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1.
Vladislav Cepk 《Journal of phycology》1993,29(6):844-852
DNA containing structures (nucleoids) were visualized by 4′, 6-diamidino-2-phenylindole (DAPI) fluorescent staining in two groups of cyanophytes (59 filamentous oscillatorialean species and 12 coccal Synechococcus-like organisms) to test the possibility of using nucleoid morphology in cyanophyte taxonomy. The morphology of nucleoids (size, shape, and structure) in oscillatorialean species is specific for individual families. The morphology of the nucleoid in Synechococcus-like species agrees from the proposed separation of the genus Cyanothece from Synechococcus. A much different nucleoid morphology in three species of Cyanothece suggests that these species should be separated into a new genus. On the basis of other characters, the species could be returned to the genus Cyanobacterium. My results indicate that the morphology of nucleoids is a valuable character in the classification of the cyanophytes examined; thus, it is a prospective feature that could be used in the taxonomy of other groups of cyanophytes. Additionally, DAPI staining is not a complicated procedure. The new character is easy to see in samples taken from nature, both living and preserved. 相似文献
2.
Summary A method for quantification of distances between amide hydrogens using only the 3D NOESY-HMQC experiment recorded on a 15N-labelled protein is presented. This method is based on an approximate expression of the NOE intensities between amide hydrogens obtained from continuum modelling of the non-amide spins; this expression is used in a distance calculation algorithm. The algorithm has been named CROWD, standing for Continuum approximation of Relaxati On path Ways between Dilute spins. This approximation as well as the CROWD algorithm are tested on a simulated case; the CROWD algorithm is then applied to experimental data, measured on a fragment of bacteriorhodopsin. 相似文献
3.
Konstantin K Turoverov Vladislav V Verkhusha Mikhail M Shavlovsky Alexander G Biktashev Olga I Povarova Irina M Kuznetsova 《Biochemistry》2002,41(3):1014-1019
The kinetics of actin unfolding induced by guanidine hydrochloride has been studied. On the basis of obtained experimental data a new kinetic pathway of actin unfolding was proposed. We have shown that the transition from native to inactivated actin induced by guanidine hydrochloride (GdnHCl) passes through essential unfolding of the protein. This means that inactivated actin should be considered as the off-pathway species rather than an intermediate conformation between native and completely unfolded states of actin, as has been assumed earlier. The rate constants of the transitions that give rise to the inactivated actin were determined. At 1.0-2.0 M GdnHCl the value of the rate constant of the transition from native to essentially unfolded actin exceeds that of the following step of inactivated actin formation. It leads to the accumulation of essentially unfolded macromolecules early in the unfolding process, which in turn causes the minimum in the time dependencies of tryptophan fluorescence intensity, parameter A, characterizing the intrinsic fluorescence spectrum position, and tryptophan fluorescence anisotropy. 相似文献
4.
Vladislav B. Bergo Oleg A. Sineshchekov Joel M. Kralj Ranga Partha Elena N. Spudich Kenneth J. Rothschild John L. Spudich 《The Journal of biological chemistry》2009,284(5):2836-2843
Proteorhodopsins (PRs), photoactive retinylidene membrane proteins
ubiquitous in marine eubacteria, exhibit light-driven proton transport
activity similar to that of the well studied bacteriorhodopsin from halophilic
archaea. However, unlike bacteriorhodopsin, PRs have a single highly conserved
histidine located near the photoactive site of the protein. Time-resolved
Fourier transform IR difference spectroscopy combined with visible absorption
spectroscopy, isotope labeling, and electrical measurements of light-induced
charge movements reveal participation of His-75 in the proton translocation
mechanism of PR. Substitution of His-75 with Ala or Glu perturbed the
structure of the photoactive site and resulted in significantly shifted
visible absorption spectra. In contrast, His-75 substitution with a positively
charged Arg did not shift the visible absorption spectrum of PR. The mutation
to Arg also blocks the light-induced proton transfer from the Schiff base to
its counterion Asp-97 during the photocycle and the acid-induced protonation
of Asp-97 in the dark state of the protein. Isotope labeling of histidine
revealed that His-75 undergoes deprotonation during the photocycle in the
proton-pumping (high pH) form of PR, a reaction further supported by results
from H75E. Finally, all His-75 mutations greatly affect charge movements
within the PR and shift its pH dependence to acidic values. A model of the
proteorhodopsin proton transport process is proposed as follows: (i) in the
dark state His-75 is positively charged (protonated) over a wide pH range and
interacts directly with the Schiff base counterion Asp-97; and (ii)
photoisomerization-induced transfer of the Schiff base proton to the Asp-97
counterion disrupts its interaction with His-75 and triggers a histidine
deprotonation.A variety of unicellular microorganisms contain primary proton pumps that
convert solar energy into a transmembrane electrochemical proton gradient,
which is subsequently used by membrane ATP synthases to generate chemical
energy. Well known examples of such pumps are the haloarchaeal rhodopsins,
photoactive, seven-helix membrane proteins, which include the well studied
proton pump bacteriorhodopsin
(BR)4 from
Halobacterium salinarum and BR homologs in other haloarchaea.
