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101.
Cultivation of Mesophilic Soil Crenarchaeotes in Enrichment Cultures from Plant Roots 总被引:2,自引:1,他引:2
Holly M. Simon Courtney E. Jahn Luke T. Bergerud Marek K. Sliwinski Paul J. Weimer David K. Willis Robert M. Goodman 《Applied microbiology》2005,71(8):4751-4760
Because archaea are generally associated with extreme environments, detection of nonthermophilic members belonging to the archaeal division Crenarchaeota over the last decade was unexpected; they are surprisingly ubiquitous and abundant in nonextreme marine and terrestrial habitats. Metabolic characterization of these nonthermophilic crenarchaeotes has been impeded by their intractability toward isolation and growth in culture. From studies employing a combination of cultivation and molecular phylogenetic techniques (PCR-single-strand conformation polymorphism, sequence analysis of 16S rRNA genes, fluorescence in situ hybridization, and real-time PCR), we present evidence here that one of the two dominant phylotypes of Crenarchaeota that colonizes the roots of tomato plants grown in soil from a Wisconsin field is selectively enriched in mixed cultures amended with root extract. Clones recovered from enrichment cultures were found to group phylogenetically with sequences from clade C1b.A1. This work corroborates and extends our recent findings, indicating that the diversity of the crenarchaeal soil assemblage is influenced by the rhizosphere and that mesophilic soil crenarchaeotes are found associated with plant roots, and provides the first evidence for growth of nonthermophilic crenarchaeotes in culture. 相似文献
102.
103.
Llorenç Milà i Canals Christian Bauer Jochen Depestele Alain Dubreuil Ruth Freiermuth Knuchel Gérard Gaillard Ottar Michelsen Ruedi Müller-Wenk Bernt Rydgren 《The International Journal of Life Cycle Assessment》2007,12(1):5-15
Background, Aim and Scope
Land use by agriculture, forestry, mining, house-building or industry leads to substantial impacts, particularly on biodiversity
and on soil quality as a supplier of life support functions. Unfortunately there is no widely accepted assessment method so
far for land use impacts. This paper presents an attempt, within the UNEP-SETAC Life Cycle Initiative, to provide a framework
for the Life Cycle Impact Assessment (LCIA) of land use.
Materials and Methods:
This framework builds from previous documents, particularly the SETAC book on LCIA (Lindeijer et al. 2002), developing essential
issues such as the reference for occupation impacts; the impact pathways to be included in the analysis; the units of measure
in the impact mechanism (land use interventions to impacts); the ways to deal with impacts in the future; and bio-geographical
differentiation.
Results:
The paper describes the selected impact pathways, linking the land use elementary flows (occupation; transformation) and parameters
(intensity) registered in the inventory (LCI) to the midpoint impact indicators and to the relevant damage categories (natural
environment and natural resources). An impact occurs when the land properties are modified (transformation) and also when
the current man-made properties are maintained (occupation).
Discussion:
The size of impact is the difference between the effect on land quality from the studied case of land use and a suitable reference
land use on the same area (dynamic reference situation). The impact depends not only on the type of land use (including coverage
and intensity) but is also heavily influenced by the bio-geographical conditions of the area. The time lag between the land
use intervention and the impact may be large; thus land use impacts should be calculated over a reasonable time period after
the actual land use finishes, at least until a new steady state in land quality is reached.
Conclusions:
Guidance is provided on the definition of the dynamic reference situation and on methods and time frame to assess the impacts
occurring after the actual land use. Including the occupation impacts acknowledges that humans are not the sole users of land.
Recommendations and Perspectives:
The main damages affected by land use that should be considered by any method to assess land use impacts in LCIA are: biodiversity
(existence value); biotic production potential (including soil fertility and use value of biodiversity); ecological soil quality
(including life support functions of soil other than biotic production potential). Bio-geographical differentiation is required
for land use impacts, because the same intervention may have different consequences depending on the sensitivity and inherent
land quality of the environment where it occurs. For the moment, an indication of how such task could be done and likely bio-geographical
parameters to be considered are suggested. The recommendation of indicators for the suggested impact categories is a matter
of future research. 相似文献
104.
Lisa M. Stout Ruth E. Blake James P. Greenwood Anna M. Martini & Eben C. Rose 《FEMS microbiology ecology》2009,70(3):70-80
The volcanic Sulphur Springs, St. Lucia, present an extreme environment due to high temperatures, low pH values, and high concentrations of sulfate and boron. St. Lucia offers some unique geochemical characteristics that may shape the microbial communities within the Sulphur Springs area. We chose six pools representing a range of geochemical characteristics for detailed microbial community analyses. Chemical concentrations varied greatly between sites. Microbial diversity was analyzed using 16S rRNA gene clone library analyses. With the exception of one pool with relatively low concentrations of dissolved ions, microbial diversity was very low, with Aquificales sequences dominating bacterial communities at most pools. The archaeal component of all pools was almost exclusively Acidianus spp. and did not vary between sites with different chemical characteristics. In the pool with the highest boron and sulfate concentrations, only archaeal sequences were detected. Compared with other sulfur springs such as those at Yellowstone, the microbial diversity at St. Lucia is very different, but it is similar to that at the nearby Lesser Antilles island of Montserrat. While high elemental concentrations seem to be related to differences in bacterial diversity here, similarities with other Lesser Antilles sites suggest that there may be a biogeographical component as well. 相似文献
105.
