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1.
Vibrio cholerae is autochthonous to various aquatic niches and is the etiological agent of the life-threatening diarrheal disease cholera. The persistence of V. cholerae in natural habitats is a crucial factor in the epidemiology of cholera. In contrast to the well-studied V. cholerae-chitin connection, scarce information is available about the factors employed by the bacteria for the interaction with collagens. Collagens might serve as biologically relevant substrates, because they are the most abundant protein constituents of metazoan tissues and V. cholerae has been identified in association with invertebrate and vertebrate marine animals, as well as in a benthic zone of the ocean where organic matter, including collagens, accumulates. Here, we describe the characterization of the V. cholerae putative collagenase, VchC, encoded by open reading frame VC1650 and belonging to the subfamily M9A peptidases. Our studies demonstrate that VchC is an extracellular collagenase degrading native type I collagen of fish and mammalian origin. Alteration of the predicted catalytic residues coordinating zinc ions completely abolished the protein enzymatic activity but did not affect the translocation of the protease by the type II secretion pathway into the extracellular milieu. We also show that the protease undergoes a maturation process with the aid of a secreted factor(s). Finally, we propose that V. cholerae is a collagenovorous bacterium, as it is able to utilize collagen as a sole nutrient source. This study initiates new lines of investigations aiming to uncover the structural and functional components of the V. cholerae collagen utilization program.  相似文献   
2.
Unlike other antiapoptotic Bcl-2 family members, Mcl-1 also mediates resistance to cancer therapy by uniquely inhibiting chemotherapy-induced senescence (CIS). In general, Bcl-2 family members regulate apoptosis at the level of the mitochondria through a common prosurvival binding groove. Through mutagenesis, we determined that Mcl-1 can inhibit CIS even in the absence of its apoptotically important mitochondrion-localizing domains. This finding prompted us to generate a series of Mcl-1 deletion mutants from both the N and C termini of the protein, including one that contained a deletion of all of the Bcl-2 homology domains, none of which impacted anti-CIS capabilities. Through subsequent structure-function analyses of Mcl-1, we identified a previously uncharacterized loop domain responsible for the anti-CIS activity of Mcl-1. The importance of the loop domain was confirmed in multiple tumor types, two in vivo models of senescence, and by demonstrating that a peptide mimetic of the loop domain can effectively inhibit the anti-CIS function of Mcl-1. The results from our studies appear to be highly translatable because we discerned an inverse relationship between the expression of Mcl-1 and of various senescence markers in cancerous human tissues. In summary, our findings regarding the unique structural properties of Mcl-1 provide new approaches for targeted cancer therapy.  相似文献   
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The carbon dioxide (CO2)-concentrating mechanism of cyanobacteria is characterized by the occurrence of Rubisco-containing microcompartments called carboxysomes within cells. The encapsulation of Rubisco allows for high-CO2 concentrations at the site of fixation, providing an advantage in low-CO2 environments. Cyanobacteria with Form-IA Rubisco contain α-carboxysomes, and cyanobacteria with Form-IB Rubisco contain β-carboxysomes. The two carboxysome types have arisen through convergent evolution, and α-cyanobacteria and β-cyanobacteria occupy different ecological niches. Here, we present, to our knowledge, the first direct comparison of the carboxysome function from α-cyanobacteria (Cyanobium spp. PCC7001) and β-cyanobacteria (Synechococcus spp. PCC7942) with similar inorganic carbon (Ci; as CO2 and HCO3) transporter systems. Despite evolutionary and structural differences between α-carboxysomes and β-carboxysomes, we found that the two strains are remarkably similar in many physiological parameters, particularly the response of photosynthesis to light and external Ci and their modulation of internal ribulose-1,5-bisphosphate, phosphoglycerate, and Ci pools when grown under comparable conditions. In addition, the different Rubisco forms present in each carboxysome had almost identical kinetic parameters. The conclusions indicate that the possession of different carboxysome types does not significantly influence the physiological function of these species and that similar carboxysome function may be possessed by each carboxysome type. Interestingly, both carboxysome types showed a response to cytosolic Ci, which is of higher affinity than predicted by current models, being saturated by 5 to 15 mm Ci. This finding has bearing on the viability of transplanting functional carboxysomes into the C3 chloroplast.Cyanobacteria inhabit a diverse range of ecological habitats, including both freshwater and marine ecosystems. The flexibility to occupy these different habitats is thought to come in part from the carbon-concentrating mechanism (CCM) present