Recently, a much larger new family of light-driven proton pumps, the
proteorhodopsins (PRs), was identified in marine proteobacteria throughout the
oceans
(1–3).
Despite the diverse properties of PRs, including different visible absorption
maxima and photocycle rates
(4–6),
they all share with BR several key conserved residues as well as an
all-trans-retinylidene chromophore in their unphotolyzed state, which
is covalently bound to transmembrane helix G via a protonated Schiff base
linkage.Many of the molecular events that occur in PRs following light activation
are similar to those of BR, including an initial ultrafast
all-trans→13-cis-retinal isomerization, which triggers
a sequence of protein conformational changes, including several intramolecular
proton transfer reactions. The two key carboxylate groups involved in proton
pumping in helix C of BR are conserved in PRs, and in the first found and most
commonly studied PR, the Monterey Bay variant eBAC31A08, also known as
green-absorbing proteorhodopsin (GPR), the helix C residues Asp-97 and Glu-108
undergo protonation changes during the photocycle similar to those of the
homologous carboxylate residues in BR. Initial FTIR studies on GPR identified
the role of Asp-97 as the Schiff base counterion and proton acceptor during
Schiff base deprotonation and concomitant M formation and Glu-108 as the
proton donor that reprotonates the Schiff base during N formation
(7,
8). Studies of other variants
indicate these roles of the two carboxylic acid residues are general in the
proteorhodopsin
family.5One major difference between BR and the PRs is the presence of a highly
conserved histidine residue at position 75, near the middle of transmembrane
helix B in the latter pigments. The His-75 homolog is not present in BR nor
thus far found in other microbial rhodopsins
(9). The proximity of His-75 to
the protein active site and specifically to the Schiff base counterion Asp-97
inferred from the x-ray crystal structure of BR suggests its involvement in
spectral tuning of the visible absorption
(10) and potentially PR
photochemical reactions. Because the pKa of histidine in
solution is close to neutral pH
(11), its imidazole group
often plays a major role in intramolecular proton transfers in enzymes,
including NADPH oxidase (12),
alcohol dehydrogenase (13),
carbonic anhydrase II (14),
and serine proteases (15).In this study we have used a combination of time-resolved FTIR difference
spectroscopy, visible absorption spectroscopy, isotope labeling, kinetic
charge displacement measurements, and site-directed mutagenesis to study the
role of His-75 in GPR. We report evidence that protonated His-75 interacts
directly with Asp-97 in the unphotolyzed protein and during the photocycle
undergoes a deprotonation in response to the protonation of Asp-97. 相似文献
5.
Paul D. Piehowski Vladislav A. Petyuk John D. Sandoval Kristin E. Burnum Gary R. Kiebel Matthew E. Monroe Gordon A. Anderson David G. Camp II Richard D. Smith 《Proteomics》2013,13(5):766-770
For bottom‐up proteomics, there are wide variety of database‐searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid‐search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection‐–referred to as STEPS‐–utilizes user‐defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal “parameter set” for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true‐positive identifications are demonstrated using datasets derived from immunoaffinity‐depleted blood serum and a bacterial cell lysate, two common proteomics sample types. 相似文献
6.
