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51.
P Singh C Raghukumar P Verma Y Shouche 《World journal of microbiology & biotechnology》2012,28(2):659-667
Increasing evidence of the fungal diversity in deep-sea sediments has come from amplification of environmental DNA with fungal
specific or eukaryote primer sets. In order to assess the fungal diversity in deep-sea sediments of the Central Indian Basin
(CIB) at ~5,000 m depth, we amplified sediment DNA with four different primer sets. These were fungal-specific primer pair
ITS1F/ITS4 (internal transcribed spacers), universal 18S rDNA primers NS1/NS2, Euk18S-42F/Euk18S-1492R and Euk18S-555F/Euk18S-1269R.
One environmental library was constructed with each of the primer pairs, and 48 clones were sequenced per library. These sequences
resulted in 8 fungal Operational Taxonomic Units (OTUs) with ITS and 19 OTUs with 18S rDNA primer sets respectively by taking
into account the 2% sequence divergence cut-off for species delineation. These OTUs belonged to 20 distinct fungal genera
of the phyla Ascomycota and Basidiomycota. Seven sequences were found to be divergent by 79–97% from the known sequences of
the existing database and may be novel. A majority of the sequences clustered with known sequences of the existing taxa. The
phylogenetic affiliation of a few fungal sequences with known environmental sequences from marine and hypersaline habitat
suggests their autochthonous nature or adaptation to marine habitat. The amplification of sequences belonging to Exobasidiomycetes
and Cystobasidiomycetes from deep-sea is being reported for the first time in this study. Amplification of fungal sequences
with eukaryotic as well as fungal specific primers indicates that among eukaryotes, fungi appear to be a dominant group in
the sampling site of the CIB. 相似文献
52.
Background
A contemporary view of the cancer genome reveals extensive rearrangement compared to normal cells. Yet how these genetic alterations translate into specific proteomic changes that underpin acquiring the hallmarks of cancer remains unresolved. The objectives of this study were to quantify alterations in protein expression in two HER2+ cellular models of breast cancer and to infer differentially regulated signaling pathways in these models associated with the hallmarks of cancer.Results
A proteomic workflow was used to identify proteins in two HER2 positive tumorigenic cell lines (BT474 and SKBR3) that were differentially expressed relative to a normal human mammary epithelial cell line (184A1). A total of 64 (BT474-184A1) and 69 (SKBR3-184A1) proteins were uniquely identified that were differentially expressed by at least 1.5-fold. Pathway inference tools were used to interpret these proteins in terms of functionally enriched pathways in the tumor cell lines. We observed "protein ubiquitination" and "apoptosis signaling" pathways were both enriched in the two breast cancer models while "IGF signaling" and "cell motility" pathways were enriched in BT474 and "amino acid metabolism" were enriched in the SKBR3 cell line.Conclusion
While "protein ubiquitination" and "apoptosis signaling" pathways were common to both the cell lines, the observed patterns of protein expression suggest that the evasion of apoptosis in each tumorigenic cell line occurs via different mechanisms. Evidently, apoptosis is regulated in BT474 via down regulation of Bid and in SKBR3 via up regulation of Calpain-11 as compared to 184A1. 相似文献53.
Valeric acid and 2-methylbutyric acid serve as chemical intermediates for a variety of applications such as plasticizers, lubricants and pharmaceuticals. The commercial process for their production uses toxic intermediates like synthesis gas and relies on non-renewable petroleum-based feedstock. In this work, synthetic metabolic pathways were constructed in Escherichia coli for the renewable production of these chemicals directly from glucose. The native leucine and isoleucine biosynthetic pathways in E. coli were expanded for the synthesis of valeric acid and 2-methylbutyric acid (2MB) respectively by the introduction of aldehyde dehydrogenases and 2-ketoacid decarboxylases. Various aldehyde dehydrogenases and 2-ketoacid decarboxylases were investigated for their activities in the constructed pathways. Highest titers of 2.59 g/L for 2-mthylbutyric acid and 2.58 g/L for valeric acid were achieved in shake flask experiments through optimal combinations of these enzymes. This work demonstrates the feasibility of renewable production of these high volume aliphatic carboxylic acids. 相似文献
54.
