyzed further, providing useful clues about the function of these genes.
The Puzzle of Rice Domestication
Authors: Sang Tao , Ge Song 
Published: June 2007

AbstractThe origin of cultivated rice has puzzled plant biologists for decades. This is due, at least in part, to the complex evolutionary dynamics in rice cultivars and wild progenitors, particularly rapid adaptive differentiation and continuous gene flow within and between cultivated and wild rice. The long‐standing controversy over single versus multiple and annual versus perennial origins of cultivated rice has been brought into shaper focus with the rapid accumulation of genetic and phylogenetic data. Molecular phylogenetic analyses revealed ancient genomic differentiation between rice cultivars, suggesting that they were domesticated from divergent wild populations. However, the recently cloned domestication gene sh4, responsible for the reduction of grain shattering from wild to cultivated rice, seems to have originated only once. Herein, we propose two models to reconcile apparently conflicting evidence regarding rice domestication. The snow‐balling model considers a single origin of cultivated rice. In this model, a core of critical domestication alleles was fixed in the founding cultivar and then acted to increase the genetic diversity of cultivars through hybridization with wild populations. The combination model considers multiple origins of cultivated rice. In this model, initial cultivars were domesticated from divergent wild populations and fixed different sets of domestication alleles. Subsequent crosses among these semi‐domesticated cultivars resulted in the fixation of a similar set of critical domestication alleles in the contemporary cultivars. In both models, introgression has played an important role in rice domestication. Recent and future introgression of beneficial genes from the wild gene pool through conventional and molecular breeding programs can be viewed as the continuation of domestication.
Identification, Expression and Functional Analysis of a Receptor‐like Cytoplasmic Kinase, OsRLCK1, in Rice
Authors: Kong Zhaosheng , Xu Wenying , Li Qun , Xue Yongbiao 
Published: June 2007

AbstractPollination involves a series of complex cellular interactions and signal transduction events. Numerous reports have suggested a central role for protein kinases in pollen germination and pollen tube growth and a large number of receptor‐like kinases have been detected exclusively in pollen in higher plants. However, few are well characterized, especially for the receptor‐like cytoplasmic kinases. Here we report a receptor‐like kinase gene, OsRLCK1, which belongs to the receptor‐like cytoplasmic kinase VIII subfamily. Real‐time quantitative polymerase chain reaction analysis and whole mount RNA in situ hybridization showed that OsRLCK1 is a pollen‐specific gene and expressed only in the mature pollen. When expressed in the onion epidermal cells, the OsRLCK1‐GFP fusion protein was diffused throughout the cell, indicating its cytoplasmic and nuclear localization. The Maltose Binding Protein‐OsRLCK1 recombinant protein was found to be capable of autophosphorylation on threonine residue, showing that it encodes a functional kinase. These results suggest that OsRLCK1 is likely to play a role in a signaling pathway associated with pollen performance during pollination in rice.
Super Hybrid Rice Breeding in China: Achievements and Prospects
Authors: Cheng Shi‐Hua , Cao Li‐Yong , Zhuang Jie‐Yun , Chen Shen‐Guang , Zhan Xiao‐Deng , Fan Ye‐Yang , Zhu De‐Feng , Min Shao‐Kai 
Published: June 2007

AbstractHybrid rice has contributed greatly to the self‐sufficiency of food supply in China. To meet the future demand for rice production, a national program on super rice breeding was established in China in 1996. The corresponding targets, breeding strategies and most significant advances are reviewed in this paper. New plant type models have been modified to adjust to various rice growing regions. In recognition of the importance of applying parents with intermediate subspecies differentiation in increasing F1 yield, medium type parental lines were selected from populations derived from inter‐subspecies crosses with the assistance of DNA markers for subspecies differentiation. Results also indicate that a substantial increase of biomass is the basis for further enhancement of the grain yield potential, and amelioration of leaf characteristics is helpful in increasing the photosynthetic rate. Thirty‐four super hybrid rice varieties have been released commercially, growing in a total area of 13.5 million hm2 and producing 6.7 thousand million kg more rice in 1998‐2005. Although remarkable progress has been made in super hybrid rice breeding in China, selections on the root system and integration of more biotechnological tools remain a great challenge.
Hypervelocity stars and the environment of Sgr A*
Authors: Sesana Alberto , Haardt Francesco , Madau Piero 
Published: June 2007

