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1.
Solvated electrons () are produced during water radiolysis and can interact with biological substrates, including DNA. To augment DNA damage,
radiosensitizers such as bromo-deoxyuridine (BUdR), often referred to as an “electron affinic radiosensitizer”, are incorporated
in place of isosteric thymidine. However, little is known about the primary interactions of with DNA. In the present study we addressed this problem by applying molecular modeling and molecular dynamics (MD) simulations
to a system of normal (BUdR·A)-DNA and a hydrated electron, where the excess electron was modeled as a localized (H2O)6 anionic cluster. Our goals were to evaluate the suitability of the MD simulations for this application; to characterize the
motion of around DNA (e.g., diffusion coefficients); to identify and describe configurational states of close localization to DNA; and to evaluate the structural dynamics of DNA in the presence of . The results indicate that has distinct space-preferences for forming close contacts with DNA and is more likely to interact directly with nucleotides
other than BUdR. Several classes of DNA - contact sites, all within the major groove, were distinguished depending on the structure of the intermediate water layer
H-bonding pattern (or its absence, i.e., a direct H-bonding of with DNA bases). Large-scale structural perturbations were identified during and after the approached the DNA from the major groove side, coupled with deeper penetration of sodium counterions in the minor groove.
Figure A rare configuration showing direct interaction between the solvated electron and DNA, where (yellow) and N7(A16) are H-bonded. The close approach from the major groove side invokes deep Na+ (magenta) penetration into the minor DNA groove (Fig. 7a). 相似文献
2.
3.
A 3D QSAR analysis has been performed on a series of 67 benzodiazepine analogues reported as γ-secretase inhibitors using
molecular field analysis (MFA), with G/PLS to predict steric and electrostatic molecular field interaction for the activity.
The MFA study was carried out using a training set of 54 compounds. The predictive ability of model developed was assessed
using a test set of 13 compounds ( as high as 0.729). The analyzed MFA model has demonstrated a good fit, having r2 value of 0.858 and cross validated coefficient, value as 0.790. The analysis of the best MFA model provided insight into possible modification of the molecules for better
activity.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
4.
Amino azobenzenes are important dyes in the food and textile industry but their application is limited due to their mutagenicity.
Computational modeling techniques were used to help understand the factors responsible for mutagenicity, and several quantitative
structure toxicity relationship (QSTR) models have been derived. HQSTR (hologram QSTR) analyses indicated that different substituents
at sites on both rings contribute to mutagenicity. Fragment parameters such as bond (B) and connectivity(C), as well as donor-acceptor
(DA)-based model provide significant results (q2 = 0.59, r2 = 0.92, ) explaining these harmful effect. HQSTR results indicated that a bulky group at ring “Y” and small group at ring “X” might
help to decrease mutagenicity. 3D-QSTR based on comparative molecular field analyses (CoMFA) and comparative molecular similarity
index analyses (CoMSIA) are also in agreement with HQSTR. The 3D QSTR studies reveal that steric and electrostatic field effects
have a strong relationship with mutagenicity (for CoMFA: q2 = 0.51, r2 = 0.95, and for CoMSIA: q2 = 0.51, r2 = 0.93 and ). In summary, negative groups and steric bulk at ring “Y” and small groups at carbon-3 of ring “X” might be helpful in reducing
the mutagenicity of azo dyes. 相似文献
5.
Effects of common soil anions and pH on the uptake and accumulation of perchlorate in lettuce 总被引:1,自引:0,他引:1
A mechanistic understanding of perchlorate () entry into plants is important for establishing the human health risk associated with consumption of contaminated produce
and for assessing the effectiveness of phytoremediation. To determine whether common soil anions affect uptake and accumulation in higher plants, a series of competition experiments using lettuce (Lactuca sativa L.) were conducted between (50 nM) and (4–12 mM), (1–10 mM), or Cl− (5–15 mM) in hydroponic solution. The effects of (0–5 mM) and pH (5.5–7.5) on uptake were also examined. Increasing in solution significantly reduced the amount of taken up by green leaf, butter head, and crisphead lettuces. Sulfate and Cl− had no significant effects on uptake in lettuce over the concentrations tested. Increasing pH significantly reduced the amount of taken up by crisphead and green leaf lettuces, whereas increasing significantly reduced uptake in butter head lettuce. The inhibition by across all lettuce genotypes suggests that may share an ion carrier with , and the decrease in uptake with increasing pH or provides macroscopic evidence for cotransport across the plasma membrane. 相似文献
6.
