生物分子水溶液的Monte Carlo模拟 III.力偏倚抽样法和Metropolis抽样法的比较

本文采用先前所用的一个中性丙氨酸分子加56个水分子的体系,对力偏倚(FB)抽样法和Metropolis抽样法进行了比较.发现用FB法,由体系的晶体点阵构型出发到达平衡态所需的循环数为Metropolis法的五分之二.为了得到较好的结构信息所需的构型数也仅为后者的五分之二.虽然每个循环所需机时为Metropolis法的1.6倍,仍是一加速收敛的好方法.本文进一步支持了以分子的平移扩散作为判别抽样效率的判据,指出接受几率在0.33——0.36之间的步长可能是合适的.此外还统计了和丙氨酸作用大于2keal/mol的分子的坚标,使它们与丙氨酸—水分子径向分布图的峰值相对应.     

牛凝乳酶原基因克隆及序列的进化分析

利用RT-PCR克隆获得牛凝乳酶原基因的cDNA序列, 测序后与GenBank中凝乳酶原基因进行序列比对和生物信息学分析。序列比对统计分析显示, 该基因为牛凝乳酶原B基因, 与已知牛和其他哺乳动物的凝乳酶原基因具有很高的同源性,18种哺乳动物凝乳酶原基因密码子一、二、三位点的碱基偏倚度分别为：6.227、1.042和1.456。这表明该基因具有整体保守性和突变位点偏倚性两个特征, 可以作为哺乳动物系统进化的研究对象。采用多种方法构建的该基因系统进化树一致表明, 偶蹄动物与灵长动物的亲缘关系比偶蹄动物与啮齿动物的亲缘关系更近, 比偶蹄动物与食肉动物的亲缘关系更远, 并且18种哺乳动物的亲缘关系与动物种系进化关系一致, 为哺乳动物系统进化关系研究提供了分子水平的佐证和依据。     

原子力显微镜拉伸吸附在金膜表面的短单链DNA分子

对单根DNA分子的操纵和拉伸可以直接研究DNA的弹性等力学性质. 首先通过将金沉积到云母表面制备了表面粗糙度小于0.3 nm的金膜,然后一段硫代的单链DNA (100 bases) 吸附到金膜表面. 利用原子力显微镜观察不同浓度的DNA吸附在金膜上的表面形貌. 进一步用原子力显微镜的力曲线模式拉伸DNA分子,在50％的情况下DNA可以被针尖拉伸,观察到了由于针尖和DNA分子间作用力的不同导致的多种不同力曲线.     

维持DNA结构稳定性的因素

对DNA分子结构的稳定性的原因进行了讨论,介绍了维持DNA分子一级结构的主要因素,即共价键和核糖上羟基的缺乏;维持DNA分子二级结构的主要因素,即氢键、碱基堆积力、正负电荷作用以及DNA分子双螺旋结构本身的一些特征.     

多分子马达输运机制的动力学研究

对多分子马达输运机制进行模拟,得到了外加负载力和货物运输速度、马达个数和货物运输距离的关系,定性半定量的解释了一些实验现象,为多分子马达研究开辟了一条全新的途径.     

原子力显微镜及其在肿瘤研究中的应用

原子力显微术是一种利用原子、分子间的相互作用力来观察物体表面超微结构的新型实验技术.介绍了原子力显微镜作为一种显微探测和操纵工具的主要特点及其在肿瘤研究中的优势,评述了国内外有关原子力显微镜在肿瘤的诊断、治疗、抗肿瘤药物开发等研究中的应用情况,展望了原子力显微镜应用于肿瘤单细胞研究的前景.     

分子佐剂C3d上调Raji细胞协同刺激分子B7-1和B7-2的表达(简报)

我们在以往研究中,引入选择性增强体液免疫效应的新型分子佐剂C3d,成功构建了重组避孕疫苗hCGB-C3d3,通过免疫Th2型优势的 BALB/c小鼠和,Th1型优势的C57BL/6小鼠,显示分子佐剂C3d在不同品系小鼠均使免疫效应从Th1型细胞免疫向Th2型体液免疫偏倚。     

以分子信标为报告分子的凝血酶检测新方法

以分子信标为报告分子,核酸适体为识别分子,发展了一种新的凝血酶检测方法.含有分子信标互补序列的核酸适体探针与凝血酶结合后,分子信标的荧光信号下降,从而得到凝血酶的浓度信息.该方法快速、灵敏,核酸适体探针无需荧光标记、设计简单,检测限达到0.83nmol/L.     