in all species (Badger et al., 2006). The CCM comprises inorganic carbon (Ci; as carbon dioxide [CO2] and HCO3) transporters for Ci uptake and protein microbodies called carboxysomes for CO2 concentration and fixation by Rubisco (Badger and Price, 2003). The CCM is believed to have evolved in response to changes in the absolute and relative levels of CO2 and oxygen (O2) in the atmosphere during the evolution of oxygenic photosynthesis in cyanobacteria (Price et al., 2008).There are two main phylogenetic groups within the cyanobacteria based on Rubisco and carboxysome phylogenies; α-cyanobacteria have α-carboxysomes with Form-IA Rubisco, whereas β-cyanobacteria have β-carboxysomes with Form-IB Rubisco (Tabita, 1999; Badger et al., 2002). Rubisco large subunit protein sequences from these two groups are closely related but nevertheless, distinguishable (Supplemental Fig. S1). In general, α-cyanobacteria and β-cyanobacteria occupy a quite different range of ecological habitats. The α-cyanobacteria are mostly marine organisms, with the majority of species living in the open ocean (Badger et al., 2006). Marine α-cyanobacteria live in very stable environments with high pH (pH 8.2) and dissolved carbon levels but low nutrients. They are characterized by small cells, very small genomes (1.6–2.8 Mb), and a few constitutively expressed carbon uptake transporters (Rae et al., 2011; Beck et al., 2012). They have been described as low flux, low energy cyanobacteria with a minimal CCM (Badger et al., 2006). Although these species are slow growing, oceanic cyanobacteria contribute as much as one-half of oceanic primary productivity (Liu et al., 1997, 1999; Field et al., 1998), suggesting that they may contribute up to 25% to net global productivity every year.In comparison, β-cyanobacteria occupy a much more diverse range of habitats, including freshwater, estuarine, and hot springs and never reach the same levels of global abundance (Badger et al., 2006). They are characterized by larger cells, larger genomes (2.2–3.6 Mb), and an array of carbon uptake transporters, including those transporters induced under low Ci (Rae et al., 2011, 2013). In addition to these broadly defined α-groups and β-groups, there are small numbers of α-cyanobacteria that have been termed transitional strains (Price, 2011; Rae et al., 2011). These species (e.g. Cyanobium spp. PCC7001, Synechococcus spp. WH5701, and Cyanobium spp. PCC6307; Supplemental Fig. S1) live in marginal marine and freshwater environments and have a number of characteristics similar to β-cyanobacteria. For example, they have a more diverse range of Ci uptake systems and a significantly larger genome than closely related α-cyanobacteria, and it has been suggested that the additional genes encoding transport systems were acquired by horizontal gene transfer (HGT) from β-cyanobacteria (Rae et al., 2011).Although the carboxysomes from α-cyanobacteria and β-cyanobacteria are very similar in overall structure, in that they share an outer protein shell of common phylogenetic origin (Kerfeld et al., 2005), they are distinguished from each other largely by differences in the proteins, which seem to make up or interact with the interior of the carboxysome compartment (Supplemental Table S1). This finding suggests that their different structures today have arisen through periods of common and convergent evolution. Certain carboxysome shell proteins from α-carboxysomes and β-carboxysomes show regions of significant sequence homology. These proteins are denoted as CsoS1 to CsoS4 (in α-cyanobacteria) and CcmKLO (in β-cyanobacteria), and the homologous regions have been termed bacterial microcompartment domains (Kerfeld et al., 2010; Rae et al., 2013). Proteins with these domains are also found in bacterial microcompartments in proteobacteria. However, other identified carboxysome proteins do not show any sequence homology between α-carboxysomes and β-carboxysomes but may perform similar functional roles. For example, carbonic anhydrase activity is essential for carboxysome function, but its activity seems to be provided by a range of different proteins (β-CcaA, β-CcmM, and α-CsoSCA; Kupriyanova et al., 2013). Similarly, β-CcmM and α-CsoS2 could play similar roles in organizing the interface between the shell and Rubisco within the carboxysomes (Gonzales et al., 2005; Long et al., 2007).The functioning of a carboxysome relies on a number of biochemical properties associated with the protein microbody structure. These properties include the biochemical/kinetic properties of Rubisco contained within carboxysomes, the conductance of the carboxysome shell to the influx of substrate ribulose-1,5-bisphosphate (RuBP) and the efflux of the carboxylation product phosphoglycerate (PGA), the conductance of the shell to the influx of bicarbonate and the efflux of CO2, and lastly, the manner in which bicarbonate is converted to CO2 within the carboxysomes. α-Carboxysomes and β-carboxysomes have the potential to differ in each of these properties. The flux of phosphorylated sugars across the shell has been postulated to be mediated by the pores in the hexameric shell proteins (Yeates et al., 2010; Kinney et al., 2011), which although similar, do differ between the