Factors affecting denitrification in agricultural headwater streams in Northeast Ohio,USA 总被引:2,自引:0,他引:2
As a result of increased anthropogenic nitrogen (N) loading in surface waters of agricultural watersheds, there is enhanced
interest to understand and quantify N removal mechanisms. Denitrification, an important N removal mechanism in aquatic systems,
may contribute to reducing N pollution in agricultural headwater streams. However, the key factors controlling this process
in lotic systems remain unclear. The objective of our study was to examine the factors regulating rates of denitrification
in the sediments of agricultural headwater streams in the mid-western USA. Denitrification rates were variable among streams
and treatments (<0.1–28.0 μg N g AFDM−1 h−1) and on average, were higher than those reported for similar headwater streams. Carbon quantity and quality, and pH had no
effect on denitrification, while temperature and nitrate (
) concentrations had a positive effect on rates of denitrification. Specifically, controlled denitrification following Michaelis-Menten kinetics. We calculated a value of km (1.0 mg -N L-1) that was comparable to other studies in aquatic sediments but was well below the median in-stream concentrations (5.2–17.4 mg -N L−1) observed at the study sites. Despite high rates of denitrification, this removal mechanism is most likely saturated in the agricultural headwater streams we examined, suggesting that these systems are not effective at removing
in-stream N.
Handling editor: D. Ryder 相似文献
7.
Wu X Xiao W Liu C Chao L Qu C Chunxiang Q Huang H Hao H Liu X Xiaoqing L Chen L Liang C Su M Mingyu S Hong F Fashui H 《Biological trace element research》2008,121(3):258-265
Lead (Pb2+) is a well-known highly toxic element. The mechanisms of the Pb2+ toxicity are not well understood for nitrogen metabolism of higher plants. In this paper, we studied the effects of various
concentrations of PbCl2 on the nitrogen metabolism of growing spinach. The experimental results showed that Pb2+ treatments significantly decreased the nitrate nitrogen absorption and inhibited the activities of nitrate reductase, glutamate dehydrogenase, glutamine synthase, and glutamic–pyruvic
transaminase of spinach, and inhibited the synthesis of organic nitrogen compounds such as protein and chlorophyll. However,
Pb2+ treatments increased the accumulation of ammonium nitrogen in spinach cell. It implied that Pb2+ could inhibit inorganic nitrogen to be translated into organic nitrogen in spinach, thus led to the reduction in spinach
growth. 相似文献
8.
de Magalhães Erismann N Caruso Machado E Sant' Anna Tucci ML 《Photosynthesis research》2008,96(2):163-172
Photosynthetic limitations under moderate water deficit were evaluated in ‘Valência’ orange trees grafted on three different
rootstocks, in pots. Net CO2 assimilation rate (A
N), stomatal conductance (g
s), and photosystem II (PS II) operating efficiency (
) in response to changing intercellular CO2 partial pressure (C
i) were analyzed under controlled conditions. Drought decreased A
N and g
s, whereas remained unchanged. This resulted in a higher ratio between electron transport rate (ETR) and gross CO2 assimilation rate (A
G). Since the comparison of A
N–C
i gas exchange curves can lead to incorrect conclusions, a normalization of C
i values () of stressed leaves was applied. Then, the relationship established for irrigated trees between the ETR/A
G ratio and C
i was used to estimate the from ETR/A
G ratios measured under water stress. The response of A
N to suggests that the CO2 diffusional restriction is the main factor that limits photosynthesis in orange leaves under moderate water deficit. 相似文献
9.
Summary A set of three-dimensional triple-resonance experiments is described which provide
,
,
and
coupling constants. The pulse sequences generate E.COSY-like multiplet patterns and comprise a magnetization transfer from
the amide proton to the α-proton or vice versa via the directly bound heteronuclei. For residues with the 1Hα spin resonating close to the H2O signal, a modified HNCA experiment can be employed to measure the vicinal 1HN,1Hα couplings. Ambiguities associated with the conversion of
values into ϕ-angle constraints for protein structure determination can be resolved with the knowledge of the heteronuclear
3J-couplings. In favourable cases, stereospecific assignments of glycine α-protons can be obtained by employing the experiments
described here in combination with NOE data. The methods are applied to flavodoxin from Desulfovibrio vulgaris. 相似文献
10.
