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71.
72.
GW Patton R Stephens IA Sidorov X Xiao RA Lempicki DS Dimitrov RH Shoemaker G Tudor 《BMC bioinformatics》2006,7(1):81
Background
Microarrays used for gene expression studies yield large amounts of data. The processing of such data typically leads to lists of differentially-regulated genes. A common terminal data analysis step is to map pathways of potentially interrelated genes. 相似文献73.
74.
Yvonne Welte James Adjaye Hans R Lehrach Christian RA Regenbrecht 《Cell communication and signaling : CCS》2010,8(1):1-10
Background
The fibroblast growth factor receptor (FGFR) interprets concentration gradients of FGF ligands and structural changes in the heparan sulfate (HS) co-receptor to generate different cellular responses. However, whether the FGFR generates different signals is not known.Results
We have previously shown in rat mammary fibroblasts that in cells deficient in sulfation, and so in HS co-receptor, FGF-2 can only stimulate a transient phosphorylation of p42/44MAPK and so cannot stimulate DNA synthesis. Here we demonstrate that this is because in the absence of HS, FGF-2 fails to stimulate the phosphorylation of the adaptor FGFR substrate 2 (FRS2). In cells possessing the HS co-receptor, FGF-2 elicits a bell-shaped dose response: optimal concentrations stimulate DNA synthesis, but supramaximal concentrations (≥ 100 ng/mL) have little effect. At optimal concentrations (300 pg/mL) FGF-2 stimulates a sustained dual phosphorylation of p42/44MAPK and tyrosine phosphorylation of FRS2. In contrast, 100 ng/mL FGF-2 only stimulates a transient early peak of p42/44MAPK phosphorylation and fails to stimulate appreciably the phosphorylation of FRS2 on tyrosine.Conclusions
These results suggest that the nature of the FGFR signal produced is determined by a combination of the HS co-receptor and the concentration of FGF ligand. Both the phosphorylation of the adaptor FRS2, the kinetics (sustained or transient) of phosphorylation of p42/44(MAPK) are varied, and so differing cellular responses are produced. 相似文献75.
76.
77.
Culture conditions required for obtaining maximum recombinant protein concentrations from two cell lines, Spodoptera frugiperda (IPLBeta-Sf21-AE) and Trichoplusia ni (Tn 5Beta-1-4), were determined in this work. Conditions studied include mode of culture (suspended vs attached), agitation rates, inoculum sizes, cell concentration at the time of infection, and various serum-free media (SFM). Results were compared with the performance of attached cultures in TnM-FH with 10% fetal bovine serum. Growth rates in the different culture media tested were similar, but the cell numbers achieved (i.e., yield) improved 2 to 2.7-fold in SFM over cultures in TnM-FH. Agitation rates of 150-160 rpm were necessary for maximum growth of suspended Tn 5Beta-1-4 cells compared to 125-150 rpm for Sf-21 cells. An inoculum size of 5 x 10(5) cells/mL gave good growth rates and optimum biomass yields for both cell lines. Cultures of both cell lines were infected with viruses encoding for beta-galactosidase or human secreted alkaline phosphatase (seAP). Protein expression in TnM-FH in attached culture showed that Tn 5Beta-1-4 cells are 2-4.5 times more productive on a per cell basis than Sf-21 cells grown under similar conditions. Production of beta-galactosidase in Sf-21 cells increased 50% in suspension cultures with SFM compared to attached cultures in TnM-FH, but seAP expression was essentially unchanged by culture techniques. The Tn 5Beta-1-4 cells produced 2.6-4.4 and 2.7-3 times more beta-galactosidase and seAP, respectively, in SFM in suspension compared to Sf-21 cells. EX-CELL 401 and Sf900-II were formulated as optimized SFM for Sf cell lines. However, in Sf-21 cultures EX-CELL 400 performed better than the other two media, as it increased the beta-galactosidase yield up to 25%. Surprisingly, EX-CELL 401 was the best medium for the production of beta-galactosidase by Tn 5Beta-1-4 cells, resulting in 25% and 69% higher volumetric and specific yields, respectively, compared to EX-CELL 405 which was formulated for this specific cell line. These results show that even when culture media are designed for maximal growth of a specific cell line, other media may provide the best conditions for protein production. 相似文献
78.
