排序方式: 共有61条查询结果,搜索用时 46 毫秒
1.
K Rippe N B Ramsing R Klement T M Jovin 《Journal of biomolecular structure & dynamics》1990,7(6):1199-1209
DNA oligonucleotides with appropriately designed complementary sequences can form a duplex in which the two strands are paired in a parallel orientation and not in the conventional antiparallel double helix of B-DNA. All parallel stranded (ps) molecules reported to date have consisted exclusively of dA.dT base pairs. We have substituted four dA.dT base pairs of a 25-nt parallel stranded linear duplex (ps-D1.D2) with dG.dC base pairs. The two strands still adopt a duplex structure with the characteristic spectroscopic properties of the ps conformation but with a reduced thermodynamic stability. Thus, the melting temperature of the ps duplex with four dG.dC base pairs (ps-D5.D6) is 10-16 degrees C lower and the van't Hoff enthalpy difference delta HvH for the helix-coil transition is reduced by 20% (in NaCl) and 10% (in MgCl2) compared to that of ps-D1.D2. Based on energy minimizations of a ps-[d(T5GA5).d(A5CT5)] duplex using force field calculations we propose a model for the conformation of a trans dG.dC base pair in a ps helix. 相似文献
2.
Distribution of sulfate-reducing bacteria, O2, and H2S in photosynthetic biofilms determined by oligonucleotide probes and microelectrodes. 总被引:15,自引:10,他引:5
下载免费PDF全文
![点击此处可从《Applied microbiology》网站下载免费的PDF全文](/ch/ext_images/free.gif)
The vertical distribution of sulfate-reducing bacteria (SRB) in photosynthetic biofilms from the trickling filter of a sewage treatment plant was investigated with oligonucleotide probes binding to 16S rRNA. To demonstrate the effect of daylight and photosynthesis and thereby of increased oxygen penetration, we incubated two 4-mm-thick biofilm samples in darkness or exposed to light at natural intensity. Gradients of O2, H2S, and pH were examined with microelectrodes during incubation. The samples were subsequently frozen with liquid nitrogen and sliced on a cryomicrotome in 20-microns vertical slices. Fluorescent-dye-conjugated oligonucleotides were used as "phylogenetic" probes to identify single cells in the slices. Oligonucleotide sequences were selected which were complementary to short sequence elements (16 to 20 nucleotides) within the 16S rRNA of sulfate-reducing bacteria. The probes were labeled with fluorescein or rhodamine derivatives for subsequent visualization by epifluorescence microscopy. Five probes were synthesized for eukaryotes, eubacteria, SRB (including most species of the delta group of purple bacteria), Desulfobacter spp., and a nonhybridizing control. The SRB were unevenly distributed in the biofilm, being present in all states from single scattered cells to dense clusters of several thousand cells. To quantify the vertical distribution of SRB, we counted cells along vertical transects through the biofilm. This was done in a blind experiment to ascertain the reliability of the staining. A negative correlation between the vertical distribution of positively stained SRB cells and the measured O2 profiles was found. The distribution differed in light- and dark-incubated samples presumably because of the different extensions of the oxic surface layer. In both cases the SRB were largely restricted to anoxic layers. 相似文献
3.
4.
Ammonia-oxidizing bacteria on root biofilms and their possible contribution to N use efficiency of different rice cultivars 总被引:12,自引:0,他引:12
Briones Aurelio M. Okabe Satoshi Umemiya Yoshiaki Ramsing Niels-Birger Reichardt Wolfgang Okuyama Hidetoshi 《Plant and Soil》2003,250(2):335-348
Ammonia-oxidizing bacteria (AOB) populations were studied on the root surface of different rice cultivars by PCR coupled with denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH). PCR-DGGE of the ammonium monooxygenase gene (amoA) showed a generally greater diversity on root samples compared to rhizosphere and unplanted soil. Sequences affiliated with Nitrosomonas spp. tended to be associated with modern rice hybrid lines. Root-associated AOB observed by FISH were found within a discrete biofilm coating the root surface. Although the total abundance of AOB on root biofilms of different rice cultivars did not differ significantly, there were marked contrasts in their population structure, indicating selection of Nitrosomonas spp. on roots of a hybrid cultivar. Observations by FISH on the total bacterial community also suggested that different rice cultivars support different bacterial populations even under identical environmental conditions. The presence of active AOB in the root environment predicts that a significant proportion of the N taken up by certain rice cultivars is in the form of NO3
–-N produced by the AOB. Measurement of plant growth of hydroponically grown plants showed a stronger response of hybrid cultivars to the co-provision of NH4
+ and NO3
–. In soil-grown plants, N use efficiency in the hybrid was improved during ammonium fertilization compared to nitrate fertilization. Since ammonium-fertilized plants actually receive a mixture of NH4
+ and NO3
– with ratios depending on root-associated nitrification activity, these results support the advantage of co-provision of ammonium and nitrate for the hybrid cultivar. 相似文献
5.
Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs 总被引:9,自引:4,他引:5
Presence of the dihydrouridine (D) stem in the mitochondrial cysteine tRNA
is unusually variable among lepidosaurian reptiles. Phylogenetic and
comparative analyses of cysteine tRNA gene sequences identify eight
parallel losses of the D-stem, resulting in D-arm replacement loops.
Sampling within the monophyletic Acrodonta provides no evidence for
reversal. Slipped-strand mispairing of noncontiguous repeated sequences
during replication or direct replication slippage can explain repeats
observed within cysteine tRNAs that contain a D-arm replacement loop. These
two mechanisms involving replication slippage can account for the loss of
the cysteine tRNA D-stem in several lepidosaurian lineages, and may
represent general mechanisms by which the secondary structures of
mitochondrial tRNAs are altered.
相似文献
6.
H Daims N B Ramsing K H Schleifer M Wagner 《Applied and environmental microbiology》2001,67(12):5810-5818
Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has found widespread application for analyzing the composition of microbial communities in complex environmental samples. Although bacteria can quickly be detected by FISH, a reliable method to determine absolute numbers of FISH-stained cells in aggregates or biofilms has, to our knowledge, never been published. In this study we developed a semiautomated protocol to measure the concentration of bacteria (in cells per volume) in environmental samples by a combination of FISH, confocal laser scanning microscopy, and digital image analysis. The quantification is based on an internal standard, which is introduced by spiking the samples with known amounts of Escherichia coli cells. This method was initially tested with artificial mixtures of bacterial cultures and subsequently used to determine the concentration of ammonia-oxidizing bacteria in a municipal nitrifying activated sludge. The total number of ammonia oxidizers was found to be 9.8 x 10(7) +/- 1.9 x 10(7) cells ml(-1). Based on this value, the average in situ activity was calculated to be 2.3 fmol of ammonia converted to nitrite per ammonia oxidizer cell per h. This activity is within the previously determined range of activities measured with ammonia oxidizer pure cultures, demonstrating the utility of this quantification method for enumerating bacteria in samples in which cells are not homogeneously distributed. 相似文献
7.
Carsten Lassen Ronnie N. Glud Niels B. Ramsing Niels Peter Revsbech 《Journal of phycology》1998,34(1):89-93
To determine gross photosynthesis in benthic microalgal communities, oxygen microelectrodes were used to measure the rate of decrease within the first 4 s after extinction of light. Photosynthetic rates calculated from third-order polynomial fits to the curve of decreasing O2 concentration were compared to the rates obtained by the traditional method, where rates were estimated from linear regression. When photosynthesis was calculated for the fitted initial rates of O2 decrease, maximum rates in microbial mats were up to 32% higher, and the depth-integrated gross photosynthesis was 5%–10% higher than the rates determined by the traditional method. The determinations from fitted initial rates also resulted in a more detailed profile of photosynthetic rate than that normally obtained. Computer simulation based on diffusion models, where the estimated initial rates of O2 decrease were assumed to represent actual photosynthesis rates, verified the validity of the curve-fitting procedure for obtaining high-resolution photosynthesis profiles. 相似文献
8.
