Genome of Geobacter sulfurreducens: metal reduction in subsurface environments

The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity.     

Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis

The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than a quarter of the genome consists of probable mobile or foreign DNA. One of the predicted mobile elements is a previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing conjugative plasmids, one encoding a previously undescribed pheromone inhibitor. The apparent propensity for the incorporation of mobile elements probably contributed to the rapid acquisition and dissemination of drug resistance in the enterococci.     

The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota

Mucosal surfaces constantly encounter microbes. Toll-like receptors (TLRs) mediate recognition of microbial patterns to eliminate pathogens. By contrast, we demonstrate that the prominent gut commensal Bacteroides fragilis activates the TLR pathway to establish host-microbial symbiosis. TLR2 on CD4(+) T cells is required for B. fragilis colonization of a unique mucosal niche in mice during homeostasis. A symbiosis factor (PSA, polysaccharide A) of B. fragilis signals through TLR2 directly on Foxp3(+) regulatory T cells to promote immunologic tolerance. B. fragilis lacking PSA is unable to restrain T helper 17 cell responses and is defective in niche-specific mucosal colonization. Therefore, commensal bacteria exploit the TLR pathway to actively suppress immunity. We propose that the immune system can discriminate between pathogens and the microbiota through recognition of symbiotic bacterial molecules in a process that engenders commensal colonization.     

Global metabolomic analysis of blood from mice infected with Brucella abortus

To better understanding Brucella abortus infection, serum metabolites of B. abortus-infected and -uninfected mice were analyzed and twenty-one metabolites were tentatively identified at 3 and 14 days post-infection (d.p.i.). Level of most lysophosphatidylcholines (LPCs) was found to increase in infected mice at 3 d.p.i., while it was decreased at 14 d.p.i. as compared to uninfected mice. In contrast, acylcarnitines were initially reduced at 3 d.p.i then elevated after two-weeks of infection, while hydroxysanthine was increased at 14 d.p.i. in infected mice. Our findings suggest that the significant changes in LPCs and other identified metabolites may serve as potential biomarkers in acute phase of B. abortus infection.     

Diversity in Phenotypic Profiles in Landrace Populations of Vietnamese Rice: A Case Study of Agronomic Characters for Conserving Crop Genetic Diversity on Farm

Phenotypic variation of agronomic characters in aromatic rice (Oryza sativa L.) was analyzed in order to elucidate the genetic diversity of the populations of rice landraces. Thirteen populations in Namdinh province, in the Red River Delta of Vietnam, were studied in both of farmers fields and an experimental field. Only small differences were found in agronomic characters among the populations, including populations containing different varieties. Variations among the populations in the frequency distributions of several characters suggested different degrees of diversity among the populations even among populations with the same variety name. The phenotypic profiles of farmers fields were different from those in an experimental field suggesting the environmental differences between them. One variety cultivated in the Myloc district had different phenotypic characters from the other varieties in the Haihau district more clearly in the experimental field. Since the small phenotypic variation in each of farm might be due to the genetic drift and selection by the farmers, on farm conservation of the landraces of rice is considered to be under a force to decrease phenotypic diversity. The present study suggests that the targeting several farms with different phenotypic profiles contribute to the conservation of regional genetic diversity of the landraces of rice.     

Atmospheric measurements of nitrogen dioxide with a sensitive luminol instrument

A highly sensitive, lightweight, portable instrument has been developed for continuous monitoring of N0₂ in air. It operates by detecting the chemiluminescence produced when N0₂ encounters a surface wetted with a specially formulated solution containing luminol. Unlike other chemiluminescent instruments it measures N0₂ directly and does not require prior conversion of N0₂ to NO. It does not respond to H₂0₂, NO, HNO₃, NH₃, CO, C0₂, S0₂ or organic nitrates. The only interferences encountered to date are from 0₃ and PAN with the response to 0₃ being less than 0.2% of its response to N0₂. The response time of the instrument is less than 1 s and its sensitivity is better than 5 pptv. The instrument shows a negative temperature dependence of about 2% °C^?1 which is compensated electronically. Measurements have been made with the instrument during a number of field missions in polluted urban and relatively clean rural air. The relative influences of photochemistry and transport from local sources has been observed. Simultaneous measurements made with this instrument and the unequivocal tunable diode laser absorption spectroscopy method have shown excellent agreement.     