55.
Yogesh Mishra Hanna Johansson Jänkänpää Anett Z Kiss Christiane Funk Wolfgang P Schröder Stefan Jansson 《BMC plant biology》2012,12(1):6
Background
Plants exhibit phenotypic plasticity and respond to differences in environmental conditions by acclimation. We have systematically compared leaves of Arabidopsis thaliana plants grown in the field and under controlled low, normal and high light conditions in the laboratory to determine their most prominent phenotypic differences. 相似文献56.
B-cell lymphoma (Bcl-2) protein is an anti-apoptotic member of the Bcl-2 family. It is functionally demarcated into four Bcl-2
homology (BH) domains: BH1, BH2, BH3, BH4, one flexible loop domain (FLD), a transmembrane domain (TM), and an X domain. Bcl-2’s
BH domains have clearly been elucidated from a structural perspective, whereas the conformation of FLD has not yet been predicted,
despite its important role in regulating apoptosis through its interactions with JNK-1, PKC, PP2A phosphatase, caspase 3,
MAP kinase, ubiquitin, PS1, and FKBP38. Many important residues that regulate Bcl-2 anti-apoptotic activity are present in
this domain, for example Asp34, Thr56, Thr69, Ser70, Thr74, and Ser87. The structural elucidation of the FLD would likely
help in attempts to accurately predict the effect of mutating these residues on the overall structure of the protein and the
interactions of other proteins in this domain. Therefore, we have generated an increased quality model of the Bcl-2 protein
including the FLD through modeling. Further, molecular dynamics (MD) simulations were used for FLD optimization, to predict
the flexibility, and to determine the stability of the folded FLD. In addition, essential dynamics (ED) was used to predict
the collective motions and the essential subspace relevant to Bcl-2 protein function. The predicted average structure and
ensemble of MD-simulated structures were submitted to the Protein Model Database (PMDB), and the Bcl-2 structures obtained
exhibited enhanced quality. This study should help to elucidate the structural basis for Bcl-2 anti-apoptotic activity regulation
through its binding to other proteins via the FLD. 相似文献
57.
Ectomycorrhizal (ECM) fungal species, a "Symbiotic" relationship between tress and fungi in forest has a great ecological and economic importance. Here is an attempt to describe database named "EctomycorrhizalDB", addressing ECM diversity of Central Himalaya (Kumaun region), with special emphasis on their characterization, physical properties and morphological features along with specifications. This database would help the scientific community to draw a better understanding of the environmental factors that affects species diversity. AVAILABILITY: The database is available for free at http://www.kubic.nic.in/ectomychorhiza. 相似文献
58.
Joshi AA Kanekar PP Kelkar AS Shouche YS Vani AA Borgave SB Sarnaik SS 《Microbial ecology》2008,55(2):163-172
Aerobic, alkaliphilic bacteria were isolated and characterized from water and sediment samples collected in the winter season,
January 2002 from alkaline Lonar lake, India, having pH 10.5. The total number of microorganisms in the sediment and water
samples was found to be 102–106 cfu g−1 and 102–104 cfu ml−1, respectively. One hundred and ninety-six strains were isolated using different enrichment media. To study the bacterial
diversity of Lonar lake and to select the bacterial strains for further characterization, screening was done on the basis
of pH and salt tolerance of the isolates. Sixty-four isolates were subjected to phenotypic, biochemical characterization and
16S rRNA sequencing. Out of 64, 31 bacterial isolates were selected on the basis of their enzyme profile and further subjected
to phylogenetic analysis. Phylogenetic analysis indicated that most of the Lonar lake isolates were related to the phylum
Firmicutes, containing Low G+C, Gram-positive bacteria, with different genera: Bacillus, Paenibacillus, Alkalibacillus, Exiguobacterium, Planococcus, Enterococcus and Vagococcus. Seven strains constituted a Gram-negative bacterial group, with different genera: Halomonas, Stenotrophomonas and Providencia affiliated to γ-Proteobacteria, Alcaligenes to β-Proteobacteria and Paracoccus to α-Proteobacteria. Only five isolates were High G+C, Gram-positive bacteria associated with phylum Actinobacteria, with
various genera: Cellulosimicrobium, Dietzia, Arthrobacter and Micrococcus. Despite the alkaline pH of the Lonar lake, most of the strains were alkalitolerant and only two strains were obligate alkaliphilic.
