Complete Genomic Structure of the Cultivated Rice Endophyte Azospirillum sp. B510

We determined the nucleotide sequence of the entire genome of a diazotrophic endophyte, Azospirillum sp. B510. Strain B510 is an endophytic bacterium isolated from stems of rice plants (Oryza sativa cv. Nipponbare). The genome of B510 consisted of a single chromosome (3 311 395 bp) and six plasmids, designated as pAB510a (1 455 109 bp), pAB510b (723 779 bp), pAB510c (681 723 bp), pAB510d (628 837 bp), pAB510e (537 299 bp), and pAB510f (261 596 bp). The chromosome bears 2893 potential protein-encoding genes, two sets of rRNA gene clusters (rrns), and 45 tRNA genes representing 37 tRNA species. The genomes of the six plasmids contained a total of 3416 protein-encoding genes, seven sets of rrns, and 34 tRNAs representing 19 tRNA species. Eight genes for plasmid-specific tRNA species are located on either pAB510a or pAB510d. Two out of eight genomic islands are inserted in the plasmids, pAB510b and pAB510e, and one of the islands is inserted into trnfM-CAU in the rrn located on pAB510e. Genes other than the nif gene cluster that are involved in N2 fixation and are homologues of Bradyrhizobium japonicum USDA110 include fixABCX, fixNOQP, fixHIS, fixG, and fixLJK. Three putative plant hormone-related genes encoding tryptophan 2-monooxytenase (iaaM) and indole-3-acetaldehyde hydrolase (iaaH), which are involved in IAA biosynthesis, and ACC deaminase (acdS), which reduces ethylene levels, were identified. Multiple gene-clusters for tripartite ATP-independent periplasmic-transport systems and a diverse set of malic enzymes were identified, suggesting that B510 utilizes C4-dicarboxylate during its symbiotic relationship with the host plant

Structural Analysis of the pRhico Plasmid of Azospirillum brasilense Sp7 and Phenotypical Characterization of pRhico Genes involved in Cell Surface Composition

status: publishe

Genetic and physical map of the pLAFR1 vector

This paper presents the complete sequencing and annotation of the pLAFR1 vector. pLAFR is a tetracycline-resistant "cosmid" cloning vector, which is derived from the 20 kb plasmid pRK290, a RK2-derivative. Due to its broad host range, the pLAFR1 vector has been widely used in the genetic analysis of a broad number of gram-negative bacterial species. The availability of the complete pLAFR1 sequence will most definitely help in the construction and analysis of clone libraries based on pRK290 or pLAFR vectors

Adaptive Bitrate Maximizing TEQ Design for DMT-based Systems

In a previous paper, we proposed a bitrate maximizing (BM) design criterion for the time-domain equalizer (TEQ) in a discrete multitone receiver. This BM-TEQ and the closely related BM per-group equalizers (PGEQ) get close to the performance of the so-called per-tone equalization (PTEQ). In this paper, we show that the BM-TEQ criterion, despite its nonlinear nature, is well suited for a recursive Levenberg-Marquardt (RLM) based design. This adaptive BM-TEQ also allows to track slow variations of the transmission channel and the noise. This RLM-based design uses the same second-order statistics (SOS) as the earlier presented recursive least-squares (RLS) based adaptive PTEQ and opens up a complete range of adaptive BM equalizers: from the computationally efficient RLS-based PTEQ with largest memory cost, over the RLM-based BM-PGEQ with intermediate memory cost, towards an RLM-based BM-TEQ with considerably smaller memory cost, but larger equalizer updating complexity

Split SR-RLS for the Joint Initialization of the Per-Tone Equalizers and Per-Tone Echo Cancelers in DMT-Based Receivers

In asymmetric digital subscriber lines (ADSL), the available bandwidth is divided in subcarriers or tones which are assigned to the upstream and/or downstream transmission direction. To allow efficient bidirectional communication over one twisted pair, echo cancellation is required to separate upstream and downstream channels. In addition, intersymbol interference and intercarrier interference have to be reduced by means of equalization. In this paper, a computationally efficient algorithm for adaptively initializing the per-tone equalizers (PTEQ) and per-tone echo cancelers (PTEC) is presented. For a given number of equalizer and echo canceler taps per-tone, it was shown that the joint PTEQ/PTEC receiver structure is able to maximize the signal-to-noise ratio (SNR) on each subcarrier and hence also the achievable bit rate. The proposed initialization scheme is based on a modification of the square root recursive least squares (SR-RLS) algorithm to reduce computational complexity and memory requirement compared to full SR-RLS, while keeping the convergence rate acceptably fast. Our performance analysis will show that the proposed method converges in the mean and an upper bound for the step size is given. Moreover, we will indicate how the presented initialization method can be reused in several other ADSL applications