two carboxysomes types. Bicarbonate and CO2 uptake processes are less well-defined but probably involve aspects of the way in which unique shell interface proteins interact with Rubisco, which also differs in that CsoS2 and CsoSCA are probably the interacting proteins involved in α-carboxysomes (Espie and Kimber, 2011), whereas CcmM and β-carboxysomal CA are variably involved in β-carboxysomes (Long et al., 2010). Finally, the Form-IA and Form-IB Rubisco proteins at the heart of carboxylation, although similar, have the potential to show different kinetic properties. Although Form-IB Rubiscos from β-cyanobacteria are well-characterized, the Form-IA counterparts have received very little attention. In addition, the CCM of very few strains of cyanobacteria have been studied at the level of biochemistry and physiology, and they have been almost exclusively β-cyanobacteria. As a result, there are significant gaps in our knowledge about the similarities and differences in functional traits between α-cyanobacterial and β-cyanobacterial strains. One important question that remains to be answered is whether α-carboxysomes and β-carboxysomes have intrinsic differences in their biochemical properties that influence the nature of the CCM, which is established within each broad cell type.Because of the difficulties in isolating and assaying intact carboxysomes in vitro, the characterization of biochemical properties of carboxysomes is not easily addressed. One way forward is to study the properties of the CCM in detail in a model representative strain from each group and compare their characteristics to contrast the intracellular function of α-cell types and β-cell types. In the past, it has been restricted because of the difficulties in growing many of the open ocean α-cyanobacteria and their very different natures in relation to inorganic transporter composition. However, the availability of α-cyanobacteria transition strains, which grow well in the laboratory, has provided an opportunity to address this question. The α-cyanobacteria Cyanobium spp. PCC7001 (hereafter Cyanobium spp.), in particular, grows in standard freshwater media (BG11) and has growth and photosynthetic performance properties that closely match the model β-cyanobacteria, Synechococcus spp. PCC7942 (hereafter Synechococcus spp.); for this reason, Cyanobium spp. is ideal for a balanced comparison of the in vivo physiological properties of α-carboxysomes and β-carboxysomes in two species with relatively similar Ci-uptake properties.Genome analysis of both strains indicates that Cyanobium spp. have many of the same carbon uptake systems present in Synechococcus spp. (Rae et al., 2011). In using two strains with such similar transport capacities, we aimed to shed light on aspects of the functional properties of carboxysomes in each strain and how these properties affect the operation of the CCM in α-cyanobacteria and β-cyanobacteria. Using both membrane inlet mass spectrometry (MIMS) and silicon oil centrifugation, we investigated Ci pool sizes and CO2 uptake rates in both species for cells grown at high and low CO2. Comparative Rubisco properties and photosynthetic rates of each species were determined, and intracellular pools of RuBP and PGA were measured. In addition, we characterized a number of cellular properties to determine differences in the biochemical environments in which each carboxysome type exists. Together, the results provide a unique functional comparison of two distinct carboxysome types from phylogenetically disparate cyanobacteria.  相似文献   
6.
The mixing performance of gastric contents during digestion is expected to have a major role on the rate and final bioavailability of nutrients within the body. The aim of this study was to characterize the ability of the human stomach to advect gastric contents with different rheological properties. The flow behavior of two Newtonian fluids (10−3 Pa s, 1 Pa s) and a pseudoplastic solution (K=0.223 Pa s0.59) during gastric digestion were numerically characterized within a simplified 3D model of the stomach geometry and motility during the process (ANSYS-FLUENT). The advective performances of each of these gastric flows were determined by analyzing the spatial distribution and temporal history of their stretching abilities (Lagrangian analysis). Results illustrate the limited influence that large retropulsive and vortex structures have on the overall dynamics of gastric flows. Even within the distal region, more than 50% of the flow experienced velocity and shear values lower than 10% of their respective maximums. While chaotic, gastric advection was always relatively poor (with Lyapunov exponents an order of magnitude lower than those of a laminar stirred tank). Contrary to expectations, gastric rheology had only a minor role on the advective properties of the flow (particularly within the distal region). As viscosity increased above 1 St, the role of fluid viscosity became largely negligible. By characterizing the fluid dynamic and mixing conditions that develop during digestion, this work will inform the design of novel in vitro systems of enhanced biomechanical performance and facilitate a more accurate diagnosis of gastric digestion processes.  相似文献   
7.