一种新的DNA分子克隆方法

DNA分子克隆是基本的分子生物学实验技术,传统的分子克隆方法大多需经过酶切链接过程,但在某些情况下,没有合适的酶切位点往往会成为阻碍克隆进行的障碍.本文描述了一种新的分子克隆方法,称为不依赖酶切和链接的分子克隆（RLIC）.利用RLIC,将3种不同大小的DNA片段克隆到3种不同载体,证明了这种方法的有效性和可靠性.由于该方法不受限制性酶切序列限制,省去了酶切连接步骤,因此具有很大的灵活性和简便性,在分子生物学研究方面有广泛应用前景.     

微卫星标记在分子生态学中的应用及其位点的分离策略

微卫星DNA作为一种优良的遗传标记在分子生态学领域得到了广泛应用,本文综述了其在分子种群生物学、分子环境遗传学、分子适应等研究领域中的应用情况.微卫星位点的获得是开展各项研究的前提,传统的构建微卫星文库再杂交筛选的方法工作量大、效率低,因而在实践过程中又产生了富集文库法、PIMA法、FIASCO法等新的分离策略.本文对几种微卫星位点分离技术进行介绍并对其进行分析比较,为分子生态学研究过程中微卫星位点筛选方法的选择提供参考.     

Developmental bias in evolution: evolutionary accessibility of phenotypes in a model evo-devo system

SUMMARY The success of the modern synthesis has resulted in forces of evolutionary change other than natural selection being marginalized. However, recent work has attempted to show the importance of non-selective influences in shaping organic form. One such force is developmental bias, in which phenotypes are differentially produced. We use a simulation model of neural development to explore questions of general interest about developmental systems. From this analysis, we find that the pattern of developmental bias varies strongly with the genotype even among phenotypically-neutral genotypes. In addition to this genotype-dependent developmental bias ( local bias ), an intrinsic bias exists in the developmental system ( global bias ). We also show that developmental bias varies among related genotypes that produce the same phenotype. Finally, we illustrate how a pattern of bias emerges from the manner in which mutations affect the regulatory structure of the wild-type genotype. These results suggest that developmental bias could have a strong influence on the direction of evolutionary modification.     

Unfolding and extraction of a transmembrane alpha-helical peptide: dynamic force spectroscopy and molecular dynamics simulations

An atomic force microscope (AFM) was used to visualize CWALP(19)23 peptides ((+)H(3)N-ACAGAWWLALALALALALALWWA-COO(-)) inserted in gel-phase DPPC and DSPC bilayers. The peptides assemble in stable linear structures and domains. A model for the organization of the peptides is given from AFM images and a 20 ns molecular dynamics (MD) simulation. Gold-coated AFM cantilevers were used to extract single peptides from the bilayer through covalent bonding to the cystein residue. Experimental and simulated force curves show two distinct force maxima. In the simulations these two maxima correspond to the extraction of the two pairs of tryptophan residues from the membrane. Unfolding of the peptide precedes extraction of the second distal set of tryptophans. To probe the energies involved, AFM force curves were obtained from 10 to 10(4) nm/s and MD force curves were simulated with 10(8)-10(11) nm/s pulling velocities (V). The velocity relationship with the force, F, was fitted to two fluctuation adhesive potential models. The first assumes the pulling produces a constant bias in the potential and predicts an F approximately ln (V) relationship. The second takes into account the ramped bias that the linker feels as it is being driven out of the adhesion complex and scales as F approximately (ln V)2/3.     

Comprehensive Analysis of Synonymous Codon Usage Bias for Complete Genomes and E2 Gene of Atypical Porcine Pestivirus

Atypical porcine pestivirus (APPV) is an emerging novel pestivirus causing the congenital tremor (CT) in piglets. The worldwide distribution characteristic of APPV make it a threat to global swine health. E2 is the major envelope glycoprotein of APPV and the crucial target for vaccine development. Considering the genetic variability of APPV complete genomes and its E2 gene as well as gaps for codon analysis, a comprehensive analysis of codon usage patterns was performed. Relative synonymous codon usage (RSCU) and effective number of codon (ENC) analyses showed that a relatively instable change existed and a slight low codon usage bias (CUB) were displayed in APPV genomes. ENC-plot analysis and correlation analyses of nucleotide compositions and ENC showed that mutation pressure and natural selection both affected the codon usage bias of the APPV and natural selection had a more obvious influence for E2 gene compared with complete genomes. Principal component analysis (PCA) and correlation analyses confirmed the above results. Correlation analyses between Gravy and Aromaticity values and the codon bias showed that natural selection played an important role in shaping the synonymous codon bias. Furthermore, neutrality plot analysis showed that natural selection was the main force while mutation pressure was a minor force influencing the codon usage pattern of the APPV E2 gene and complete genomes. The results could illustrate the codon usage patterns of APPV genomes and provided valuable basic data for further fundamental research of evolution of APPV.

