Genetic organization of aromatic rice as revealed by RAPD markers: A case study in conserving crop genetic resources on farm

Summary On-farm conservation of landraces is one strategy to maintain the diversity of crop germplasm in local agro-ecosystems. The genetic structures of landraces are a key biological factor in on-farm conservation strategies. To accumulate a genetic understanding that will help establish a methodology for on-farm conservation, the genetic organization of landraces of aromatic rice in Namdinh province, Vietnam was analyzed using RAPD markers. Eighteen RAPD markers detected 38 genotypes among 320 aromatic rice samples growing at 23 sites of farmers' fields and in the experimental field that derived from 13 sites. Geographical variation was observed in the frequency of genotypes, whereas individual landraces could not be distinguished by RAPD markers. Genetic variation within a site was generally smaller than that among sites. The degree of genetic similarity of the plants in a site varied among sites, as did the number of genotypes. Changes in genetic structure over time were investigated using experimental populations each derived from approximately 30 plants from 13 farmers' fields. The differences detected by DNA markers between the genetic structural in the farmers' fields and those in experimental fields suggested that genetic drift is a major cause of these differences. The present study suggests that DNA markers are an essential means to monitor the genetic structures of heterogeneous landraces of rice, and are useful for selecting study sites for the on-farm conservation of genetic diversity as well as for successive monitoring.     

Genetic variability for resistance to sorghum downy mildew (Peronosclerospora sorghi) and Rajasthan downy mildew (P. heteropogoni) in the tropical/sub-tropical Asian maize germplasm

Downy mildews cause considerable damage to maize (Zea mays L.) worldwide, particularly in the tropical Asia. We have evaluated a set of 42 tropical/sub-tropical maize inbred lines developed in different countries in Asia (India, Thailand and Philippines), and Mexico, for analysing the genetic variability for resistance to sorghum downy mildew [Peronosclerospora sorghi; SDM] and Rajasthan downy mildew [P. heteropogoni; RDM]. Experiments were carried out in replicated trials under artificial infection in field conditions against SDM and RDM at Mandya in Karnataka, India, and Udaipur in Rajasthan, India, respectively, during 1999 and 2000. The study resulted in identification of five inbred lines offering consistent and strong resistance to both SDM and RDM, while several inbred lines revealed resistance only to RDM. It was also revealed that the SDM-resistant inbreds are invariably resistant to RDM, while the RDM-resistant inbreds might show differential responses to the SDM. The maize inbred lines identified in this study with broad-spectrum resistance to downy mildews could be potentially useful for basic and applied research work on downy mildews in tropical Asia. This revised version was published online in August 2006 with corrections to the Cover Date.     

Enzymatic modification of pectin to increase its calcium sensitivity while preserving its molecular weight

A commercial high-methoxy citrus pectin was treated with a purified salt-independent pectin methylesterase (PME) isozyme isolated from Valencia orange peel to prepare a series of deesterified pectins. A series of alkali-deesterified pectins was also prepared at pH 10 under conditions permitting beta-elimination. Analysis of these pectins using high-performance size exclusion chromatography (HPSEC) with on-line multiangle laser light-scattering, differential viscometer, and refractive index (RI) detectors revealed no reduction in weight-average molecular weight (M(w); 150000) in the PME-treated pectin series, whereas a 16% reduction in intrinsic viscosity (IV) occurred below a degree of esterification (DE) of 47%. In contrast, alkali deesterification rapidly reduced both M(w) and IV to less than half of that observed for untreated pectin. PME treatment of a non-calcium-sensitive citrus pectin introduced calcium sensitivity with only a 6% reduction in the DE. Triad blocks of unesterified galacturonic acid were observed in (1)H nuclear magnetic resonance spectra of this calcium-sensitive pectin (CSP). These results demonstrate that the orange salt-independent PME isozyme utilizes a blockwise mode of action. This is the first report of the preparation of a CSP by PME treatment without significant loss of the pectin's M(w) due to depolymerization.     