Scavenger receptor-mediated uptake of oxidized LDL (oxLDL) is thought to be the major mechanism of foam cell generation in atherosclerotic lesions. Recent data has indicated that native LDL is also capable of contributing to foam cell formation via low-affinity receptor-independent LDL particle pinocytosis and selective cholesteryl ester (CE) uptake. In the current investigation, Cu2+-induced LDL oxidation was found to inhibit macrophage selective CE uptake. Impairment of selective CE uptake was significant with LDL oxidized for as little as 30 min and correlated with oxidative fragmentation of apoB. In contrast, LDL aggregation, LDL CE oxidation, and the enhancement of scavenger receptor-mediated LDL particle uptake required at least 3 h of oxidation. Selective CE uptake did not require expression of the LDL receptor (LDL-R) and was inhibited similarly by LDL oxidation in LDL-R−/− versus WT macrophages. Inhibition of selective uptake was also observed when cells were pretreated or cotreated with minimally oxidized LDL, indicating a direct inhibitory effect of this oxLDL on macrophages. Consistent with the effect on LDL CE uptake, minimal LDL oxidation almost completely prevented LDL-induced foam cell formation. These data demonstrate a novel inhibitory effect of mildly oxidized LDL that may reduce foam cell formation in atherosclerosis.  相似文献   
8.
In these studies, the role of ceramide-1-phosphate (C1P) in the wound-healing process was investigated. Specifically, fibroblasts isolated from mice with the known anabolic enzyme for C1P, ceramide kinase (CERK), ablated (CERK−/− mice) and their wild-type littermates (CERK+/+) were subjected to in vitro wound-healing assays. Simulation of mechanical trauma of a wound by scratching a monolayer of fibroblasts from CERK+/+ mice demonstrated steadily increasing levels of arachidonic acid in a time-dependent manner in stark contrast to CERK−/− fibroblasts. This observed difference was reflected in scratch-induced eicosanoid levels. Similar, but somewhat less intense, changes were observed in a more complex system utilizing skin biopsies obtained from CERK-null mice. Importantly, C1P levels increased during the early stages of human wound healing correlating with the transition from the inflammatory stage to the peak of the fibroplasia stage (e.g., proliferation and migration of fibroblasts). Finally, the loss of proper eicosanoid response translated into an abnormal migration pattern for the fibroblasts isolated from CERK−/−. As the proper migration of fibroblasts is one of the necessary steps of wound healing, these studies demonstrate a novel requirement for the CERK-derived C1P in the proper healing response of wounds.  相似文献   
9.
Designed retroaldolases have utilized a nucleophilic lysine to promote carbon–carbon bond cleavage of β-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff base and to function as a general acid/base. Here we investigate an alternative active-site design in which the catalytic water molecule was replaced by the side chain of a glutamic acid. Five out of seven designs expressed solubly and exhibited catalytic efficiencies similar to previously designed retroaldolases for the conversion of 4-hydroxy-4-(6-methoxy-2-naphthyl)-2-butanone to 6-methoxy-2-naphthaldehyde and acetone. After one round of site-directed saturation mutagenesis, improved variants of the two best designs, RA114 and RA117, exhibited among the highest kcat (> 10− 3 s− 1) and kcat/KM (11–25 M− 1 s− 1) values observed for retroaldolase designs prior to comprehensive directed evolution. In both cases, the > 105-fold rate accelerations that were achieved are within 1–3 orders of magnitude of the rate enhancements reported for the best catalysts for related reactions, including catalytic antibodies (kcat/kuncat = 106 to 108) and an extensively evolved computational design (kcat/kuncat > 107). The catalytic sites, revealed by X-ray structures of optimized versions of the two active designs, are in close agreement with the design models except for the catalytic lysine in RA114. We further improved the variants by computational remodeling of the loops and yeast display selection for reactivity of the catalytic lysine with a diketone probe, obtaining an additional order of magnitude enhancement in activity with both approaches.  相似文献   
10.
Traumatic brain injury (TBI) induces severe harm and disability in many accident victims and combat‐related activities. The heat‐shock proteins Hsp70/Hsp110 protect cells against death and ischemic damage. In this study, we used mice deficient in Hsp110 or Hsp70 to examine their potential requirement following TBI. Data indicate that loss of Hsp110 or Hsp70 increases brain injury and death of neurons. One of the mechanisms underlying the increased cell death observed in the absence of Hsp110 and Hsp70 following TBI is the increased expression of reactive oxygen species‐induced p53 target genes Pig1, Pig8, and Pig12. To examine whether drugs that increase the levels of Hsp70/Hsp110 can protect cells against TBI, we subjected mice to TBI and administered Celastrol or BGP‐15. In contrast to Hsp110‐ or Hsp70i‐deficient mice that were not protected following TBI and Celastrol treatment, there was a significant improvement of wild‐type mice following administration of these drugs during the first week following TBI. In addition, assessment of neurological injury shows significant improvement in contextual and cued fear conditioning tests and beam balance in wild‐type mice that were treated with Celastrol or BGP‐15 following TBI compared to TBI‐treated mice. These studies indicate a significant role of Hsp70/Hsp110 in neuronal survival following TBI and the beneficial effects of Hsp70/Hsp110 inducers toward reducing the pathological consequences of TBI.

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