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11.
Background
Concurrent peptide fragmentation (i.e. shotgun CID, parallel CID or MSE) has emerged as an alternative to data-dependent acquisition in generating peptide fragmentation data in LC-MS/MS proteomics experiments. Concurrent peptide fragmentation data acquisition has been shown to be advantageous over data-dependent acquisition by providing greater detection dynamic range and providing more accurate quantitative information. Nevertheless, concurrent peptide fragmentation data acquisition remains to be widely adopted due to the lack of published algorithms designed specifically to process or interpret such data acquired on any mass spectrometer. 相似文献12.
13.
Fourier transform infrared spectroscopy and site-directed isotope labeling as a probe of local secondary structure in the transmembrane domain of phospholamban. 总被引:1,自引:0,他引:1
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C F Ludlam I T Arkin X M Liu M S Rothman P Rath S Aimoto S O Smith D M Engelman K J Rothschild 《Biophysical journal》1996,70(4):1728-1736
Phospholamban is a 52-amino acid residue membrane protein that regulates Ca(2+)-ATPase activity in the sarcoplasmic reticulum of cardiac muscle cells. The hydrophobic C-terminal 28 amino acid fragment of phospholamban (hPLB) anchors the protein in the membrane and may form part of a Ca(2+)-selective ion channel. We have used polarized attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy along with site-directed isotope labeling to probe the local structure of hPLB. The frequency and dichroism of the amide I and II bands appearing at 1658 cm-1 and 1544 cm-1, respectively, show that dehydrated and hydrated hPLB reconstituted into dimyristoylphosphatidycholine bilayer membranes is predominantly alpha-helical and has a net transmembrane orientation. Specific local secondary structure of hPLB was probed by incorporating 13C at two positions in the protein backbone. A small band seen near 1614 cm-1 is assigned to the amide I mode of the 13C-labeled amide carbonyl group(s). The frequency and dichroism of this band indicate that residues 39 and 46 are alpha-helical, with an axial orientation that is approximately 30 degrees relative to the membrane normal. Upon exposure to 2H2O (D2O), 30% of the peptide amide groups in hPLB undergo a slow deuterium/hydrogen exchange. The remainder of the protein, including the peptide groups of Leu-39 and Leu-42, appear inaccessible to exchange, indicating that most of the hPLB fragment is embedded in the lipid bilayer. By extending spectroscopic characterization of PLB to include hydrated, deuterated as well as site-directed isotope-labeled hPLB films, our results strongly support models of PLB that predict the existence of an alpha-helical hydrophobic region spanning the membrane domain. 相似文献
14.
H.A. Ludlam B. Nwachukwu W.C. Noble† A.V. Swan‡ I. Phillips 《Journal of applied microbiology》1989,67(4):417-423
The preservation of micro-organisms that may be found on the skin was studied by storage in liquid media at -70°C. In the first part of the study the performance of 12 varieties of suspending media was evaluated with pure cultures of 17 species of micro-organisms maintained in the laboratory. After storage for 1 year the best medium (Oxoid Nutrient Broth with 15% glycerol) showed a mean survival for all organisms studied of 83.8%, with no significant differences between organisms. Even the worst medium (distilled water) permitted greater than 40% survival at 1 year. No changes in the characteristics of these micro-organisms were detected after 6 months storage in glycerol broth. In the second part of the study nose swabs were suspended in one representative medium (Bacto Nutrient Broth containing 7% glycerol). The mean percentage survival of staphylococci in these suspensions after 1 year's storage at -70°C was 75.4%. These results indicate that coagulase-negative staphylococci in samples of skin flora may be stored under these conditions for long periods, greatly reducing the work-load in epidemiological studies of infection. 相似文献
15.
Statistical analyses of DNA sequences of globin genes (beta A, beta C, and
gamma) from goat and sheep (including new sequence information for the
second intron of sheep beta A and gamma, kindly provided by A. Davis and A.
W. Nienhuis) indicate that the rates of nonsynonymous substitution in these
genes have been greatly accelerated following the gene duplication
separating gamma and the ancestor of beta A and beta C and the gene
duplication separating beta A and beta C. In both cases the acceleration
was apparently due to relaxation of purifying selection (functional
constraints) rather than advantageous mutations because acceleration
occurred only in less important parts of the beta globin chain. The rates
of nonsynonymous substitution in these genes are estimated to be about 2.3
x 10(-9) per site per year, which is three times higher than that for the
divergence between human beta and mouse beta major globin genes. Our
analyses further suggest that the rate of synonymous substitution in
functional genes and the rate of substitution in pseudogenes are
approximately equal and are between 2.8 x 10(-9) and 5.0 x 10(-9) and that
the rate of substitution in introns is about 3.0 x 10(-9). The divergence
time between beta A and beta C and that between gamma and the beta A-beta C
pair are about 12 and 30 million years, respectively. The proportion of
transition mutations is estimated to be 64%, two times higher than expected
under random mutation but considerably lower than the 96% estimated for
animal mitochondrial DNA.
相似文献
16.
17.
Discontinuous sequence change of human immunodeficiency virus (HIV) type 1 env sequences in plasma viral and lymphocyte-associated proviral populations in vivo: implications for models of HIV pathogenesis. 总被引:45,自引:36,他引:9
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P Simmonds L Q Zhang F McOmish P Balfe C A Ludlam A J Brown 《Journal of virology》1991,65(11):6266-6276
Sequence change in different hypervariable regions of the external membrane glycoprotein (gp120) of human immunodeficiency virus type 1 (HIV-1) was studied. Viral RNA associated with cell-free virus particles circulating in plasma and proviral DNA present in HIV-infected peripheral blood mononuclear cells (PBMCs) were extracted from blood samples of two currently asymptomatic hemophiliac patients over a 5-year period. HIV sequences were amplified by polymerase chain reaction to allow analysis in the V3, V4, and V5 hypervariable regions of gp120. Rapid sequence change, consisting of regular replacements by a succession of distinct viral populations, was found in both plasma virus and PBMC provirus populations. Significant differences between the frequencies of sequence variants in DNA and RNA populations within the same sample were observed, indicating that at any one time point, the predominant plasma virus variants were antigenically distinct from viruses encoded by HIV DNA sequences in PBMCs. How these findings contribute to current models of HIV pathogenesis is discussed. 相似文献
18.
C Ludlam W Palinski P G?r?g G V Born 《Proceedings of the Royal Society of London. Series B, Containing papers of a Biological character. Royal Society (Great Britain)》1988,235(1279):139-144
Male Wistar rats were heparinized and killed with pentobarbital. The upper and lower ends of the aortae were cannulated and the blood was washed out with saline until the washings contained calcium and sialic-acid-reacting material at minimal concentrations. The aortae were perfused with neuraminidase for 15 min. This caused the appearance of calcium as well as of sialic acids in the perfusate in total amounts of about 5.3 nmol and about 3.6 nmol per aorta respectively. The molar ratio of about 1.5 is sufficiently close to that determined for the association of calcium with sialic acids in vitro to suggest that their association is similar in vivo. 相似文献
19.
20.