Distribution of sulfate-reducing bacteria in a stratified fjord (Mariager Fjord, Denmark) as evaluated by most-probable-number counts and denaturing gradient gel electrophoresis of PCR-amplified ribosomal DNA fragments. 总被引:37,自引:27,他引:10
下载免费PDF全文
![点击此处可从《Applied microbiology》网站下载免费的PDF全文](/ch/ext_images/free.gif)
The sulfate-reducing bacterial populations of a stratified marine water column, Mariager Fjord, Denmark, were investigated by molecular and culture-dependent approaches in parallel. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA and DNA encoding rRNA (rDNA) isolated from the water column indicated specific bacterial populations in different water column layers and revealed a highly differentiated pattern of rRNA- and rDNA-derived PCR amplificates, probably reflecting active and resting bacterial populations. Hybridization of DGGE patterns with rRNA probes indicated the increased presence and activity (by at least 1 order of magnitude) of sulfate-reducing bacteria within and below the chemocline. Parallel to this molecular approach, an approach involving most-probable-number (MPN) counts was used, and it found a similar distribution of cultivable sulfate-reducing bacteria in the water column of Mariager Fjord, Approximately 25 cells and 250 cells per ml above and below the chemocline, respectively, were found. Desulfovibrio- and Desulfobulbus-related strains occurred in the oxic zone. DGGE bands from MPN cultures were sequenced and compared with those obtained from nucleic acids extracted from water column samples. The MPN isolates were phylogenetically affiliated with sulfate-reducing delta subdivision proteobacteria (members of the genera Desulfovibrio, Desulfobulbus, and Desulfobacter), whereas the molecular isolates constituted an independent lineage of the delta subdivision proteobacteria. DGGE of PCR-amplified nucleic acids with general eubacterial PCR primers conceptually revealed the general bacterial population, whereas the use of culture media allowed cultivable sulfate-reducing bacteria to be selected. A parallel study of Mariager Fjord biogeochemistry, bacterial activity, and bacterial counts complementing this investigation has been presented elsewhere (N.B. Ramsing, H. Fossing, T. G. Ferdelman, F. Andersen, and B. Thamdrup, Appl. Environ. 相似文献
9.
Morphological and metabolic responses to starvation by the dissimilatory metal-reducing bacterium Shewanella alga BrY. 总被引:1,自引:0,他引:1
下载免费PDF全文
![点击此处可从《Applied microbiology》网站下载免费的PDF全文](/ch/ext_images/free.gif)
The response of the dissimilatory metal-reducing bacterium Shewanella alga BrY to carbon and nitrogen starvation was examined. Starvation resulted in a gradual decrease in the mean cell volume from 0.48 to 0.2 micron 3 and a dramatic decrease in Fe(III) reductase activity. Growth of starved cultures was initiated with O2, ferric oxyhydroxide, Co(III)-EDTA, or Fe(III)-bearing subsurface materials as the sole electron acceptor. Microbially reduced subsurface materials reduced CrO(4)2-. Starvation of dissimilatory metal-reducing bacteria may provide a means of delivering this metabolism to contaminated subsurface environments for in situ bioremediation. 相似文献
10.
Michael Kühl Ronnie Nhr Glud Helle Ploug Niels Birger Ramsing 《Journal of phycology》1996,32(5):799-812
The photosynthetic performance of an epilithic cyano-bacterial biofilm was studied in relation to the in situ light field by the use of combined microsensor measurements of O2, photosynthesis, and spectral scalar irradiance. The high density of the dominant filamentous cyanobacteria (Oscillatoria sp.) embedded in a matrix of exopolymers and bacteria resulted in a photic zone of < 0.7 mm. At the biofilm surface, the prevailing irradiance and spectral composition were significantly different from the incident light. Multiple scattering led to an intensity maximum for photic light (400–700 nm) of ca. 120% of incident quantum irradiance at the biofilm surface. At the bottom of the euphotic zone in the biofilm, light was attenuated strongly to < 5–10% of the incident surface irradiance. Strong spectral signals from chlorophyll a (440 and 675 nm) and phycobilins (phycoerythrin 540–570 nm, phycocyanin 615–625 nm) were observed as distinct maxima in the scalar irradiance attenuation spectra in the upper 0.0–0.5 mm of the biofilm. The action spectrum for photosynthesis in the cyanobacterial layer revealed peak photosynthetic activity at absorption wavelengths of phycobilins, whereas only low photosynthesis rates were induced by light absorption of carotenoids (450–550 nm). Respiration rates in light- and dark-incubated biofilms were determined using simple flux calculations on measured O2 concentration profiles and photosynthetic rates. A significantly higher areal O2 consumption was found in illuminated biofilms than in dark-incubated biofilms. Although photorespiration accounted for part of the increase, the enhanced areal O2 consumption of illuminated biofilms could also be ascribed to a deeper oxygen penetration in light as well as an enhanced volumetric O2 respiration in and below the photic zone. Gross photosynthesis was largely unaffected by increasing flow velocities, whereas the O2 flux out of the photic zone, that is, net photosynthesis, increased with flow velocity. Consequently, the amount of produced O2 consumed within the biofilm decreased with increasing flow velocity. Our data indicated a close coupling of photosynthesis and respiration in biofilms, where the dissolved inorganic carbon requirement of the photo-synthetic population may largely be covered by the respiration of closely associated populations of heterotrophic bacteria consuming a significant part of the photosynthetically produced oxygen and organic carbon. 相似文献