作者机构：
Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA.;Hunan Agr Univ, Dept Plant Pathol, Changsha 410128, Hunan, Peoples R China.;Michigan State Univ, Ctr Microbial Ecol, E Lansing, MI 48824 USA.;[Zhou, JZ] Oak Ridge Natl Lab, Div Environm Sci, POB 2008, Oak Ridge, TN 37831 USA.
通讯机构：
[Zhou, JZ] O;Oak Ridge Natl Lab, Div Environm Sci, POB 2008, Oak Ridge, TN 37831 USA.
摘要：
The detection and identification of microorganisms in natural communities is a great challenge to biologists. Microarray-based genomic technology provides a promising high-throughput alternative to traditional microbial characterization. A novel prototype microarray containing whole genomic DNA, termed community genome array (CGA), was constructed and evaluated. Microarray hybridizations at 55°C using 50% formamide permitted the examined bacteria to be distinguished at the species level, while strain-level differentiation was obtained at hybridization temperatures of 65 or 75°C. The detection limit was estimated to be approximately 0.2 ng with genomic DNA from a single pure culture using a reduced hybridization volume (3 μL). Using mixtures of known amounts of DNA or a known number of cells from 14 or 16 different species, respectively, about 5 ng of genomic DNA or 2.5 × 105 cells were detected under the hybridization conditions used. In addition, strong linear relationships were observed between hybridization signal intensity and target DNA concentrations for pure cultures, a mixture of DNA templates, and a population of mixed cells (r2 = 0.95-0.98, P < 0.01). Finally, the prototype CGA revealed differences in microbial community composition in soil, river, and marine sediments. The results suggest that CGA hybridization has potential as a specific, sensitive, and quantitative tool for detection and identification of microorganisms in environmental samples.
摘要：
The Arabidopsis thaliana CORONATINE INSENSITIVE1 (COI1) gene encodes an F-box protein to assemble SCFCOI1 complexes essential for response to jasmonates (JAs), which are a family of plant signaling molecules required for many essential functions, including plant defense and reproduction. To better understand the molecular basis of JA action, we screened for suppressors of coi1 and isolated a coi1 suppressor1 (cos1) mutant. The coi1 mutation restores the coi1-related phenotypes, including defects in JA sensitivity, senescence, and plant defense responses. The COS1 gene was cloned through a map-based approach and found to encode lumazine synthase, a key component in the riboflavin pathway that is essential for diverse yet critical cellular processes. We demonstrated a novel function for the riboflavin pathway that acts downstream of COI1 in the JA signaling pathway and is required for suppression of the COI1-mediated root growth, senescence, and plant defense.
作者机构：
[方治国; 欧阳志云; 王效科; 林学强; 胡利锋] Key Laboratory of System Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China;[胡利锋] Plant Protection College, Hunan Agricultural University, Changsha 410128, China
期刊：
Applied and Environmental Microbiology,2003年69(10):6073-6081 ISSN：0099-2240
通讯作者：
Zhou, JH
作者机构：
Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA.;Hunan Agr Univ, Dept Plant Pathol, Changsha, Hunan, Peoples R China.;Univ Washington, Sch Oceanog, Seattle, WA 98195 USA.;[Zhou, JH] Oak Ridge Natl Lab, Div Environm Sci, Bldg 1505 MS 6038,Bethel Valley Rd, Oak Ridge, TN 37831 USA.
通讯机构：
[Zhou, JH] O;Oak Ridge Natl Lab, Div Environm Sci, Bldg 1505 MS 6038,Bethel Valley Rd, Oak Ridge, TN 37831 USA.
关键词：
Genetic Variation;Sulfur-Reducing Bacteria
摘要：
This study examined the natural diversity and distributions of sulfate-reducing bacteria along a natural carbon gradient extending down the shelf-slope transition zone of the eastern Pacific continental margin. Dissimilatory (bi)sulfite reductase gene sequences (dsrAB) were PCR amplified and cloned from five different sampling sites, each at a discrete depth, from two different margin systems, one off the Pacific coast of Mexico and another off the coast of Washington State. A total of 1,762 clones were recovered and evaluated by restriction fragment length polymorphism (RFLP) analysis. The majority of the gene sequences recovered showed site and depth restricted distributions; however, a limited number of gene sequences were widely distributed within and between the margin systems. Cluster analysis identified 175 unique RFLP patterns, and nucleotide sequences were determined for corresponding clones. Several different continental margin DsrA sequences clustered with those from formally characterized taxa belonging to the delta subdivision of the class Proteobacteria (Desulfobulbus propionicus, Desulfosarcina variabilis) and the Bacillus-Clostridium (Desulfotomaculum putei) divisions, although the majority of the recovered sequences were phylogenetically divergent relative to all of the other DsrA sequences available for comparison. This study revealed extensive new genetic diversity among sulfate-reducing bacteria in continental margin sedimentary habitats, which appears to be tightly coupled to slope depth, specifically carbon bioavailability.