Monitoring of Atmospheric Mercury at a Global Atmospheric Watch (GAW) Site on An-Myun Island, Korea

In order to investigate the regional background concentration levels of mercury (Hg), measurements were routinely recorded on An-Myun Island off the coast of Korea (December 2004 to April 2006). The mean concentration of Hg computed from the entire measurement period was 4.61?±?2.21 ng m^?3 with a range of 0.10–25.4 ng m^?3 (N?=?10,485). Using these data, we inspected various aspects of Hg behavior from the relatively remote island of An-Myun in Korea. Inspection of the seasonal patterns of Hg indicated that its concentration levels generally peaked in spring, while reached a minimum in summer. The summertime deficiency of Hg along with the lack of diurnal variation suggests that the environmental behavior of Hg at the study site was strongly suppressed by heavy precipitation during specific period. The diurnal variations of Hg, typically characterized by a relative daytime dominance, are distinguishable between seasons so that such patterns disappear during the summer. The results of our analysis, when inspected in terms of long-range transport of airborne pollutants, imply that Hg concentration levels can be affected intensively by trans-boundary input processes over certain period of time. Its springtime dominance hence suggests the combined effects of various local source processes and the meteorological conditions favorable for the massive air mass transport phenomenon (such as Asian Dust storms) during that time period.     

Comparative genomics of trypanosomatid parasitic protozoa

A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.     

A reversibly switching surface

We report the design of surfaces that exhibit dynamic changes in interfacial properties, such as wettability, in response to an electrical potential. The change in wetting behavior was caused by surface-confined, single-layered molecules undergoing conformational transitions between a hydrophilic and a moderately hydrophobic state. Reversible conformational transitions were confirmed at a molecular level with the use of sum-frequency generation spectroscopy and at a macroscopic level with the use of contact angle measurements. This type of surface design enables amplification of molecular-level conformational transitions to macroscopic changes in surface properties without altering the chemical identity of the surface. Such reversibly switching surfaces may open previously unknown opportunities in interfacial engineering.     

Optimizing competitive uses of water for irrigation and fisheries

Choosing the appropriate reservoir water management strategy can be difficult when the water has multiple uses. This study examines this problem for reservoir managers where water use involves irrigation and fisheries. A stochastic dynamic programming (SDP) model is developed to facilitate reservoir management, using a case study illustration for southern Vietnam. The model includes the response of rice and fish yields to key factors including reservoir water levels, the timing and quantity of water release, and climatic conditions. The model also accounts for variation in rainfall patterns, irrigation requirements, and the demand for low water levels during the fish harvest season. Three production scenarios are examined where the reservoir's water is used for: only producing rice (scenario 1), only producing fish (scenario 2), and producing rice and fish (scenario 3). Key findings are: (1) for scenario 1, adequate water should be released to meet rice growing water requirements and residual water should be stored as a source of water in case of low rainfall, (2) for scenario 2, sufficient water needs to be released prior to the fish harvest to maximize this harvest; and (3) for scenario 3, water should be released prior to fish harvest, but sufficient water should remain to satisfy the water requirements of rice. When the reservoir is managed for joint production of rice and fish, net benefits are 6% greater than when the reservoir is managed solely for rice production. The SDP model developed in this paper could be adapted and applied to other multiple-use resources such as forests, river basins, and land.     

How do earthworms influence organic matter quantity and quality in tropical soils?

Earthworms are important regulators of soil structure and soil organic matter (SOM) dynamics; however, quantifying their influence on SOM cycling in tropical ecosystems remains little studied. Simulated rainfall was used to disrupt casts produced by Amynthas khami and their surrounding soil (control) into a range of small sized aggregates (50-250, 250-500, 500-2000 and 2000-5000 μm). To gain insight into how earthworms influence SOM biogeochemical composition in the aggregates, we carried out elemental and stable isotope analysis, and analytical pyrolysis (Py GC/MS). We also characterized their lignin component after oxidation with cupric oxide (CuO).The C content of smaller size fractions (<500 μm) in the control soil was higher than in the larger fractions. Our study therefore suggests that the aggregate hierarchy concept, which is used to understand soil aggregates and SOM dynamics in temperate soils, may not be applicable to the tropical Acrisol studied here. Earthworms modified SOM organization in soil aggregates. Although the isotope analyses were useful for highlighting SOM enrichment in the earthworm casts, aggregate fractions could not be classified according to particle size. Molecular analyses were necessary to indicate that SOM in all size fractions of casts consisted of relatively undecomposed material. Protection of the most labile SOM structures occurred in the smallest aggregate size fraction (50-250 μm). Py GC/MS showed that earthworm casts and control aggregates <2000 μm could be clearly distinguished according to the molecular properties of their SOM. Aggregates larger than 2000 μm, however, were most probably composed of all fractions and were not different. As a consequence, our results indicate that studies to determine the impact of earthworms on SOM turnover in soil are spatially dependant on the scale of observation.