人工诱导南方鲇雌核发育的最适参数

用紫外线照射南方鲇(Silurus meridionalis)精子,用遗传失活的精子人工授精,采用热休克方法抑制南方鲇第二极体的排出。根据热休克起始时间、持续时间和休克温度三因子三水平设计正交试验,探索获得人工诱导南方鲇雌核发育的最理想条件。结果表明,紫外线照射精子15 min,热休克起始时间为受精后5 min,持续时间为1 min,休克温度为41℃,对人工诱导南方鲇雌核发育最有利。该实验为进一步分析人工繁殖南方鲇的雌化机制以及南方鲇性别决定的分子机制奠定了基础。     

Differential interactions of antitumor antibiotics chromomycin A(3) and mithramycin with d(TATGCATA)(2) in presence of Mg(2+)

The antitumor antibiotics chromomycin A(3) (CHR) and mithramycin (MTR) are known to inhibit macromolecular biosynthesis by reversibly binding to double stranded DNA with a GC base specificity via the minor groove in the presence of a divalent cation such as Mg(2+). Earlier reports from our laboratory showed that the antibiotics form two types of complexes with Mg(2+): complex I with 1:1 stoichiometry and complex II with 2:1 stoichiometry in terms of the antibiotic and Mg(2+). The binding potential of an octanucleotide, d(TATGCATA)(2), which contains one potential site of association with the above complexes of the two antibiotics, was examined using spectroscopic techniques such as absorption, fluorescence, and circular dichroism. We also evaluated thermodynamic parameters for the interaction. In spite of the presence of two structural moieties of the antibiotic in complex II, a major characteristic feature was the association of a single ligand molecule per molecule of octameric duplex in all cases. This indicated that the modes of association for the two types of complexes with the oligomeric DNA were different. The association was dependent on the nature of the antibiotics. Spectroscopic characterization along with analysis of binding and thermodynamic parameters showed that differences in the mode of recognition by complexes I and II of the antibiotics with polymeric DNA existed at the oligomeric level. Analysis of the thermodynamic parameters led us to propose a partial accommodation of the ligand in the groove without the displacement of bound water molecules and supported earlier results on the DNA structural transition from B --> A type geometry as an obligatory requirement for the accommodation of the bulkier complex II of the two drugs. The role of the carbohydrate moieties of the antibiotics in the DNA recognition process was indicated when we compared the DNA binding properties with the same type of Mg(2+) complex for the two antibiotics.     

Effects of therapeutic and toxic doses of levamisole on thyroid hormones and some biochemical parameters in sheep

This study was carried out to establish the effects of therapeutic and toxic doses of levamisole on thyroid hormone levels and some biochemical parameters in sheep. Twelve Akkaraman ewes were used. Levamisole was given orally at doses of 7.5 mg kg(-1) (group 1) and 40 mg kg(-1) (group 2) to the animals. Blood samples were taken from the jugular vein at 2, 4, 8, 24, 48, 96 and 144 h after the administrations. Serum thyroid hormones and some biochemical parameters were determined on these samples. When compared with the control levels, no significant changes were observed in triiodothyronine (T3) and thyroxin (T4) levels in group 1. Although levamisole was found to increase the levels of total T3, it decreased the levels of total T4 in group 2. On the other hand, free T3 and free T4 levels were not changed in either group. While serum alkaline phosphatase (ALP) activities were decreased, aspartate aminotransferase (AST), alanine aminotransferase (ALT), lactate dehydrogenase (LDH) and creatinine kinase (CK) activities were increased significantly by levamisole. However, it increased the serum albumin and cholesterol levels, but decreased the inorganic phosphate levels in groups 1 and 2. On the other hand, when compared with the control levels, no significant changes were detected in serum sodium, potassium and calcium levels. In conclusion, therapeutic and toxic doses of levamisole were determined to affect thyroid metabolism and some biochemical parameters in sheep.     

Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme

The quality of molecular dynamics (MD) simulations of proteins depends critically on the biomolecular force field that is used. Such force fields are defined by force-field parameter sets, which are generally determined and improved through calibration of properties of small molecules against experimental or theoretical data. By application to large molecules such as proteins, a new force-field parameter set can be validated. We report two 3.5 ns molecular dynamics simulations of hen egg white lysozyme in water applying the widely used GROMOS force-field parameter set 43A1 and a new set 45A3. The two MD ensembles are evaluated against NMR spectroscopic data NOE atom–atom distance bounds, ³J_NH and ³J coupling constants, and ¹5N relaxation data. It is shown that the two sets reproduce structural properties about equally well. The 45A3 ensemble fulfills the atom–atom distance bounds derived from NMR spectroscopy slightly less well than the 43A1 ensemble, with most of the NOE distance violations in both ensembles involving residues located in loops or flexible regions of the protein. Convergence patterns are very similar in both simulations atom-positional root-mean-square differences (RMSD) with respect to the X-ray and NMR model structures and NOE inter-proton distances converge within 1.0–1.5 ns while backbone ³J_HN-coupling constants and ¹H– ¹5N order parameters take slightly longer, 1.0–2.0 ns. As expected, side-chain ³J-coupling constants and ¹H– ¹5N order parameters do not reach full convergence for all residues in the time period simulated. This is particularly noticeable for side chains which display rare structural transitions. When comparing each simulation trajectory with an older and a newer set of experimental NOE data on lysozyme, it is found that the newer, larger, set of experimental data agrees as well with each of the simulations. In other words, the experimental data converged towards the theoretical result.     

A quantitative, non-radioactive single-nucleotide insertion assay for analysis of DNA replication fidelity by using an automated DNA sequencer

A method to determine the steady-state kinetic parameters of single-nucleotide insertion in replication was developed using an automated DNA sequencer. The insertion of nucleoside 5'-triphosphates into a 6-carboxyfluorescein-labeled primer by DNA polymerase was quantified from the band pattern on a gel using GeneScan software. The parameters determined by this method were consistent with those obtained by the conventional radioisotope-labeling method. This non-radioactive, fluorescent-based method is rapid and can handle a large number of samples to assess cognate or non-cognate base pair formation between natural or unnatural bases in replication.     

Demography of the cereal rust mite Abacarus hystrix (Acari: Eriophyoidea) on quack grass

Demography parameters of the cereal rust mite Abacarus hystrix (Nalepa) on quack grass were studied to investigate its potential capacity of population increase in conditions of initially low density. The experiment was maintained under laboratory conditions at a constant temperature of 19.5-20.5 degrees C and 94 +/- 1% RH. Life-history data were used to calculate duration of developmental stages, survival of adults and rates of population increase. A new method of estimation of age-dependent fecundity is proposed. On average, eggs required 7.98 (n = 33, 95% CI: 7.68-8.21) days to develop into adults. Life expectancy of females was longer than that of males (9.72 and 5.41 days, respectively). The mean sex ratio, expressed as the proportion of females, was 0.80 (n = 122, CI: 0.71-0.86). The reproductive output for females was age-dependent and daily egg production reached a peak (3.83 eggs/day, CI: 2.50-5.15) on the 5th day, and then decreased steeply. The net reproductive rate (R0) was 10.12 female progeny per female per generation, the generation time (T) was 11.31 days, the intrinsic rate of increase (r) was 0.20 female progeny per female per day, and the finite rate of increase (lambda) was 1.23 female progeny per day. These estimates showed that A. hystrix has a great potential capacity for rapid population increase when colonising new hosts and its density is low. Therefore, we conclude that the population of the cereal rust mite on quack grass may rapidly build up to very high densities and can be a reservoir population, which may easily disperse and infest other, including cultivated, grasses.     

Activation Parameters for the Spontaneous and Pressure-Induced Phases of the Dissociation of Single-Ring GroEL (SR1) Chaperonin