Most of the isolates produced biotechnologically important enzymes at alkaline pH, while only two isolates (ARI 351 and ARI
341) showed the presence of polyhydroxyalkcanoate (PHA) and exopolysaccharide (EPS), respectively. 相似文献
59.
Alioua A Lu R Kumar Y Eghbali M Kundu P Toro L Stefani E 《The Journal of biological chemistry》2008,283(8):4808-4817
The large conductance, voltage- and Ca2+-activated potassium (MaxiK, BK) channel and caveolin-1 play important roles in regulating vascular contractility. Here, we hypothesized that the MaxiK alpha-subunit (Slo1) and caveolin-1 may interact with each other. Slo1 and caveolin-1 physiological association in native vascular tissue is strongly supported by (i) detergent-free purification of caveolin-1-rich domains demonstrating a pool of aortic Slo1 co-migrating with caveolin-1 to light density sucrose fractions, (ii) reverse co-immunoprecipitation, and (iii) double immunolabeling of freshly isolated myocytes revealing caveolin-1 and Slo1 proximity at the plasmalemma. In HEK293T cells, Slo1-caveolin-1 association was unaffected by the smooth muscle MaxiK beta1-subunit. Sequence analysis revealed two potential caveolin-binding motifs along the Slo1 C terminus, one equivalent, 1007YNMLCFGIY1015, and another mirror image, 537YTEYLSSAF545, to the consensus sequence, varphiXXXXvarphiXXvarphi. Deletion of 1007YNMLCFGIY1015 caused approximately 80% loss of Slo1-caveolin-1 association while preserving channel normal folding and overall Slo1 and caveolin-1 intracellular distribution patterns. 537YTEYLSSAF545 deletion had an insignificant dissociative effect. Interestingly, caveolin-1 coexpression reduced Slo1 surface and functional expression near 70% without affecting channel voltage sensitivity, and deletion of 1007YNMLCFGIY1015 motif obliterated channel surface expression. The results suggest 1007YNMLCFGIY1015 possible participation in Slo1 plasmalemmal targeting and demonstrate its role as a main mechanism for caveolin-1 association with Slo1 potentially serving a dual role: (i) maintaining channels in intracellular compartments downsizing their surface expression and/or (ii) serving as anchor of plasma membrane resident channels to caveolin-1-rich membranes. Because the caveolin-1 scaffolding domain is juxtamembrane, it is tempting to suggest that Slo1-caveolin-1 interaction facilitates the tethering of the Slo1 C-terminal end to the membrane. 相似文献
60.
Chakravarthy VS Gupte N Yogesh S Salhotra A 《International journal of neural systems》2008,18(2):157-164
Synchronization of chaotic low-dimensional systems has been a topic of much recent research. Such systems have found applications for secure communications. In this work we show how synchronization can be achieved in a high-dimensional chaotic neural network. The network used in our studies is an extension of the Hopfield Network, known as the Complex Hopfield Network (CHN). The CHN, also an associative memory, has both fixed point and limit cycle or oscillatory behavior. In the oscillatory mode, the network wanders chaotically from one stored pattern to another. We show how a pair of identical high-dimensional CHNs can be synchronized by communicating only a subset of state vector components. The synchronizability of such a system is characterized through simulations. 相似文献