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1.
Sergei L Kosakovsky Pond Sadie R Wisotsky Ananias Escalante Brittany Rife Magalis Steven Weaver 《Molecular biology and evolution》2021,38(3):1184
A number of evolutionary hypotheses can be tested by comparing selective pressures among sets of branches in a phylogenetic tree. When the question of interest is to identify specific sites within genes that may be evolving differently, a common approach is to perform separate analyses on subsets of sequences and compare parameter estimates in a post hoc fashion. This approach is statistically suboptimal and not always applicable. Here, we develop a simple extension of a popular fixed effects likelihood method in the context of codon-based evolutionary phylogenetic maximum likelihood testing, Contrast-FEL. It is suitable for identifying individual alignment sites where any among the sets of branches in a phylogenetic tree have detectably different ω ratios, indicative of different selective regimes. Using extensive simulations, we show that Contrast-FEL delivers good power, exceeding 90% for sufficiently large differences, while maintaining tight control over false positive rates, when the model is correctly specified. We conclude by applying Contrast-FEL to data from five previously published studies spanning a diverse range of organisms and focusing on different evolutionary questions. 相似文献
2.
3.
Niyati Jain Christopher E. Morgan Brittany D. Rife Marco Salemi Blanton S. Tolbert 《The Journal of biological chemistry》2016,291(5):2331-2344
Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3′ acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein. 相似文献
4.
Wayne W. Poon Anthony J. Carlos Brittany L. Aguilar Nicole C. Berchtold Crystal K. Kawano Vahe Zograbyan Tim Yaopruke Michael Shelanski Carl W. Cotman 《The Journal of biological chemistry》2013,288(23):16937-16948
We previously found that BDNF-dependent retrograde trafficking is impaired in AD transgenic mouse neurons. Utilizing a novel microfluidic culture chamber, we demonstrate that Aβ oligomers compromise BDNF-mediated retrograde transport by impairing endosomal vesicle velocities, resulting in impaired downstream signaling driven by BDNF/TrkB, including ERK5 activation, and CREB-dependent gene regulation. Our data suggest that a key mechanism mediating the deficit involves ubiquitin C-terminal hydrolase L1 (UCH-L1), a deubiquitinating enzyme that functions to regulate cellular ubiquitin. Aβ-induced deficits in BDNF trafficking and signaling are mimicked by LDN (an inhibitor of UCH-L1) and can be reversed by increasing cellular UCH-L1 levels, demonstrated here using a transducible TAT-UCH-L1 strategy. Finally, our data reveal that UCH-L1 mRNA levels are decreased in the hippocampi of AD brains. Taken together, our data implicate that UCH-L1 is important for regulating neurotrophin receptor sorting to signaling endosomes and supporting retrograde transport. Further, our results support the idea that in AD, Aβ may down-regulate UCH-L1 in the AD brain, which in turn impairs BDNF/TrkB-mediated retrograde signaling, compromising synaptic plasticity and neuronal survival. 相似文献
5.
M. Stine B. B. Sears D. E. Keathley 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1989,78(6):768-774
Summary Chloroplast DNA (cpDNA) was purified from blue spruce (Picea pungens Engelm.) and white spruce [P. glauca (Moench) Voss], and was digested with several different restriction endonucleases. Restriction fragment length polymorphisms (RFLPs) were identified that differentiated the cpDNA of both species. Intraspecific conservation of the RFLPs that differentiated each species was confirmed by examining trees from across the natural range of each species. Ten F1 hybrids were examined, and the cpDNA from each showed the banding pattern of the paternal species. Cloned Petunia cpDNA containing part of the rbcL gene hybridized to polymorphic bands, while a cloned maize mtDNA probe of the coxII gene failed to hybridize to any band. 相似文献
6.
Ellen M. Johnson Linda S. Schnabelrauch Barbara B. Sears 《Molecular & general genetics : MGG》1991,225(1):106-112
Summary A bovine tRNA gene cluster has been characterized and the sequences of four tDNAs determined. Two of the tDNAs could encode tRNASer
IGA, one tDNASer
UGA, and the fourth tRNAGln
CUG. The three serine tDNAs representing the UCN codon isoacceptor family are almost identical. However, the sequence of the tDNASer
TGA differs from a previously sequenced bovine tDNASer
TGA at 12 positions (ca. 14%). This finding suggests that in the bovine genome, two subfamilies of genes might encode tRNASer
UGA. It also raises the possibility that new genes for a specific UCN isoacceptor might arise from the genes of a different isoacceptor, and could explain previously observed differences between species in the anticodons of coevolving pairs of tRNAsSer
UCN. The gene cluster also contains complete and partial copies, and fragments, of the BCS (bovine consensus sequence) SINE (short interspersed nuclear element) family, six examples of which were sequenced. Some of these elements occur in close proximity to two of the serine tDNAs. 相似文献
7.
