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71.
Kirk?K?DurstonEmail author David?KY?Chiu Andrew?KC?Wong Gary?CL?Li 《EURASIP Journal on Bioinformatics and Systems Biology》2012,2012(1):8
Background
Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families.Results
The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function.Conclusions
Our results demonstrate that the method we present here using a k- modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.72.
Changing concepts in plant hormone action 总被引:4,自引:0,他引:4
Th.?GasparEmail author C.?Kevers O.?Faivre-Rampant M.?Crèvecoeur CL.?Penel H.?Greppin J.?Dommes 《In vitro cellular & developmental biology. Plant》2003,39(2):85-106
Summary A plant hormone is not, in the classic animal sense, a chemical synthesized in one organ, transported to a second organ to
exert a chemical action to control a physiological event. Any phytohormone can be synthesized everywhere and can influence
different growth and development processes at different places. The concept of physiological activity under hormonal control
cannot be dissociated from changes in concentrations at the site of action, from spatial differences and changes in the tissue's
sensitivity to the compound, from its transport and its metabolism, from balances and interactions with the other phytohormones,
or in their metabolic relationships, and in their signaling pathways as well. Secondary messengers are also involved. Hormonal
involvement in physiological processes can appear through several distinct manifestations (as environmental sensors, homeostatic
regulators and spatio-temporal synchronizers, resource allocators, biotime adjusters, etc.), dependent on or integrated with
the primary biochemical pathways. The time has also passed for the hypothesized ‘specific’ developmental hormones, rhizocaline,
canlocaline, and florigen: root, stem, and flower formation result from a sequential control of specific events at the right
places through a coordinated control by electrical signals, the known phytohormones and nonspecific molecules of primary and
secondary metabolism, and involve both cytoplasmic and apoplastic compartments. These contemporary views are examined in this
review. 相似文献
73.
Cell suspension cultures are useful for a wide range of biochemical and physiological studies, yet their production can be
technically demanding and often unreliable. Here we describe a protocol for producing Arabidopsis cell suspension cultures
that is reliable and easy to use. 相似文献
74.
Gilbert M Wagner H Weingart I Skotnica J Nieber K Tauer G Bergmann F Fischer H Wilhelm C 《Journal of plant physiology》2004,161(6):641-651
Here we describe a newly developed thermoluminescence measuring device that employs flash excitation, peltier heating, and light detection by channel photomultipliers (CPM). The new thermoluminometer is equipped with four sample holders for simultaneous measurements of thermoinduced light emission in the temperature range from -20 degrees C to +180 degrees C. It allows one to measure leaf samples, chloroplasts, thylakoids, algae, or even bioorganic material lacking chlorophyll by means of naturally induced or artificially applied chemilumigenic probes. The temperature range of the thermoluminometer allows one to analyse the thermoinduced radical pair recombination of photosystem II in the lower temperature region as well as chemiluminescence from lipid peroxidation in the higher temperature region. Hence, plant material can be assessed concerning both its photosynthetic and its oxidative stress status. Since the device is equipped with four sample holders and four CPM channels for simultaneous detection of thermoinduced light emission, it facilitates a high throughput. Therefore, the new device is interesting, not only in ecophysiology, but also in the field of plant breeding, as it can be used to study the stress tolerance of various cultivars of cultural crop plants. 相似文献
75.
Cell-cell communication via the production and detection of chemical signal molecules has been the focus of a great deal of research over the past decade. One class of chemical signals widely used by proteobacteria consists of N-acyl-homoserine lactones, which are synthesized by proteins related to LuxI of Vibrio fischeri and are detected by proteins related to the V. fischeri LuxR protein. A related marine bacterium, Vibrio harveyi, communicates using two chemical signals, one of which, autoinducer-2 (AI-2), is a furanone borate diester that is synthesized by the LuxS protein and detected by a periplasmic protein called LuxP. Evidence from a number of laboratories suggests that AI-2 may be used as a signal by diverse groups of bacteria, and might permit intergeneric signalling. These two families of signalling systems have been studied from the perspectives of physiology, ecology, biochemistry, and more recently, structural biology. Here, we review the biochemistry and structural biology of both acyl-homoserine-lactone-dependent and AI-2-dependent signalling systems. 相似文献
76.
77.