摘要：
Application of modem genetic manipulation has been limited in pepper (Capsicum annuum L.) due to the lack of an efficient transformation system. Following the development of an efficient protocol for in vitro regeneration of pepper cotyledons, we investigated the key factors affecting transformation and established a highly efficient genetic transformation system using the pepper cotyledon as starting material. In this system, cotyledon explants are preconditioned for 2 days on kanamycin (km)-free DM1 medium [Murashige and Skoog (MS) salts/Gamborg B5 vitamins basal medium supplemented with 20 g/l sucrose, 5,000 mg/l DJ nutrients and a hormone combination of 1.0 mg/l indoleacetic acid (IAA) and 5.0 mg/l 6-benzyladenine (BA) solidified with 0.7% agar, pH 5.8], followed by co-cultivation with Agrobacterium tumefaciens on DM1 for 2 days and delay selection on DM1 with 500 mg/1 carbenicillin (carb) for 2 days. The explants are then placed on DM1 containing 10 mg/l AgNO<inf>3</inf>, 50 mg/l km-sulfate and 500 mg/l carb. After 4-5 weeks, the explants with buds are transferred to EM1 medium (MS salts/Gamborg B5 vitamins basal medium supplemented with 20 g/l sucrose, 5,000 mg/l DJ nutrients, 10 mg/l AgNO<inf>3</inf> and a hormone combination of 1.0 mg/l IAA, 3.0 mg/l BA and 2.0 mg/l gibberellic acid, solidified with 0.7% agar, pH 5.8) with 50 mg/l kanamycin and 500 mg/l carbenicillin for the elongation of buds. After 3-6 weeks, 1- to 2-cm-long elongated shoots are excised and planted on RM1 medium (MS basal medium supplemented with a hormone combination of 0.2 mg/l NAA and 0.1 mg/l IAA, solidified with 0.8% agar, pH 5.8) with 25 mg/l km and 200 mg/l carb for rooting. We tested four genotypes of pepper, and all presented a high differentiation efficiency (81.3% on average), elongation rate (61.5%) and rooting efficiency (89.5%). Polymerase chain reaction analysis results showed that 40.8% of the regenerated plantlets were transgenic plants.
期刊：
Applied and Environmental Microbiology,2003年69(6):3549-3560 ISSN：0099-2240
通讯作者：
Zhou, JZ
作者机构：
Oak Ridge Natl Lab, Div Environm Sci, Oak Ridge, TN 37831 USA.;Hunan Agr Univ, Dept Plant Pathol, Changsha, Hunan, Peoples R China.;Univ Wisconsin Stout, Dept Biol, Menomonie, WI 54751 USA.;Univ Washington, Sch Oceanog, Seattle, WA 98295 USA.;Michigan State Univ, Ctr Microbial Ecol, E Lansing, MI 48824 USA.
通讯机构：
[Zhou, JZ] O;Oak Ridge Natl Lab, Div Environm Sci, POB 2008, Oak Ridge, TN 37831 USA.
摘要：
To understand the composition and structure of denitrifying communities in the oxygen-deficient zone off the Pacific coast of Mexico, the molecular diversity of nir genes from sediments obtained at four stations was examined by using a PCR-based cloning approach. A total of 50 operational taxonomic units (OTUs) for nirK and 82 OTUs for nirS were obtained from all samples. Forty-four of the nirS clones and 31 of the nirK clones were sequenced; the levels of similarity of the nirS clones were 52 to 92%, and the levels of similarity of the nirS clones were 50 to 99%. The percentages of overlapping OTUs between stations were 18 to 30% for nirS and 5 to 8% for nirK. Sequence analysis revealed that 26% of the nirS clones were related to the nirS genes of Alcaligenesfaecalis (80 to 94% similar) and Pseudomonas stutzeri (80 to 99%), whereas 3 to 31% of the nirK clones were closely related to the nirK genes of Pseudomonas sp. strain G-179 (98 to 99%), Bradyrhizobium japonicum (91%), Blastobacter denitrificans (83%), and Alcaligenes xylosoxidans (96%). The rest of the clones, however, were less than 80% similar to nirS and nirK sequences available in sequence databases. The results of a principalcomponent analysis (PCA) based on the percentage of OTUs and biogeochemical data indicated that the nitrate concentration and oxygen have an effect on the denitrifying communities. The communities at the stations in oxygen-deficient zones were more similar than the communities at the stations in the oxygenated zone. The denitrifying communities were more similar at the stations that were closer together and had similar nitrate levels. Also, the results of PCA based on biogeochemical properties suggest that geographic location and biogeochemical conditions, especially the nitrate and oxygen levels, appear to be the key factors that control the structure of denitrifying communities.
作者机构：
[丁学知] Department of Biochemistry, College of Life Science, Hunan Normal University, Changsha 410081, China;[丁学知; 高必达] Department of Phytopathology, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
