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61.
Human BAC ends quality assessment and sequence analyses 总被引:8,自引:0,他引:8
End sequences from bacterial artificial chromosomes (BACs) provide highly specific sequence markers in large-scale sequencing projects. To date, we have generated >300,000 end sequences from >186,000 human BAC clones with an average read length of >460 bp for a total of 141 Mb covering approximately 4.7% of the genome. Over 60% of the clones have BAC end sequences (BESs) from both ends representing more than fivefold coverage of the human genome by the paired-end clones. Our quality assessments and sequence analyses indicate that BESs from human BAC libraries developed at The California Institute of Technology (CalTech) and Roswell Park Cancer Institute have similar properties. The analyses have highlighted differences in insert size for different segments of the CalTech library. Problems with the fidelity of tracking of sequence data back to physical clones have been observed in some subsets of the overall BES dataset. The annotation results of BESs for the contents of available genomic sequences, sequence tagged sites, expressed sequence tags, protein encoding regions, and repeats indicate that this resource will be valuable in many areas of genome research. 相似文献
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Hyojeong Yi Han Song Junghyun Hwang Karan Kim William C. Nierman Heenam Stanley Kim 《PLoS genetics》2014,10(9)
Expansion or shrinkage of existing tandem repeats (TRs) associated with various biological processes has been actively studied in both prokaryotic and eukaryotic genomes, while their origin and biological implications remain mostly unknown. Here we describe various duplications (de novo TRs) that occurred in the coding region of a β-lactamase gene, where a conserved structure called the omega loop is encoded. These duplications that occurred under selection using ceftazidime conferred substrate spectrum extension to include the antibiotic. Under selective pressure with one of the original substrates (amoxicillin), a high level of reversion occurred in the mutant β-lactamase genes completing a cycle back to the original substrate spectrum. The de novo TRs coupled with reversion makes a genetic toggling mechanism enabling reversible switching between the two phases of the substrate spectrum of β-lactamases. This toggle exemplifies the effective adaptation of de novo TRs for enhanced bacterial survival. We found pairs of direct repeats that mediated the DNA duplication (TR formation). In addition, we found different duos of sequences that mediated the DNA duplication. These novel elements—that we named SCSs (same-strand complementary sequences)—were also found associated with β-lactamase TR mutations from clinical isolates. Both direct repeats and SCSs had a high correlation with TRs in diverse bacterial genomes throughout the major phylogenetic lineages, suggesting that they comprise a fundamental mechanism shaping the bacterial evolution. 相似文献
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Schaap FG Nierman MC Berbée JF Hattori H Talmud PJ Vaessen SF Rensen PC Chamuleau RA Kuivenhoven JA Groen AK 《Journal of lipid research》2006,47(10):2333-2339
The relevance of apolipoprotein A-V (apoA-V) for human lipid homeostasis is underscored by genetic association studies and the identification of truncation-causing mutations in the APOA5 gene as a cause of type V hyperlipidemia, compatible with an LPL-activating role of apoA-V. An inverse correlation between plasma apoA-V and triglyceride (TG) levels has been surmised from animal data. Recent studies in human subjects using (semi)quantitative immunoassays, however, do not provide unambiguous support for such a relationship. Here, we used a novel, validated ELISA to measure plasma apoA-V levels in patients (n = 28) with hypertriglyceridemia (HTG; 1.8-78.7 mmol TG/l) and normolipidemic controls (n = 42). Unexpectedly, plasma apoA-V levels were markedly increased in the HTG subjects compared with controls (1,987 vs. 258 ng/ml; P < 0.001). In the HTG group, apoA-V and TG were positively correlated (r = +0.44, P = 0.02). In addition, we noted an increased level of the LPL-inhibitory protein apoC-III in the HTG group (45.8 vs. 10.6 mg/dl in controls; P < 0.001). The correlation between apoA-V and TG levels in the HTG group disappeared (partial r = +0.09, P = 0.65) when controlling for apoC-III levels. In contrast, apoC-III and TG remained positively correlated in this group when controlling for apoA-V (partial r = +0.43, P = 0.025). Our findings suggest that in HTG patients, increased TG levels are accompanied by high plasma levels of apoA-V and apoC-III, apolipoproteins with opposite modes of action. This study provides evidence for a complex interaction between apoA-V and apoC-III in patients with severe HTG. 相似文献
69.
A single lineage of r2 retrotransposable elements is an active, evolutionarily stable component of the Drosophila rDNA locus 总被引:1,自引:0,他引:1
R2 elements are non-long-terminal-repeat (non-LTR) retrotransposons that
insert specifically in the 28S rRNA genes of many insects. Previous reports
concerning this element in the genus Drosophila have suggested that R2
elements are absent from many species of this genus, particularly those
species from the subgenus Drosophila. In this report, we present an
extensive study of the distribution and evolution of R2 elements in
Drosophila. A PCR survey of 59 species from 23 species groups of the two
major Drosophila subgenera found that R2 elements are present in all but
two species of the melanogaster species subgroup. Phylogenetic analysis
based on partial nucleotide sequences of R2 elements from 23 species
demonstrates that the relationships of R2 elements are congruent with those
of the Drosophila species phylogeny, suggesting that these elements have
been vertically inherited since the divergence of this genus some 60 MYA.
Sequence variation between different copies of R2 elements within each
species was less than 0.16%, indicating that these elements are undergoing
concerted evolution similar to that of the 28S genes. Several properties of
the R2 sequences suggest that these elements depend on retrotransposition
in addition to simple recombination to remain within the rDNA locus: the
rates of synonymous substitutions averaged 4.8 times the rate of
replacement substitutions, 82 of 83 R2 copies partially sequenced contained
intact open reading frames, and, finally, length variation associated with
the poly(A) 3' tails indicated that many R2 copies are the direct result of
retrotransposition.
相似文献
70.
Wilkinson JR Yu J Bland JM Nierman WC Bhatnagar D Cleveland TE 《Applied microbiology and biotechnology》2007,74(6):1308-1319
Aflatoxins are toxic and carcinogenic secondary metabolites produced by the fungi Aspergillus flavus and Aspergillus parasiticus. To better understand the molecular mechanisms that regulate aflatoxin production, the biosynthesis of the toxin in A. flavus and A. parasticus grown in yeast extract sucrose media supplemented with 50 mM tryptophan (Trp) were examined. Aspergillus flavus grown in the presence of 50 mM tryptophan was found to have significantly reduced aflatoxin B1 and B2 biosynthesis, while A. parasiticus cultures had significantly increased B1 and G1 biosynthesis. Microarray analysis of RNA extracted from fungi grown under these conditions revealed 77 genes that are expressed
significantly different between A. flavus and A. parasiticus, including the aflatoxin biosynthetic genes aflD (nor-1), aflE (norA), and aflO (omtB). It is clear that the regulatory mechanisms of aflatoxin biosynthesis in response to Trp in A. flavus and A. parasiticus are different. These candidate genes may serve as regulatory factors of aflatoxin biosynthesis. 相似文献