A statistical analysis of the nucleotide sequence variability in 14
published hepatitis B virus (HBV) genomes was carried out using parametric
and nonparametric methods. A parametric statistical model revealed that the
different regions of the genome differed significantly in their
variability. The conclusion was supported by a nonparametric kernel-density
model of the HBV genome. Genes S, C, and P, region X, the precore region,
and the pre-S2/pre-S1 regions were ranked in order of increasing
variability. In many instances, conserved regions of the genome identified
with sequences of known function in HBV biology. However, other
characterized regions (such as pre-S) showed much variability despite the
involvement of their encoded peptides in specific functions. Point
mutations that may result in the formation of stop codons and amino acid
changes may affect the clinical picture of HBV infection and may be
reflected in atypical serological patterns.
相似文献
78.
Sequence, organization, and evolution of the A+T region of Drosophila melanogaster mitochondrial DNA 总被引:2,自引:0,他引:2
The long (4.6-kb) A+T region of Drosophila melanogaster mitochondrial DNA
has been cloned and sequenced. The A+T region is organized in two large
arrays of tandemly repeated DNA sequence elements, with nonrepetitive
intervening and flanking sequences comprising only 22% of its length. The
first repeat array consists of five repeats of 338-373 bp. The second
consists of four intact 464-bp repeats and a fifth partial repeat of 137
bp. Three DNA sequence elements are found to be highly conserved in D.
melanogaster and in several Drosophila species with short A+T regions.
These include a 300-bp DNA sequence element that overlaps the DNA
replication origin and two thymidylate stretches identified on opposite DNA
strands. We conclude that the length heterogeneity observed in the A+T
regulatory region in mitochondrial DNAs from the genus Drosophila results
from the expansion (and contraction) of the number of repeated DNA sequence
elements. We also propose that the 300-bp conserved DNA sequence element,
in conjunction with another primary sequence determinant, perhaps the
adjacent thymidylate stretch, functions in the regulation of mitochondrial
DNA replication.
相似文献
79.
PCR fingerprinting using primers corresponding to repetitive (ERIC and REP) and insertion sequences (IS50) was investigated as a method to distinguish the pathovars of Pseudomonas syringae . After amplification of total DNA with the ERIC-, REP-, and IS50-PCR followed by agarose gel electrophoresis. most of the tested pathovars showed specific patterns of PCR products. The differences between the fingerprints among strains within a pathovar were small, with the exception of pathovars syringae, aptata , and atrofaciens . The fingerprints of the related pathovars savastanoi, phaseolicola, glycinea, morsprunorum, tabaci, lachrymans , and mori generated with the ERIC- and REP-primers were found to be very similar, showing the potential of this technique for taxonomical studies. In contrast, the IS50-PCR fingerprints of these pathovars were clearly distinguishable. The fingerprint patterns of a strain were highly reproducible with all three tested primer sets, also when whole cells were added to the reaction mixture. Thus, the PCR technique with the ERIC-, REP-, and IS50-primers is a rapid, simple, reproducible, and low cost method to identify and classify strains of the Pseudomonas syringae pathovars. 相似文献
80.
Significant amounts of ethylene were produced by Pseudomonas syringae pv. glycinea, pv. phaseolicola (which had been isolated from viny weed Pueraria lobata [Willd.] Ohwi [common name, kudzu]), and pv. pisi in synthetic medium. On the other hand, the bean strains of P. syringae pv. phaseolicola and strains of 17 other pathovars did not produce ethylene. P. syringae pv. glycinea and P. syringae pv. phaseolicola produced nearly identical levels of ethylene (about 5 x 10(sup-7) nl h(sup-1) cell(sup-1)), which were about 10 times higher than the ethylene level of P. syringae pv. pisi. Two 22-bp oligonucleotide primers derived from the ethylene-forming enzyme (efe) gene of P. syringae pv. phaseolicola PK2 were investigated for their ability to detect ethylene-producing P. syringae strains by PCR analysis. PCR amplification with this primer set resulted in a specific 0.99-kb fragment in all ethylene-producing strains with the exception of the P. syringae pv. pisi strains. Therefore, P. syringae pv. pisi may use a different biosynthetic pathway for ethylene production or the sequence of the efe gene is less conserved in this bacterium. P. syringae pv. phaseolicola isolated from kudzu and P. syringae pv. glycinea also produced ethylene in planta. It could be shown that the enhanced ethylene production in diseased tissue was due to the production of ethylene by the inoculated bacteria. Ethylene production in vitro and in planta was strictly growth associated. 相似文献