Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions.

The correspondence between the transversion/transition ratio and the neighboring base composition in chloroplast DNA is examined. For 18 noncoding regions of the chloroplast genome, alignments between rice (Oryza sativa) and maize (Zea mays) were generated by two different methods. Difficulties of aligning noncoding DNA are discussed, and the alignments are analyzed in a manner that reduces alignment artifacts. Sequence divergence is < 10%, so multiple substitutions at a site are assumed to be rare. Observed substitutions were analyzed with respect to the A+T content of the two immediately flanking bases. It is shown that as this content increases, the proportion of transversions also increases. When both the 5'- and 3'-flanking nucleotides are G or C (A+T content of 0), only 25% of the observed substitutions are transversions. However, when both the 5'- and 3'-flanking nucleotides are A or T (A+T content of 2), 57% of the observed substitutions are transversions. Therefore, the influence of flanking base composition on substitutions, previously reported for a single noncoding region, is a general feature of the chloroplast genome.

Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes.

Fluorescence in situ hybridization (FISH) is a powerful tool for physical mapping in human and other mammalian species. However, application of the FISH technique has been limited in plant species, especially for mapping single- or low-copy DNA sequences, due to inconsistent signal production in plant chromosome preparations. Here we demonstrate that bacterial artificial chromosome (BAC) clones can be mapped readily on rice (Oryza sativa L.) chromosomes by FISH. Repetitive DNA sequences in BAC clones can be suppressed efficiently by using rice genomic DNA as a competitor in the hybridization mixture. BAC clones as small as 40 kb were successfully mapped. To demonstrate the application of the FISH technique in physical mapping of plant genomes, both anonymous BAC clones and clones closely linked to a rice bacterial blight-resistance locus, Xa21, were chosen for analysis. The physical location of Xa21 and the relationships among the linked clones were established, thus demonstrating the utility of FISH in plant genome analysis.

Fish diversity and traditional fishing methods in semiarid irrigated system in the Bajo Vinalopó region, Southeastern Spain

The aim of this paper is to obtain a comprehensive picture of the importance of the fish fauna in the wetlands and coastal lagoons of the Bajo Vinalopó region (Alicante, South eastern Spain) and the ecological, historical and cultural value of the traditional knowledge on fishing maintained by local people. We have compiled data from different information sources: (1) the revision of historical archives, (2) personal interviews and collaborative research, and (3) ecological and water quality data. The results show that the area sustains important fish fauna diversity (17 species) and that local people have inherited a considerable traditional knowledge on fishing methods (11 modalities), on the maintenance and sound management of the water system and on the ecology and behaviour of fish. We conclude that a comprehensive consideration of all these ecological, historical and socio-cultural aspects related to fish and fishing shows clearly the value of this ecological and cultural heritage and provides a necessary base for a sustainable management of the area.

Polarimetric Response of Rice Fields at C-Band: Analysis and Phenology Retrieval

A set of ten RADARSAT-2 images acquired in fully polarimetric mode over a test site with rice fields in Seville, Spain, has been analyzed to extract the main features of the C-band radar backscatter as a function of rice phenology. After observing the evolutions versus phenology of different polarimetric observables and explaining their behavior in terms of scattering mechanisms present in the scene, a simple retrieval approach has been proposed. This algorithm is based on three polarimetric observables and provides estimates from a set of four relevant intervals of phenological stages. The validation against ground data, carried out at parcel level for a set of six stands and up to nine dates per stand, provides a 96% rate of coincidence. Moreover, an equivalent compact-pol retrieval algorithm has been also proposed and validated, providing the same performance at parcel level. In all cases, the inversion is carried out by exploiting a single satellite acquisition, without any other auxiliary information.

Estimation of Key Dates and Stages in Rice Crops Using Dual-Polarization SAR Time Series and a Particle Filtering Approach

Information of crop phenology is essential for evaluating crop productivity. In a previous work, we determined phenological stages with remote sensing data using a dynamic system framework and an extended Kalman filter (EKF) approach. In this paper, we demonstrate that the particle filter is a more reliable method to infer any phenological stage compared to the EKF. The improvements achieved with this approach are discussed. In addition, this methodology enables the estimation of key cultivation dates, thus providing a practical product for many applications. The dates of some important stages, as the sowing date and the day when the crop reaches the panicle initiation stage, have been chosen to show the potential of this technique.

Influence of Incidence Angle on the Coherent Copolar Polarimetric Response of Rice at X-Band

The coherent nature of the acquisition by TerraSAR-X of both copolar channels (HH and VV) enables the generation of many different polarimetric observables with physical interpretation, as have recently been used for monitoring rice fields. In this letter, the influence of incidence angle upon these polarimetric observables is analyzed by comparing three stacks of images that were acquired simultaneously at different incidence angles (22°, 30°, and 40°) during a whole cultivation campaign. We show that the response of observables related to dominance (entropy, ratios of components) and type of scattering mechanisms (alpha angles) is not greatly influenced by incidence angle at some stages: early and advanced vegetative phases, and maturation. Moreover, the acquisition geometry drives the sensitivity to the presence of the initial stems and tillers, being detected earlier at shallower angles. This analysis is a necessary step before studying potential methodologies for combining different orbits and beams for reducing the time between acquisitions for monitoring purposes.

Payment order for Samuel Adams on behalf of John Rice, 1772 July 1

Handwritten order to John Sale to pay scholarship funds to Samuel Adams for use by student John Rice (Harvard AB 1774), signed by Charles Chauncey, Thomas Waite, Jonathan Williams, and Daniel Marsh.