The pathway and ab initio direct kinetics of the decomposition 5-aminotetrazole (5-ATZ) to HN3 and NH2CN was investigated. Reactant, products and transition state were optimized with MP2 and B3LYP methods using 6–311G** and
aug-cc-pVDZ basis sets. The intrinsic reaction coordinate curve of the reaction was calculated using the MP2 method with 6–311G**
basis set. The energies were refined using CCSD(T)/6–311G**. Rate constants were evaluated by conventional transition-state
theory (CVT) and canonical variational transition-state theory (TST), with tunneling effect over 300 to 2,500 K. The results
indicated that the tunneling effect and the variational effect are small for the calculated rate constants. The fitted three-parameter
expression calculated using the CVT and TST methods are and , respectively.
Figure The mechanism of the decomposition process of 5-ATZ to HN3 and NH2CN 相似文献
11.
The biosorption of metal ions (Cr+3,
, Cu+2, and Ni+2) on two algal blooms (designated HD-103 and HD-104) collected locally was investigated as a function of the initial metal
ion concentration. The main constituent of HD-103 is Cladophora sp., while Spirulina sp. is present significantly in the bloom HD-104. Algal biomass HD-103 exhibited the highest Cu+2 uptake capacity (819 mg/g). This bloom adsorbed Ni+2 (504 mg/g), Cr+3 (347 mg/g), and (168 mg/g). Maximum of Ni+2 (1108 mg/g) is taken by HD-104. This species takes up 306, 202, and 576 mg/g Cr+3, , and Cu+2, respectively. Equilibrium data fit very well to both the Langmuir and the Freundlich isotherm models. The sorption process
followed the Freundlich model better. Pseudo-first-order kinetic model could describe the kinetic data. Infrared (IR) spectroscopic
data were employed to identify the site(s) of bonding. It was found that phosphate and peptide moieties participate in the
metal uptake by bloom HD-103. In the case of bloom HD-104, carboxylate and phosphate are responsible for the metal uptake.
The role of protein in metal uptake by HD-103 was investigated using polyacrylamide gel electrophoresis. 相似文献
12.
P. Pic 《Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology》1978,123(2):155-162
Summary In seawater (SW)-adaptedMugil andFundulus, gill effluxes of Na+
and of Cl–
and the simultaneously recorded transgill potential (P.D.) differ according to whether they are measured in stressed or rested animals.In rested animals of the two species, transfer to Ringer's solution considerably reduces the P.D. but not
. InFundulus,
is also decreased. Transfer of the two species from SW to fresh water (FW) reduces
and
by 75 to 85% and leads to a large inversion of P.D. When K+ is added to FW, a gill depolarization occurs, as well as a large increase of
and
.These results suggest that: 1) the P.D. originates primarily from the diffusion of cations, the gill permeability to Na+ (
) being greater than that to Cl– (
), 2) a Cl–/Cl– exchange independent of P.D. is associated with the Cl– pump; 3) Cl– pump activity is linked to Na+/K+ exchange which in turn is associated to a Na+/Na+ exchange diffusion mechanism.In stressed individuals of the two species, the P.D. in SW, as well as the P.D. changes observed during transfer experiments, are considerably reduced. The decrease of
and
observed after transfer from SW to FW are also minimised. Changes are smaller inFundulus. The decrease of P.D. characterizing stressed animals may be at least in part due to a 3 to 4 fold increase of
which becomes equal to
in both species.As a result of stress, the K+-activated Na+ and Cl– excretion mechanisms are totally inhibited inFundulus and partially so inMugil.Stress response seems more intense inFundulus and recovery from stress faster inMugil. 相似文献
13.
A. Robic D. Bertrand J.-F. Sassi Y. Lerat M. Lahaye 《Journal of applied phycology》2009,21(4):451-456
The water-soluble cell wall polysaccharides from green seaweeds of Ulva spp. (Ulvales, Chlorophyta), referred to as ulvan, demonstrate composition- and structure-related functional properties.
