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.     

猫扣带回前部内脏伤害感受神经元的膜电学特性

目的：研究猫扣带回前部内脏大神经刺激相关神经元的膜电生理特性,以便从神经元水平进一步了解大脑皮质内脏伤害感受的特性及机制,为痛觉理论“特异性学说”提供新的实验依据。方法：应用在体玻璃微电极细胞内电位记录技术及细胞内注入极化电流的方法,测量和计算神经元的膜电学参数。结果：将20只猫扣带回前部176个内脏大神经刺激相关神经元,分为内脏伤害(148个)和非伤害(28个)感受神经元。发现它们在膜电阻、时间常数、膜电容及I—V曲线等方面存在差异。注入去极化电流引发的放电幅值及频率也存在差异。结论：扣带回前部内脏伤害与非伤害感受神经元可能在细胞膜结构、细胞大小等形态学方面存有差别。     

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.     

Modulation of hematology changes by polymorphism of glutathione S-transferase M1 and T1

Workers in the petroleum distribution trades experience relatively low-level exposures to gasoline vapors whose consequences have not been fully elucidated. The purpose of this study was to investigate changes in the hematological parameters among filling station workers who were occupationally exposed to gasoline. The target group for the study consisted of 41 workers from eight filling stations of Shiraz (south of Iran). The control group consisted of 27 healthy subjects matched for age and sex from general population. The complete blood count analysis was done in one laboratory. Using PCR-based method, the genotypes of glutathione S-transferase T1 (GSTT1) and M1 (GSTM1) were determined. Workers were divided into three exposure groups according to employment history: duration less than 1 year, 1-5 years, and more than 5 years. Comparison was performed using Kruskal-Wallis test. In the individuals with the presence of both GSTT1 and GSTM1 functional alleles, comparison between four exposure groups revealed no significant difference for studied hematological variables. There were statistically significant differences between study groups, with only one functional allele, either GSTT1 or GSTM1, for relative number of lymphocytes (chi(2)=9.147, df=3, P=0.027) and neutrophils (chi(2)=9.951, df=3, and P=0.019), and absolute number of lymphocytes (chi(2)=9.135, df=3, and P=0.028), and RBC (chi(2)=10.586, df=3, and P=0.014). These findings could indicate the possible protective effect of concurrent presence of GSTM1 and GSTT1 enzymes on the hematopoietic system of filling station workers.     

Development of an automation system for a tablet coater

An instrumentation and automation system for a side-vented pan coater with a novel air-flow rate measurement system for monitoring the film-coating process of tablets was designed and tested. The instrumented coating system was tested and validated by film-coating over 20 pilot-scale batches of tablets with aqueous-based hydroxypropyl methylcellulose (HPMC). Thirteen different process parameters were continuously measured and monitored, and the most significant ones were logged for analysis. Laser profilometry was used to measure the surface roughness of the coated tablets. The instrumentation system provided comprehensive and quantitative information on the process parameters monitored. The measured process parameters and the responses of the film-coated tablet batches showed that the coating process is reproducible. The inlet air-flow rate influenced the coating process and the subsequent quality of the coated tablets. Increasing the inlet flow rate accelerated the drying of the tablet surface. At high inlet flow rate, obvious film-coating defects (ie, unacceptable surface roughness of the coated tablets) were observed and the loss of coating material increased. The instrumented and automated pancoating system described, including historical data storage capability and a novel air-flow measurement system, is a useful tool for controlling and characterizing the tablet film-coating process. Monitoring of critical process parameters increases the overall coating process efficiency and predictability.     

Effects of excessive copper intake on hematological and hemorheological parameters

Copper plays an important role in the structure and function of metalloproteins and in the absorption of iron. The present study deals with the effects of excessive copper intake on hematological and hemorheological parameters. Drinking water containing 250 μg/mL copper for a period of 9 wk, Wistar albino rats showed increased erythrocyte count, blood viscosity, and hematocrit values (p<0.05) and lower hemoglobin (p<0.05) than controls fed a normal diet. The two groups also had differences in the erythrocyte deformability index. The results suggest that excessive copper intake results in hematological and hemorheological changes affecting both the protein content of the erythrocyte membrane and heme synthesis.     

