A complete sequence of a chromosome centromere is necessary for fully understanding centromere function. We reported the sequence structures of the first complete rice chromosome centromere through sequencing a large insert bacterial artificial chromosome clone-based contig, which covered the rice chromosome 4 centromere. Complete sequencing of the 124-kb rice chromosome 4 centromere revealed that it consisted of 18 tracts of 379 tandemly arrayed repeats known as CentO and a total of 19 centromeric retroelements (CRs) but no unique sequences were detected. Four tracts, composed of 65 CentO repeats, were located in the opposite orientation, and 18 CentO tracts were flanked by 19 retroelements. The CRs were classified into four types, and the type I retroelements appeared to be more specific to rice centromeres. The preferential insert of the CRs among CentO repeats indicated that the centromere-specific retroelements may contribute to centromere expansion during evolution. The presence of three intact retrotransposons in the centromere suggests that they may be responsible for functional centromere initiation through a transcription-mediated mechanism.

Unlike other bacteria that use FNR to regulate anaerobic respiration, Shewanella oneidensis MR-1 uses the cyclic AMP receptor protein (CRP) for this purpose. Three putative genes, cyaA, cyaB, and cyaC, predicted to encode class I, class IV, and class III adenylate cyclases, respectively, have been identified in the genome sequence of this bacterium. Functional validation through complementation of an Escherichia coli cya mutant confirmed that these genes encode proteins with adenylate cyclase activities. Chromosomal deletion of either cyaA or cyaB did not affect anaerobic respiration with fumarate, dimethyl sulfoxide (DMSO), or Fe(III), whereas deletion of cyaC caused deficiencies in respiration with DMSO and Fe(III) and, to a lesser extent, with fumarate. A phenotype similar to that of a crp mutant, which lacks the ability to grow anaerobically with DMSO, fumarate, and Fe(III), was obtained when both cyaA and cyaC were deleted. Microarray analysis of gene expression in the crp and cyaC mutants revealed the involvement of both genes in the regulation of key respiratory pathways, such as DMSO, fumarate, and Fe(III) reduction. Additionally, several genes associated with plasmid replication, flagellum biosynthesis, and electron transport were differentially expressed in the cyaC mutant but not in the crp mutant. Our results indicated that CyaC plays a major role in regulating anaerobic respiration and may contribute to additional signaling pathways independent of CRP.Shewanella oneidensis MR-1 is a metal reducer that uses more than 14 terminal electron acceptors for respiration. These electron acceptors include oxygen, nitrate, fumarate, dimethyl sulfoxide (DMSO), Fe(III) oxides, uranium, and chromium (21,25,26). In Escherichia coli and other bacteria, the shift from aerobic respiration to anaerobic respiration requires activation of the global transcriptional regulator FNR (11,34). FNR is an oxygen-sensing protein that is activated under anaerobic conditions by the formation of a [4Fe-4S] cluster (14). The S. oneidensis FNR homolog, EtrA, complements an E. coli FNR mutant (27) but does not appear to have the same role as the E. coli protein in S. oneidensis (17). Our previous findings demonstrated that instead of EtrA, the cyclic AMP (cAMP) receptor protein (CRP) controls anaerobic respiration in S. oneidensis MR-1 (28). crp mutants are deficient in anaerobic respiration of Fe(III), Mn(IV), fumarate, nitrate, and DMSO. Furthermore, fumarate, DMSO, and nitrate reductase activities are either severely decreased or undetectable in the crp mutants, suggesting that CRP regulates the expression of these anaerobic reductases (28).Although genetic and phenotypic data clearly have implicated CRP in the activation of anaerobic reductase systems in S. oneidensis MR-1, the mechanisms of this regulation remain unclear. CRP lacks obvious redox-sensing domains and is not expected to respond to changes in oxygen concentrations like FNR. Complementation of the S. oneidensis crp mutants with E. coli crp indicates that CRP is activa...

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Modification of silicon nitride nanopores under electron beam (e-beam) irradiation was investigated using a scanning electron microscope (SEM). Under e-beam irradiation, all pores with diameters ranging from 40to200nm undergo shrinkage, and the shrinkage rate increases with the rate of energy deposition. By using the selected-area scanning tool in the SEM, the silicon nitride nanopores can be selectively reshaped based on localized e-beam irradiation, with a characteristic dimension smaller than 10nm. A selected-area shaping technique was proposed to controllably shrink and shape the nanopores to a special structure.

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