The phylogenetic origin of the bifunctional tyrosine-pathway protein in the enteric lineage of bacteria 总被引:5,自引:0,他引:5
Because bifunctional enzymes are distinctive and highly conserved products
of relatively infrequent gene-fusion events, they are particularly useful
markers to identify clusters of organisms at different hierarchical levels
of a phylogenetic tree. Within the subdivision of gram-negative bacteria
known as superfamily B, there are two distinctive types of tyrosine-pathway
dehydrogenases: (1) a broad- specificity dehydrogenase (recently termed
cyclohexadienyl dehydrogenase [CDH]) that can utilize either prephenate or
L-arogenate as alternative substrates and (2) a bifunctional CDH that also
posseses chorismate mutase activity. (T-proteins). The bifunctional
T-protein, thought to be encoded by fused ancestral genes for chorismate
mutase and CDH, was found to be present in enteric bacteria (Escherichia,
Shigella, Salmonella, Citrobacter, Klebsiella, Erwinia, Serratia,
Morganella, Cedecea, Kluyvera, Hafnia, Edwardsiella, Yersinia, and Proteus)
and in Aeromonas and Alteromonas. Outside of the latter "enteric lineage,"
the T-protein is absent in other major superfamily-B genera, such as
Pseudomonas (rRNA homology group I), Xanthomonas, Acinetobacter, and
Oceanospirillum. Hence, the T-protein must have evolved after the
divergence of the enteric and Oceanospirillum lineages.
3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase-phe, an early-pathway
isozyme sensitive to feedback inhibition by L- phenylalanine, has been
found in each member of the enteric lineage examined. The absence of both
the T-protein and DAHP synthase-phe elsewhere in superfamily B indicates
the emergence of these character states at approximately the same
evolutionary time.
相似文献
79.
Biotinyl-oligosaccharides are a relatively new generation of saccharide
probes that enable immobilization of desired oligosaccharides on
streptavidin matrices for studies of carbohydrate-protein interactions.
Here we describe the facile preparation of biotinyl-l-3-(2-naphthyl)-
alanine hydrazide (BNAH) derivatives of oligosaccharides, containing a
strong UV absorbing and fluorescent group, in which the ring of the
reducing-end monosaccharide is nonreduced. We evaluate reactivities of
immobilized BNAH- N -glycans with plant lectins that recognize aspects of
the oligosaccharide core or outer-arms. We make some comparisons with
2-amino-6-amidobiotinyl-pyridine (BAP) derivatives obtained by reductive
amination, and 6-(biotinyl)-aminocaproyl-hydrazide (BACH) derivatives which
have a longer spacer-arm. N -Glycan-BNAH and-BAP derivatives have, overall,
comparable reactivities with lectins which recognize N -glycan outer-arms
or the trimannosyl core, but only BNAH and BACH derivatives are bound by
lectins which recognize the non- reduced core. Moreover, with Pisum sativum
agglutinin (PSA) which additionally requires the fucosyl- N-
glycan-asparaginyl core for high affinity binding, the immobilized BNAH
derivative (which is an alanine hydrazide beta-glycoside) can substitute
for the natural beta- glycosylasparaginyl core, whereas the BACH derivative
(aminocaproyl- hydrazide-beta-glycoside) is less effective. BNAH is a
derivatization reagent of choice, therefore, for solid phase
carbohydrate-binding experiments with immobilized N -glycans.
相似文献
80.
Multidimensional heteronuclear NMR studies have been applied to the
resonance assignment and conformational analysis of 13C-enriched
Neu5Acalpha2-3Galbeta1-4Glc. It is demonstrated that three-dimensional
ROESY-HSQC experiments provide through-space distance restraints which
cannot be observed with conventional homonuclear 1H techniques due to
resonance overlap. In particular, connectivities demonstrating the
existence of the "anti" conformation about the Galbeta1-4Glc glycosidic
linkage are unambiguously observed. It is shown that 13C isotopic
enrichment of the trisaccharide at a level >95% enables straightforward
measurement of trans-glycosidic 1H-13C and 13C-13C coupling constants and a
Karplus-type relation is derived for the latter. In total 15 conformational
restraints were obtained for the trisaccharide in aqueous solution, all of
which were in excellent agreement with theoretical parameters computed from
a 5 ns molecular dynamics simulation of the glycan.
相似文献