Differential expression analysis for sequence count data 总被引:22,自引:0,他引:22
High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form
of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability
throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution,
with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package. 相似文献
106.
We have developed a telomerase assay that can quickly and accurately rank the ability of molecules to inhibit telomerase activity. It is based on the method of Orlando and co-workers which utilizes PicoGreen to detect dsDNA formed during the polymerase chain reaction (PCR) amplification of telomerase products. PCR cycles were optimized to give as linear a signal as possible relative to telomerase products; 96-well streptavidin-coated PCR plates were used to isolate the preamplification telomerase products and to wash inhibitors away before the amplification step. The inhibitor removal step is critical to prevent false positives potentially caused by inhibition of Taq polymerase during amplification. Use of the streptavidin-coated PCR plate allows this step to be done much more rapidly than use of the liquid/liquid extraction adopted by others. We have demonstrated that this assay can correctly order the ability of four inhibitors to inhibit telomerase and reproduce within a factor of two the absolute IC(50) values determined by the more time-consuming direct assay. We have shown that the difference in IC(50) values determined in this assay versus the direct assay can be corrected for by using the standard curve appropriately. Using this method 96 compounds can be assessed in 3-5h. 相似文献
107.
Elsabbagh M Mercure E Hudry K Chandler S Pasco G Charman T Pickles A Baron-Cohen S Bolton P Johnson MH;BASIS Team 《Current biology : CB》2012,22(4):338-342
Autism spectrum disorders (henceforth autism) are diagnosed in around 1% of the population [1]. Familial liability confers risk for a broad spectrum of difficulties including the broader autism phenotype (BAP) [2, 3]. There are currently no reliable predictors of autism in infancy, but characteristic behaviors emerge during the second year, enabling diagnosis after this age [4, 5]. Because indicators of brain functioning may be sensitive predictors, and atypical eye contact is characteristic of the syndrome [6-9] and the BAP [10, 11], we examined whether neural sensitivity to eye gaze during infancy is associated with later autism outcomes [12, 13]. We undertook a prospective longitudinal study of infants with and without familial risk for autism. At 6-10 months, we recorded infants' event-related potentials (ERPs) in response to viewing faces with eye gaze directed toward versus away from the infant [14]. Longitudinal analyses showed that characteristics of ERP components evoked in response to dynamic eye gaze shifts during infancy were associated with autism diagnosed at 36 months. ERP responses to eye gaze may help characterize developmental processes that lead to later emerging autism. Findings also elucidate the mechanisms driving the development of the social brain in infancy. 相似文献
108.
109.
SM Lank BA Golbach HM Creager RW Wiseman DB Keskin EL Reinherz V Brusic DH O'Connor 《BMC genomics》2012,13(1):378
ABSTRACT: BACKGROUND: High-resolution HLA genotyping is a critical diagnostic and research assay. Current methods rarely achieve unambiguous high-resolution typing without making population-specific frequency inferences due to a lack of locus coverage and difficulty in exon-phase matching. Achieving high-resolution typing is also becoming more challenging with traditional methods as the database of known HLA alleles increases. RESULTS: We designed a cDNA amplicon-based pyrosequencing method to capture 94% of the HLA class I open-reading-frame with only two amplicons per sample, and an analogous method for class II HLA genes, with a primary focus on sequencing the DRB loci. We present a novel Galaxy server-based analysis workflow for determining genotype. During assay validation, we performed two GS Junior sequencing runs to determine the accuracy of the HLA class I amplicons and DRB amplicon at different levels of multiplexing. When 116 amplicons were multiplexed, we unambiguously resolved 99%of class I alleles to four- or six-digit resolution, as well as 100% unambiguous DRB calls. The second experiment, with 271 multiplexed amplicons, missed some alleles, but generated high-resolution, concordant typing for 93% of class I alleles, and 96% for DRB1 alleles. In a third, preliminary experiment we attempted to sequence novel amplicons for other class II loci with mixed success. CONCLUSIONS: The presented assay is higher-throughput and higher-resolution than existing HLA genotyping methods, and suitable for allele discovery or large cohort sampling. The validated class I and DRB primers successfully generated unambiguously high-resolution genotypes, while further work is needed to validate additional class II genotyping amplicons. 相似文献
110.
Hiltrud White Herbert Lebertz Iordanes Thanos Helmut Simon 《FEMS microbiology letters》1987,43(2):173-176
Whole cells of Clostridium thermoaceticum, crude extracts of such cells as well as the supernatant of 100 000 × g centrifugations catalyse the reduction of carbon monoxide to methanol in the presence of viologens or cobalt sepulchrate. Without such a mediator methanol could not be detected. The reaction shows a marked optimum at pH 5. The incubation of [5-14C]methyltetrahydrofolate led only to the formation of 14C-labeled ethanol; the radioactivity in methanol was negligible. The reaction seems to be catalysed by carbon monoxide dehydrogenase. 相似文献