Mid-infrared spectroscopy combined with chemometric techniques was investigated as a means to rapidly predict the chemical
composition of ulvan extracts. A calibration was realized with 41 ulvan extracts from two Ulva species. The variables studied included the constituent sugars (rhamnose, xylose, glucose, galactose, glucuronic acid, iduronic
acid), protein, and sulfate contents. The correlation between Fourier transform infrared and chemical data was developed using
partial least squares (PLS) regression with full cross-validation (leave one out). The coefficients of determination in cross-validation
() and the standard error in cross-validation were determined for each variable. The PLS model validation resulted in a coefficient
of determination () and a standard error in prediction. Good predictions were obtained for rhamnose ( = 0.9244), xylose ( = 0.8758), glucuronic acid ( = 0.9415), and sulfate ( = 0.9218), which are the main ulvan constituents. However, minor components such as proteins, glucose, galactose, and iduronic
acid were not correctly predicted. This study showed that mid-infrared spectroscopy combined with PLS regression is a reliable
and fast method for the quantification of the main chemical constituents of ulvan extracts. 相似文献
14.
Long-term changes in nutrient concentrations of the Changjiang River and principal tributaries 总被引:5,自引:0,他引:5
We present long-term nutrient data on the Changjiang River (Yangtze River) at six hydrological stations and eight principal
tributaries during the period 1958–1985. Three patterns of temporal changes were observed in nitrate
and nitrite : minimal variations in the upper catchment area, rapid increases in the middle watershed towards the end of the 1970s, and
a gradual increase in the lower drainage basin. Prior to the 1970s, the level of throughout the Changjiang River system remained fairly constant. In the 1980s, however, this changed, with the lowest values
in the upper Changjiang changing rapidly to the highest in the middle reaches and then declining slowly but steadily in the
lower courses. Compared to and ammonium and soluble reactive phosphorus (SRP) showed smaller increases or no long-term variations, while dissolved silica (DSi) concentration
generally decreased at most stations. These three patterns of and changes in the Changjiang River system were reflective of the difference in chemical fertilizer use and landscape features
(e.g., slope, soil type and water body area) of the drainage basins of the primary tributaries. The decreases in DSi were
most likely attributed to a reduction in suspended sediment loading due to dam constructions and increasing diatom consumption.
The increase in and with a reduction in DSi concentrations in the Changjiang River could have significant effects on the stoichiometric balance
of nutrients delivered to the East China Sea and the ecosystem in this dynamic region. 相似文献
15.
Christoph Kuhn 《Journal of biological physics》2006,32(6):563-572
A simple theoretical model of a Darwinian system (a periodic system with a multiplication phase and a selection phase) of
entities (initial form of polymer strand, primary mutant and satellite mutants) is given. First case: one mutant is considered.
One individual of the mutant appears in the multiplication phase of the first generation. The probabilities to find N individuals of the mutant after the multiplication phase M of the n-th generation (with probability δ of an error in the replication, where all possible errors are fatal errors) and after the following selection phase S (with probability β that one individual survives) are given iteratively. The evolutionary tree is evaluated. Averages from the distributions
and the probability of extinction are obtained. Second case: two mutants are considered (primary mutant and new form). One individual of the primary mutant
appears in the multiplication phase of the first generation. The probabilities to find N
p individuals of the primary mutant and N
m individuals of the new form after the multiplication phase M of the n-th generation (probability ɛ of an error in the replication of the primary mutant giving the new form) and after the following selection phase S (probabilities β
p and β
m that one individual each of the primary mutant and of the new form survives) are given iteratively. Again the evolutionary
tree is evaluated. Averages from the distributions are obtained.
The online version of the original article can be found at . 相似文献
16.
A most common problem encountered in radiosterilization of solid drugs is discoloration or yellowing. By pharmacopoeia method,
discoloration can be assessed by measuring absorbance of solutions of irradiated solid samples at 450 nm. We propose to evaluate
discoloration of solid samples directly by recording their diffuse reflectance spectra. Further, the reflectance spectrum
is used to compute various color parameters: CIE XYZ tristimulus value, CIE Lab, (color difference), yellowness index (YI), dominant wavelength, and excitation purity by CIE method. The investigation of
difference reflectance spectra and color parameters revealed that for fluoroquinolones, e-beam was more damaging than gamma
radiation, whereas for cephalosporins, trend was reversed. The quantum of discoloration with gamma radiation and e-beam is
found to be nearly equal when assessed by pharmacopeia method, and it is therefore inadequate to assess small color differences.
The color parameters and ΔYI are found to be reliable indicators of discoloration. The tolerance limits proposed in terms of and ΔYI are ±2 and ±10 U, respectively. The dominant wavelength for all compounds has shifted to higher values indicating
change in hue but defining color tolerance limit with this parameter requires adjunct excitation purity value. 相似文献
17.