Interrelations between EEG Parameters and Personality Characteristics in Parkinsonian Patients

We studied a number of EEG parameters and indices of personality characteristics (evaluated with the use of the MMPI questionnaire) in sixty 44- to 73-year-old patients with Parkinson's disease (PD). According to the intensity of the symptoms, they were classified into groups 1 and 2, with an initial or moderate level of disease manifestation. In group-2 patients, the powers of the - and -range rhythms were greater, as compared with those in group 1. This was combined with higher indices in scales 2 (depression, D), 8 (individualism, Sc), and 0 (introversion/extraversion, Si). A clear correlations between the EEG parameters and indices of personality structure were found. There were positive correlations between the normalized power of ₂-rhythm and values of a few MMPI scales: 1 (supercontrol, Hs), 2 (depression, D), 4 (impulsivity, Pd), 7 (anxiety, Pt), 8 (individualism, Sc), and 0 (introversion/extraversion, Si). We also found negative correlations between the frequency of -rhythm and indices of supercontrol and anxiety scales. Correlations between different EEG parameters and MMPI scale indices depended on the level of disease manifestation. Our results allow us to assume a certain generality of the neurophysiological mechanisms determining modifications of the integral electrical activity of the brain and formation of individual psychological characteristics in parkinsonian patients.     

Estimation of genetic parameters for growth,carcass and overfeeding traits in a white geese strain

In an experimental strain of white plumage geese created in 1989, two experiments were carried out from 1993 to 1995 in order to estimate genetic parameters for growth, and carcass composition traits in non-overfed animals, and genetic parameters for growth and fatty liver formation in overfed animals. Four hundred and thirty-one non-overfed animals were bred and slaughtered at 11 weeks of age; they were measured for forearm length, keel bone length, chest circumference and breast depth before and after slaughtering. The carcasses were partly dissected in order weigh breast, breast muscle and skin + fat, and abdominal fat. Four hundred and seventy-seven overfed animals were slaughtered at 20 weeks of age; they were measured for "paletot" (breast meat, bone and meat from wings, bone and meat from thigh and legs) weight and liver weight. In these two experiments, the weights had moderate to high heritability values. Breast depth measured on live animals showed a low heritability value. In overfed animals, liver weight showed a high heritability value. Liver weight could be increased by selection without a great effect on "paletot" weight. Thus, obtaining a white plumage geese strain for fatty liver production by selection would be difficult because only 20% of overfed animals had fatty liver. The results did not allow to conclude on the influence of selection on liver weight on carcass traits such as muscle or fatty tissue weight.     

Density dependence and population differentiation of genetic architecture in Impatiens capensis in natural environments

We identified environment-dependent constraints on the evolution of plasticity to density under natural conditions in two natural populations of Impatiens capensis. We also examined the expression of population divergence in genetic variance-covariance matrices in these natural environments. Inbred lines, originally collected from a sunny site with high seedling densities and a woodland site with low seedling densities, were planted in both original sites at natural high densities and at low density. Morphological and life-history characters were measured. More genetic variation for plastic responses to density was expressed in the sun site than in the woodland site, so the evolutionary potential of plasticity was greater in the sun site. Strong genetic correlations between the same character expressed at different densities and correlations among different characters could constrain the evolution of plasticity in both sites. Genetically based trade-offs in meristem allocation to vegetative growth and reproduction were apparent only in the high-resource environment with no overhead canopy and no intraspecific competition. Therefore, genetic constraints on the evolution of plasticity depended on the site and density in which plants were grown, and correlated responses to selection on plastic characters are also expected to differ between sites and densities. Population differentiation in genetic variance-covariance matrices was detected, but matrix structural differences, as opposed to proportional differences, were detected between populations only in the sun site at natural high density. Thus, population divergence in genetic architecture can occur rapidly and on a fine spatial scale, but the expression of such divergence may depend on the environment.