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31.
H Tabara M Sarkissian W G Kelly J Fleenor A Grishok L Timmons A Fire C C Mello 《Cell》1999,99(2):123-132
Double-stranded (ds) RNA can induce sequence-specific inhibition of gene function in several organisms. However, both the mechanism and the physiological role of the interference process remain mysterious. In order to study the interference process, we have selected C. elegans mutants resistant to dsRNA-mediated interference (RNAi). Two loci, rde-1 and rde-4, are defined by mutants strongly resistant to RNAi but with no obvious defects in growth or development. We show that rde-1 is a member of the piwi/sting/argonaute/zwille/eIF2C gene family conserved from plants to vertebrates. Interestingly, several, but not all, RNAi-deficient strains exhibit mobilization of the endogenous transposons. We discuss implications for the mechanism of RNAi and the possibility that one natural function of RNAi is transposon silencing. 相似文献
32.
Wei Ching Khor Suat Moi Puah Jin Ai Mary Anne Tan SD Puthucheary Kek Heng Chua 《PloS one》2015,10(12)
Gram-negative bacilli of the genus Aeromonas are primarily inhabitants of the aquatic environment. Humans acquire this organism from a wide range of food and water sources as well as during aquatic recreational activities. In the present study, the diversity and distribution of Aeromonas species from freshwater lakes in Malaysia was investigated using glycerophospholipid-cholesterol acyltransferase (GCAT) and RNA polymerase sigma-factor (rpoD) genes for speciation. A total of 122 possible Aeromonas strains were isolated and confirmed to genus level using the API20E system. The clonality of the isolates was investigated using ERIC-PCR and 20 duplicate isolates were excluded from the study. The specific GCAT-PCR identified all isolates as belonging to the genus Aeromonas, in agreement with the biochemical identification. A phylogenetic tree was constructed using the rpoD gene sequence and all 102 isolates were identified as: A. veronii 43%, A. jandaei 37%, A. hydrophila 6%, A. caviae 4%, A. salmonicida 2%, A. media 2%, A. allosaccharophila 1%, A. dhakensis 1% and Aeromonas spp. 4%. Twelve virulence genes were present in the following proportions—exu 96%, ser 93%, aer 87%, fla 83%, enolase 70%, ela 62%, act 54%, aexT 33%, lip 16%, dam 16%, alt 8% and ast 4%, and at least 2 of these genes were present in all 102 strains. The ascV, aexU and hlyA genes were not detected among the isolates. A. hydrophila was the main species containing virulence genes alt and ast either present alone or in combination. It is possible that different mechanisms may be used by each genospecies to demonstrate virulence. In summary, with the use of GCAT and rpoD genes, unambiguous identification of Aeromonas species is possible and provides valuable data on the phylogenetic diversity of the organism. 相似文献
33.
Studies of esterase 6 in Drosophila melanogaster. XVIII. Biochemical differences between the slow and fast allozymes 总被引:1,自引:0,他引:1
Most natural populations of Drosophila melanogaster are polymorphic for two
major electrophoretic variants at the esterase-6 locus. The frequency of
the EST 6F allozyme is greatest in populations in warmer latitudes, whereas
the EST 6S allozyme is predominant in colder latitudes. Latitudinal clines
in electromorph frequencies are found on three continents. Purified
preparations of the allozymes have been characterized for their pH optimum,
substrate specificity, organophosphate inhibition, alcohol activation,
thermal stability, and kinetic parameters. These and previous analyses of
the EST 6 allozymes reveal that the two variants have differences in their
physical and kinetic properties that may provide a basis for the selective
maintenance of the polymorphisms and an explanation of the clinal variation
observed in natural populations.
相似文献
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36.
Recent progress in bioinformatics research has led to the accumulation of huge quantities of biological data at various data sources.
The DNA microarray technology makes it possible to simultaneously analyze large number of genes across different samples.
Clustering of microarray data can reveal the hidden gene expression patterns from large quantities of expression data that in turn
offers tremendous possibilities in functional genomics, comparative genomics, disease diagnosis and drug development. The k-
¬means clustering algorithm is widely used for many practical applications. But the original k-¬means algorithm has several
drawbacks. It is computationally expensive and generates locally optimal solutions based on the random choice of the initial
centroids. Several methods have been proposed in the literature for improving the performance of the k-¬means algorithm. A
meta-heuristic optimization algorithm named harmony search helps find out near-global optimal solutions by searching the entire
solution space. Low clustering accuracy of the existing algorithms limits their use in many crucial applications of life sciences. In
this paper we propose a novel Harmony Search-K means Hybrid (HSKH) algorithm for clustering the gene expression data.
Experimental results show that the proposed algorithm produces clusters with better accuracy in comparison with the existing
algorithms. 相似文献
37.