We investigated the dissociation of single-ring heptameric GroEL (SR1) by high hydrostatic pressure in the range 0.5-3.0 kbar. The kinetics were studied as a function of temperature in the range 15-35 degrees C. The dissociation processes at each pressure and temperature showed biphasic behavior. The slower rate (k1,obs) was confirmed to be the self-dissociation of SR1 at any specific temperature at atmospheric pressure. This dissociation was pressure independent and followed concentration-dependent first-order kinetics. The self-dissociation rates followed normal Eyring plots (In k1,obs/T vs. 1/T) from which the free energy of activation (deltaG++ = 22 +/- 0.3 kcal mol(-1)), enthalpy of activation (deltaH++ = 18 +/- 0.5 kcal mol(-1)), and entropy of activation (deltaS++ = -15 +/- 1 kcal mol(-1)) were evaluated. The effect of pressure on the dissociation rates resulted in nonlinear behavior (ln k2,obs vs. pressure) at all the temperatures studied indicating that the activation volumes were pressure dependent. Activation volumes at zero pressure (V++o) and compressibility factors (beta++) for the dissociation rates at the specific temperatures were calculated. This is the first systematic study where the self-dissociation of an oligomeric chaperonin as well as its activation parameters are reported.     

Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library

Accurate prediction of the placement and comformations of protein side chains given only the backbone trace has a wide range of uses in protein design, structure prediction, and functional analysis. Prediction has most often relied on discrete rotamer libraries so that rapid fitness of side-chain rotamers can be assessed against some scoring function. Scoring functions are generally based on experimental parameters from small-molecule studies or empirical parameters based on determined protein structures. Here, we describe the NCN algorithm for predicting the placement of side chains. A predominantly first-principles approach was taken to develop the potential energy function incorporating van der Waals and electrostatics based on the OPLS parameters, and a hydrogen bonding term. The only empirical knowledge used is the frequency of rotameric states from the PDB. The rotamer library includes nearly 50,000 rotamers, and is the most extensive discrete library used to date. Although the computational time tends to be longer than most other algorithms, the overall accuracy exceeds all algorithms in the literature when placing rotamers on an accurate backbone trace. Considering only the most buried residues, 80% of the total residues tested, the placement accuracy reaches 92% for chi(1), and 83% for chi(1 + 2), and an overall RMS deviation of 1 A. Additionally, we show that if information is available to restrict chi(1) to one rotamer well, then this algorithm can generate structures with an average RMS deviation of 1.0 A for all heavy side-chains atoms and a corresponding overall chi(1 + 2) accuracy of 85.0%.     

The burgeoning field of statistical phylogeography

In the newly emerging field of statistical phylogeography, consideration of the stochastic nature of genetic processes and explicit reference to theoretical expectations under various models has dramatically transformed how historical processes are studied. Rather than being restricted to ad hoc explanations for observed patterns of genetic variation, assessments about the underlying evolutionary processes are now based on statistical tests of various hypotheses, as well as estimates of the parameters specified by the models. A wide range of demographical and biogeographical processes can be accommodated by these new analytical approaches, providing biologically more realistic models. Because of these advances, statistical phylogeography can provide unprecedented insights about a species' history, including decisive information about the factors that shape patterns of genetic variation, species distributions, and speciation. However, to improve our understanding of such processes, a critical examination and appreciation of the inherent difficulties of historical inference and challenges specific to testing phylogeographical hypotheses are essential. As the field of statistical phylogeography continues to take shape many difficulties have been resolved. Nonetheless, careful attention to the complexities of testing historical hypotheses and further theoretical developments are essential to improving the accuracy of our conclusions about a species' history.     

Soft Picture of Lateral Heterogeneity in Biomembranes

Standard methods of characterization of electron paramagnetic resonance (EPR) spectra of spin-labeled biomembranes limit the resolution of lateral heterogeneity to only two or three domain types. This disables examination of the structure—function relationship in complex membranes, which might be composed of a larger number of different domain types. To enable exploration of this kind, a new approach based on analysis of EPR spectra with multi-run, hybrid evolutionary optimization is proposed here. From the multiple runs a quasi-continuous distribution of membrane spectral parameters (order parameter, proportion of spectral component, polarity correction factor, rotational correlation time and broadening constant) can be constructed and presented by a new presentation technique CODE (colored distribution of EPR spectral parameters). Through this the concept of a soft picture of membrane heterogeneity is introduced, in contrast to the standard discrete domain picture. The soft characterization method, established on synthetic spectra, was used to examine the lateral heterogeneity of liposome membranes as well as of membranes of neutrophils from healthy and asthmatic horses. In liposome membranes the determined number of domain types was the same as already established by standard procedures of EPR spectra line-shape interpretation. In membranes of neutrophils a quasi-continuous distribution of membrane domain properties was detected by the new method.