Abstract
Hypervelocity stars (HVSs) are a natural consequence of the presence of a massive nuclear black hole (Sgr A*) in the Galactic Centre. Here we use the Brown et al. sample of unbound and bound HVSs together with numerical simulations of the propagation of HVSs in the Milky Way halo to constrain three plausible ejection mechanisms: (i) the scattering of stars bound to Sgr A* by an in-spiralling intermediate-mass black hole (IMBH); (ii) the disruption of stellar binaries in the tidal field of Sgr A*; and (iii) the two-body scattering of stars off a cluster of stellar-mass black holes orbiting Sgr A*. We compare the predicted radial and velocity distributions of HVSs with the limited-statistics data set currently available, and show that the IMBH model appears to produce a spectrum of ejection velocities that is too flat. Future astrometric and deep wide-field surveys of HVSs should shed unambiguous light on the stellar ejection mechanism and probe the Milky Way potential on scales as large as 200 kpc.
Mechanisms of hypotonic inhibition of the sodium, proton exchanger type 1 (NHE1) in a biliary epithelial cell line (Mz‐Cha‐1)
Authors: Elsing C. , Gosch I. , Hennings J. C. , Hübner C. A. , Herrmann T. 
Published: June 2007

AbstractAim:  To elucidate the cellular events that results in inhibition of Na+, H+ exchanger type 1 (NHE1) by hypotonicity.Methods:  Intracellular pH (pHi) was measured in biliary epithelial cells, with the pH‐sensitive fluorochrome 2′,7′‐bis‐(carboxyethyl)‐5(6)‐carboxyfluorescein (BCECF) using a spectrophotometer. Regulatory volume decrease (RVD) was analysed from confocal images. Changes in NHE1 membrane content were visualized by confocal laser scanning microscopy after transfection of Mz‐Cha‐1 cells with a NHE1–cMyc fusion protein.Results:  In Mz‐Cha‐1 cells hypotonicity (−80 mmol L−1 NaCl) inhibited endogenous Na+, H+ exchange. Tyrosine and serine kinase inhibitors were incapable to prevent inhibition. As several signalling pathways influence Na+, H+ exchange, we tested the effect of the Ca++, Calmodulin, protein kinase C or the cAMP, protein kinase A system on inhibition of Na+, H+ exchange by hypotonic challenge, but neither system was involved. In contrast, cytoskeleton did influence the effect of hypotonicity. Inhibition of microtubule polymerization by colchicine prevented inhibition of NHE1, and also restored Na+, H+ exchange kinetics. Specific inhibition of Src kinases with PP2, attenuated pHi recovery rate from 1.93 ± 0.16 pH units min−1 (normotonic environment) to 1.02 ± 0.50 pH units min−1 (hypotonic environment). Membrane staining of NHE1–cMyc fusion protein was maintained after hypotonic exposure in colchicine pre‐treated cells as was RVD. Microfilament inhibition by cytochalasin preserved NHE1 activity. Inhibition of phosphatidylinositol‐3′‐kinase was unable to restore Na+, H+ exchange activity.Conclusion:  We conclude that regulation of Na+, H+ exchange during RVD is mediated by cytoskeletal elements. This receptor independent pathway is regulated by Src.
Physiology and pathology of collagen receptors
Authors: Popova S. N. , Lundgren‐Åkerlund E. , Wiig H. , Gullberg D. 
Published: June 2007

AbstractJust before the transition from pre‐genomic to the post‐genomic era, the two latest members of the mammalian integrin family were identified. These integrins, which were named α10β1 and α11β1, are both collagen receptors and are related. Rather than being twins, they can be regarded as close cousins. They both belong to the subfamily of integrins that contain an I‐domain in the α subunit. This domain is also the part that endows these integrins with the capacity to bind the GFOGER sequence in collagens. In the current review, we summarize and update the current knowledge about the in vitro and in vivo functions of these integrins.