Magnetic separation technology, using magnetic particles, is quick and easy method for sensitive and reliable capture of specific proteins, genetic material and other biomolecules. The technique offers an advantage in terms of subjecting the analyte to very little mechanical stress compared to other methods. Secondly, these methods are non-laborious, cheap and often highly scalable. Moreover, techniques employing magnetism are more amenable to automation and miniaturization. Now that the human genome is sequenced and about 30,000 genes are annotated, the next step is to identify the function of these individual genes, carrying out genotyping studies for allelic variation and SNP analysis, ultimately leading to identification of novel drug targets. In this post-genomic era, technologies based on magnetic separation are becoming an integral part of todays biology laboratory. This article briefly reviews the selected applications of magnetic separation techniques in the field of biotechnology, biomedicine and drug discovery. 相似文献
38.
Alternatively activated macrophages in intestinal helminth infection: effects on concurrent bacterial colitis 总被引:2,自引:0,他引:2
Weng M Huntley D Huang IF Foye-Jackson O Wang L Sarkissian A Zhou Q Walker WA Cherayil BJ Shi HN 《Journal of immunology (Baltimore, Md. : 1950)》2007,179(7):4721-4731
The distribution of several pathogenic helminth infections coincides geographically with many devastating microbial diseases, including enteric bacterial infections. To dissect the mechanisms by which helminths modulate the host's response to enteric bacteria and bacteria-mediated intestinal inflammation, we have recently established a coinfection model and shown that coinfection with the helminth Heligmosomoides polygyrus exacerbates colitis induced by infection with the gram-negative bacterial pathogen Citrobacter rodentium. The disease severity of the coinfected mice was correlated with high Citrobacter loads in the gut, translocation of the bacteria into mucosal and systemic immune compartments, delayed bacterial clearance, and a significantly enhanced colonic TNF-alpha response. In the present study, using our in vivo coinfection model as well as in vitro approaches, we test the hypothesis that the phenotypic and functional alterations in macrophages induced by the helminth-driven T cell response may contribute to the observed alterations in the response to C. rodentium. We show that via a STAT6-dependent mechanism H. polygyrus coinfection results in a marked infiltration into the colonic lamina propria of F4/80+ cells that have the phenotype of alternatively activated macrophages. Functional analysis of these macrophages further shows that they are impaired in their killing of internalized bacteria. Yet, these cells produce an enhanced amount of TNF-alpha in response to C. rodentium infection. These results demonstrate that helminth infection can impair host protection against concurrent enteric bacterial infection and promote bacteria-induced intestinal injury through a mechanism that involves the induction of alternatively activated macrophages. 相似文献
39.
Sanne Boessenkool Kristian Hanghøj Heidi M. Nistelberger Clio Der Sarkissian Agata T. Gondek Ludovic Orlando James H. Barrett Bastiaan Star 《Molecular ecology resources》2017,17(4):742-751
The feasibility of genome‐scale studies from archaeological material remains critically dependent on the ability to access endogenous, authentic DNA. In the majority of cases, this represents a few per cent of the DNA extract, at most. A number of specific pre‐extraction protocols for bone powder aimed to improve ancient DNA recovery before library amplification have recently been developed. Here, we test the effects of combining two of such protocols, a bleach wash and a predigestion step, on 12 bone samples of Atlantic cod and domestic horse aged 750–1350 cal. years before present. Using high‐throughput sequencing, we show that combined together, bleach wash and predigestion consistently yield DNA libraries with higher endogenous content than either of these methods alone. Additionally, the molecular complexity of these libraries is improved and endogenous DNA templates show larger size distributions. Other library characteristics, such as DNA damage profiles or the composition of microbial communities, are little affected by the pre‐extraction protocols. Application of the combined protocol presented in this study will facilitate the genetic analysis of an increasing number of ancient remains and will reduce the cost of whole‐genome sequencing. 相似文献
40.
Oligogalacturonic acids (OGAs), derived from plant cell wall pectin, have
been implicated in a number of signal transduction pathways involved in
growth, development and defense responses of higher plants. This study
investigates the size range of OGAs capable of inducing ethylene synthesis
in tomato plants, and demonstrates that in contrast with many other
effects, only short chain OGAs are active. Oligomers across a range of DP
from 2-15 were separated and purified to homogeneity by QAE-Sephadex anion
exchange chromatography using a novel elution system. The OGAs were applied
to tomato plants and assayed for their ability to induce ethylene gas
release and changes in steady state levels of mRNA encoding the ethylene
forming enzyme aminocyclopropane-1-carboxylic acid oxidase (ACO). The study
demonstrated that only OGAs in the size range of DP4-6 were active both in
eliciting ACO expression and in the production of ethylene.
相似文献