A novel molecular connectivity index, , based on the adjacency matrix of molecular graphs and novel atomic valence connectivities, , for predicting the molar diamagnetic susceptibilities of organic compounds is proposed. The is defined as: , where and Ei are the atomic valence connectivity and the valence orbital energy of atom i, respectively. A good QSPR model for molar diamagnetic
susceptibilities can be constructed from and using multivariate linear regression (MLR). The correlation coefficient r, standard error, and average absolute deviation
of the MLR model are 0.9918, 5.56 cgs, and 4.26 cgs, respectively, for the 721 organic compounds tested (training set). Cross-validation
using the leave-one-out method demonstrates that the MLR model is highly reliable statistically. Using the MLR model, the
average absolute deviations of the predicted values of molar diamagnetic susceptibility of another 360 organic compounds (test
set) is 4.34 cgs. The results show that the current method is more effective than literature methods for estimating the molar
diamagnetic susceptibility of an organic compound. The MLR method thus provides an acceptable model for the prediction of
molar diamagnetic susceptibilities of organic compounds.
Figure Plot of calculated vs experimental values of molar diamagnetic susceptibilities using the multivariate linear regression (MLR)
model (Eq. 8) 相似文献
18.
Microsomal prostaglandin E2 synthase (mPGES-1) has been identified recently as a novel target for treating pain and inflammation. The aim of this study
is to understand the binding affinities of reported inhibitors for mPGES-1 and further to design potential new mPGES-1 inhibitors.
3D-QSAR-CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis) - techniques
were employed on a series of indole derivatives that act as selective mPGES-1 inhibitors. The lowest energy conformer of the
most active compound obtained from systematic conformational search was used as a template for the alignment of 32 compounds.
The models obtained were used to predict the activities of the test set of eight compounds, and the predicted values were
in good agreement with the experimental results. The 3D-QSAR models derived from the training set of 24 compounds were all
statistically significant (CoMFA; q
2 = 0.89, r
2 = 0.95, , and CoMSIA; q
2 = 0.84, r
2 = 0.93, , ). Contour plots generated for the CoMFA and CoMSIA models reveal useful clues for improving the activity of mPGES-1 inhibitors.
In particular, substitutions of an electronegative fluorine atom or a bulky hydrophilic phenoxy group at the meta or para positions of the biphenyl rings might improve inhibitory activity. A plausible binding mode between the ligands and mPGES-1
is also proposed. 相似文献
19.
Desulfovibrio vulgaris (strain Marburg) was grown on H2 and sulfate as sole energy source in a chemostat limited by the sulfate supply. The biomass concentration and the sulfate concentration in the culture were determined as a function of the dilution rate. From the data a K
S (saturation constant) for sulfate of 10 M, a max of 0.23 h–1, and a
of 13 g/mol were calculated. The organism was also grown in chemostat culture on H2 and sulfite, H2 and thiosulfate, and pyruvate (without sulfate).
was found to be 35 g/mol,
36 g/mol, and Y
pyr
max
10 g/mol. The growth yields are discussed with respect to ATP gains in dissimilatory sulfate reduction. 相似文献
20.
Calcification, a process common to numerous marine taxa, has traditionally been considered to be a significant source of CO2 in tropical waters only. A number of relatively recent studies, however, have shown that significant amounts of CO2 are also produced in temperate waters, although none of these studies was carried out on rocky shores, which are considered
to be very productive systems. We compared the CO2 fluxes due to respiration and calcification in two temperate species, the cirripedes Chthamalus montagui and Elminius modestus. The population dynamics of both species were estimated at two sites during a 1-year experimental period in order to establish
mean organic (ash-free dry weight) and CaCO3 (dry shell weight) production. Based on these parameters, we estimated the CO2 fluxes due to respiration and calcification. CaCO3 production was estimated to be 481.0 and
at each site, representing 3.4 and respectively, of released CO2. These fluxes represent each 47% of the CO2 released as a result of respiration and calcification. The production of CaCO3 at the high-density site was: (1) among the highest values obtained for temperate organisms, and (2) comparable to the estimated
CO2 fluxes for coral reefs. As calcifying organisms are well represented in temperate ecosystems in terms of both density and
biomass, our results provide clear evidence that calcification of temperate organisms should not be underestimated. Additional
studies on other rocky shore taxa are needed before the relative importance of calcification in rocky intertidal carbon budgets
can be generalized. 相似文献