RAPD variability in rice (Oryza sativa L.) plants derived from desiccation-tolerant calli

Genetic modification from selfed progenies of 18 rice (Oryza sativa L.) plants regenerated from callus tissues which survived desiccation, were investigated at the DNA level using the random amplified polymorphic DNA (RAPD) method. Twelve 10-mer random primers were used to amplify DNA of progenies from the regenerated plants, and a total of 228 PCR products and 1780 DNA fragments were obtained by primers, generating between four to thirteen major bands. The size of the amplified fragments ranged from 0.2 to 2.55 kb. The results showed that 10 out of 12 primers produced polymorphic bands, two primers (RA31 and RA185) showed no polymorphism among plants tested. A dendrogram of the genetic distance was constructed based on their polymorphism, demonstrating that somaclonal variation exists in rice plants regenerated from callus which survived the desiccation treatment. Part of this variation can be useful in rice breeding. This revised version was published online in August 2006 with corrections to the Cover Date.     

Varietal Differences in Allelopathic Potential of Alfalfa

Alfalfa ( Medicago sativa L.) plants were found to contain water-soluble substances that inhibited the germination and seedling growth of alfalfa ( Chung and Miller 1990, Agron. J. 87, 762—767 ). Tsuzuki et al. (1999, Rep. Kyushu Branch Crop Sci. Soc. Japan 65, 39—40 ) discovered allelochemicals in alfalfa plants that could have adverse effects on the growth of some lowland weeds. This study was conducted to investigate varietal differences in allelopathic potential in alfalfa plants. Eight common varieties of Japanese alfalfa ( Medicago sativa L.), namely Batasu, Hisawakaba, Kitawakaba, Makiwakaba, Natsuwakaba, Lucerne, Tachiwakaba and Yuba, were grown by conventional methods in the Experimental Field of the Crop Science Laboratory, Faculty of Agriculture, Miyazaki University. Aqueous extracts of both fresh and dried material of alfalfa plants of all varieties significantly inhibited both germination and growth of lettuce ( Lactuca sativa L.). Leachates from germinating seeds of almost all alfalfa varieties inhibited elongation of the radicle but produced a negligible increase in germination and only slightly inhibited elongation of the hypocotyl of lettuce plants. Results demonstrated that the degree of inhibition of germination and growth of lettuce varied with the variety of alfalfa. In particular, Lucerne was identified as having the strongest allelopathic potential of the varieties studied. The results suggested that the allelopathic potential of alfalfa might be relating to a gene.     

Use of GIS and machine learning to predict disease in shrimp farmed on the east coast of the Mekong Delta,Vietnam

Diseases in shrimp farms in the Mekong Delta of Vietnam cause significant crop losses and are therefore of great concern to producers. Once a pond becomes infected, it is difficult to prevent spread of the disease to nearby shrimp farming areas. Thus, predicting the occurrence of disease is an essential part of reducing the risk for shrimp farmers. In this study, we applied an integrated geographic information system and machine learning system to predict three serious diseases of shrimp, namely, acute hepatopancreatic necrosis, white spot syndrome disease, and Enterocytozoon hepatopenaei infection, based on data collected from shrimp farms in the Tra Vinh, Bac Lieu, Soc Trang, and Ca Mau provinces of Vietnam. We first constructed a map showing the distribution of these diseases using the locations of affected farms, and then we conducted spatial analysis to acquire the geographical features of the affected locations. This latter information was combined with environmental factors and clinical signs to form the set of independent variables affecting the outbreak of diseases. The neural network model outperformed the logistic regression, random forest, and gradient boosting methods in terms of predicting infection to estimate the probability of disease occurrence in farmed areas. Acute hepatopancreatic necrosis disease infected farms downstream of the Co Chien and Hau Rivers of Tra Vinh and west of Ca Mau. Enterocytozoon hepatopenaei infection is distributed in Soc Trang Province, while white spot syndrome virus has spread to the coastal districts of Soc Trang and Bac Lieu Provinces, where it is highly associated to water from a complex canal system.