In previous work, we found that the phorbol ester drug 12-O-tetradecanoyl phorbol acetate (TPA) reversed the developmental restriction of melanogenesis that normally occurs in neural crest-derived Schwann cell precursors around embryonic Day 5 of quail development. That is, TPA treatment of dorsal root ganglia (DRG) from 7-day quail embryos caused Schwann cell precursors to regain the ability to give rise to melanocytes. In this paper, we examine other long-term effects of TPA on the differentiative and migratory properties of neural crest and crest-derived DRG cells, using heterospecific grafting methods. We report that TPA treatment in culture increased the extent of cell migration following grafting into host embryos, including some ectopic migration into the central nervous system and other locations. TPA did not, however, seem to change the fate of these crest-derived cells, except that some DRG cells underwent pigmentation, as had been observed previously. Interestingly, graft cells associated with peripheral nerves were found to be exclusively unpigmented, whereas graft cells found in all other locations, including the central nervous system, were both pigmented and unpigmented. This suggests that peripheral nerves may act in a fashion antagonistic to the effects of TPA. These findings are consistent with the notion that TPA treatment causes early crest-derived cells to regain developmental properties lost with developmental age. 相似文献
8.
Human erythrocyte spectrin binds calmodulin weakly under native conditions. This binding is enhanced in the presence of urea. The site responsible for this enhanced binding in urea has now been shown to reside in a specific region of the spectrin beta-subunit. Cleavage of spectrin with trypsin, cyanogen bromide or 2-nitro-5-thiocyanobenzoic acid generates fragments of the molecule which retain the ability to bind calmodulin under denaturing conditions. The origin of these fragments, identified by two-dimensional peptide mapping, is the terminal region of the spectrin beta-IV domain. The smallest peptide active in calmodulin binding is a 10 000 Mr fragment generated by cyanogen bromide cleavage. Only the intact 74 000 Mr fragment generated by trypsin (the complete beta-IV domain) retains the capacity to reassociate with the isolated alpha-subunit of spectrin. The position of a putative calmodulin binding site near a site for subunit-subunit association and protein 4.1 and actin binding suggests a possible role in vivo for calmodulin regulation of the spectrin-actin membrane skeleton or for regulation of subunit-subunit associations. This beta-subunit binding site in erythrocyte spectrin is found in a region near the NH2-terminus at a position analogous to the alpha-subunit calmodulin binding site previously identified in a non-erythroid spectrin by ultrastructural studies. 相似文献
9.
James V. Moroney N. E. Tolbert Barbara B. Sears 《Molecular & general genetics : MGG》1986,204(2):199-203
Summary Six independently isolated mutants of Chlamydomonas reinhardtii that require elevated CO2 for photoautotrophic growth were tested by complementation analysis. These mutants are likely to be defective in some aspect of the algal concentrating mechanism for inorganic carbon as they exhibit CO2 fixation and inorganic carbon accumulation properties different from the wild-type. Four of the six mutants defined a single complementation group and appear to be defective in an intracellular carbonic anhydrase. The other two mutations represent two additional complementation groups.Abbreviations HS
high salt medium which has 13 mM phosphate at pH 6.8
- HSA
high salt plus 36 mM acetate medium
- YA
high salt medium with 4 g yeast extract per L and 36mM acetate
- Arg
arginine
- cia-
CO2 accumulation mutants that cannot grow on low CO2
- Ci
inorganic carbon (CO2+HCO
-
3
)
- CA
carbonic anhydrase
- mt
mating type
Supported in part by the McKnight Foundation and by NSF grant PCM 8005917 and published as journal article 11924 from the Michigan State Agriculatural Experiment Station 相似文献
10.
M R Sears H H Rea R P Rothwell T V O'Donnell P E Holst A J Gillies R Beaglehole 《BMJ (Clinical research ed.)》1986,293(6558):1342-1345
Causes for the high mortality from asthma in New Zealand were investigated by comparing deaths from asthma in caucasian subjects aged 15-64 in New Zealand with those from asthma in the same age group in two regions in England. There were no significant differences in the accuracy of death certification. The verified asthma mortality in New Zealand (4.2/100,000) was over twice that in England. Many characteristics of patients and management, including poor compliance with treatment and deficiencies in long term and emergency care, were qualitatively similar in the two countries. New Zealand had an apparently higher rate of non-preventable deaths from asthma, suggesting a greater severity of asthma in New Zealand. In both countries, however, most deaths were associated with poor assessment, underestimation of severity and inappropriate treatment (over-reliance on bronchodilators and underuse of systemic corticosteroids), and delays in obtaining help. A greater frequency of some of these deficiencies in management remains a possible additional explanation for part of the excess mortality in New Zealand. 相似文献