Alexander G. Volkov Chrystelle L. Vilfranc Veronica A. Murphy Colee M. Mitchell Maia I. Volkova Lawrence O’Neal Vladislav S. Markin 《Journal of plant physiology》2013
The electrical phenomena and morphing structures in the Venus flytrap have attracted researchers since the nineteenth century. We have observed that mechanical stimulation of trigger hairs on the lobes of the Venus flytrap induces electrotonic potentials in the lower leaf. Electrostimulation of electrical circuits in the Venus flytrap can induce electrotonic potentials propagating along the upper and lower leaves. The instantaneous increase or decrease in voltage of stimulating potential generates a nonlinear electrical response in plant tissues. Any electrostimulation that is not instantaneous, such as sinusoidal or triangular functions, results in linear responses in the form of small electrotonic potentials. The amplitude and sign of electrotonic potentials depend on the polarity and the amplitude of the applied voltage. Electrical stimulation of the lower leaf induces electrical signals, which resemble action potentials, in the trap between the lobes and the midrib. The trap closes if the stimulating voltage is above the threshold level of 4.4 V. Electrical responses in the Venus flytrap were analyzed and reproduced in the discrete electrical circuit. The information gained from this study can be used to elucidate the coupling of intracellular and intercellular communications in the form of electrical signals within plants. 相似文献
7.
Xiuling Li Pavel Přibyl Kateřina Bišová Shigeyuki Kawano Vladislav Cepák Vilém Zachleder Mária Čížková Irena Brányiková Milada Vítová 《Biotechnology and bioengineering》2013,110(1):97-107
The alga Parachlorella kessleri, strain CCALA 255, grown under optimal conditions, is characterized by storage of energy in the form of starch rather than lipids. If grown in the complete medium, the cultures grew rapidly, producing large amounts of biomass in a relatively short time. The cells, however, contained negligible lipid reserves (1–10% of DW). Treatments inducing hyperproduction of storage lipids in P. kessleri biomass were described. The cultures were grown in the absence or fivefold decreased concentration of either nitrogen or phosphorus or sulfur. Limitation by all elements using fivefold or 10‐fold diluted mineral medium was also tested. Limitation with any macroelement (nitrogen, sulfur, or phosphorus) led to an increase in the amount of lipids; nitrogen limitation was the most effective. Diluted nutrient media (5‐ or 10‐fold) were identified as the best method to stimulate lipid overproduction (60% of DW). The strategy for lipid overproduction consists of the fast growth of P. kessleri culture grown in the complete medium to produce sufficient biomass (DW more than 10 g/L) followed by the dilution of nutrient medium to stop growth and cell division by limitation of all elements, leading to induction of lipid production and accumulation up to 60% DW. Cultivation conditions necessary for maximizing lipid content in P. kessleri biomass generated in a scale‐up solar open thin‐layer photobioreactor were described. Biotechnol. Bioeng. 2013; 110: 97–107. © 2012 Wiley Periodicals, Inc. 相似文献
8.
Marina V. Shirmanova Ekaterina O. Serebrovskaya Konstantin A. Lukyanov Ludmila B. Snopova Marina A. Sirotkina Natalia N. Prodanetz Marina L. Bugrova Ekaterina A. Minakova Ilya V. Turchin Vladislav A. Kamensky Sergey A. Lukyanov Elena V. Zagaynova 《Journal of biophotonics》2013,6(3):283-290
KillerRed is known to be a unique red fluorescent protein displaying strong phototoxic properties. Its effectiveness has been shown previously for killing bacterial and cancer cells in vitro. Here, we investigated the photototoxicity of the protein on tumor xenografts in mice. HeLa Kyoto cell line stably expressing KillerRed in mitochondria and in fusion with histone H2B was used. Irradiation of the tumors with 593 nm laser led to photobleaching of KillerRed indicating photosensitization reaction and caused significant destruction of the cells and activation of apoptosis. The portion of the dystrophically changed cells increased from 9.9% to 63.7%, and the cells with apoptosis hallmarks from 6.3% to 14%. The results of this study suggest KillerRed as a potential genetically encoded photosensitizer for photodynamic therapy of cancer. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim) 相似文献
9.
Asaf Zviran Nofar Mor Yoach Rais Hila Gingold Shani Peles Elad Chomsky Sergey Viukov Jason D. Buenrostro Roberta Scognamiglio Leehee Weinberger Yair S. Manor Vladislav Krupalnik Mirie Zerbib Hadas Hezroni Diego Adhemar Jaitin David Larastiaso Shlomit Gilad Sima Benjamin Jacob H. Hanna 《Cell Stem Cell》2019,24(2):328-341.e9