     

The effect of biased conversion on the mutation load

The mutation load is sensitive to changes in the segregation ratio caused, for example, by biased conversion. If the distortion, measured by the force of conversion, is greater than the loss of fitness in the mutation heterozygotes, then the mutation load will be far away from its normal value. Examples are given where a small positive bias together with realistic fitness parameters increase the mutation load by more than two orders of magnitude. In practical terms this implies that great restrictions should be placed on the use of substances and treatments that may induce mutations associated with a positive conversion bias.     

Robust biased Brownian dynamics for rate constant calculation

A reaction probability is required to calculate the rate constant of a diffusion-dominated reaction. Due to the complicated geometry and potentially high dimension of the reaction probability problem, it is usually solved by a Brownian dynamics simulation, also known as a random walk or path integral method, instead of solving the equivalent partial differential equation by a discretization method. Building on earlier work, this article completes the development of a robust importance sampling algorithm for Brownian dynamics-i.e., biased Brownian dynamics with weight control-to overcome the high energy and entropy barriers in biomolecular association reactions. The biased Brownian dynamics steers sampling by a bias force, and the weight control algorithm controls sampling by a target weight. This algorithm is optimal if the bias force and the target weight are constructed from the solution of the reaction probability problem. In reality, an approximate reaction probability has to be used to construct the bias force and the target weight. Thus, the performance of the algorithm depends on the quality of the approximation. Given here is a method to calculate a good approximation, which is based on the selection of a reaction coordinate and the variational formulation of the reaction probability problem. The numerically approximated reaction probability is shown by computer experiments to give a factor-of-two speedup over the use of a purely heuristic approximation. Also, the fully developed method is compared to unbiased Brownian dynamics. The tests for human superoxide dismutase, Escherichia coli superoxide dismutase, and antisweetener antibody NC6.8, show speedups of 17, 35, and 39, respectively. The test for reactions between two model proteins with orientations shows speedups of 2578 for one set of configurations and 3341 for another set of configurations.     

Vertebrate codon bias indicates a highly GC-rich ancestral genome

Two factors are thought to have contributed to the origin of codon usage bias in eukaryotes: 1) genome-wide mutational forces that shape overall GC-content and create context-dependent nucleotide bias, and 2) positive selection for codons that maximize efficient and accurate translation. Particularly in vertebrates, these two explanations contradict each other and cloud the origin of codon bias in the taxon. On the one hand, mutational forces fail to explain GC-richness (~ 60%) of third codon positions, given the GC-poor overall genomic composition among vertebrates (~ 40%). On the other hand, positive selection cannot easily explain strict regularities in codon preferences. Large-scale bioinformatic assessment, of nucleotide composition of coding and non-coding sequences in vertebrates and other taxa, suggests a simple possible resolution for this contradiction. Specifically, we propose that the last common vertebrate ancestor had a GC-rich genome (~ 65% GC). The data suggest that whole-genome mutational bias is the major driving force for generating codon bias. As the bias becomes prominent, it begins to affect translation and can result in positive selection for optimal codons. The positive selection can, in turn, significantly modulate codon preferences.     

Integration of Sensory Force Feedback Is Disturbed in CRPS-Related Dystonia

Complex regional pain syndrome (CRPS) is characterized by pain and disturbed blood flow, temperature regulation and motor control. Approximately 25% of cases develop fixed dystonia. The origin of this movement disorder is poorly understood, although recent insights suggest involvement of disturbed force feedback. Assessment of sensorimotor integration may provide insight into the pathophysiology of fixed dystonia. Sensory weighting is the process of integrating and weighting sensory feedback channels in the central nervous system to improve the state estimate. It was hypothesized that patients with CRPS-related dystonia bias sensory weighting of force and position toward position due to the unreliability of force feedback. The current study provides experimental evidence for dysfunctional sensory integration in fixed dystonia, showing that CRPS-patients with fixed dystonia weight force and position feedback differently than controls do. The study shows reduced force feedback weights in CRPS-patients with fixed dystonia, making it the first to demonstrate disturbed integration of force feedback in fixed dystonia, an important step towards understanding the pathophysiology of fixed dystonia.     

Mutation bias is the driving force of codon usage in the Gallus gallus genome

Synonymous codons are used with different frequencies both among species and among genes within the same genome and are controlled by neutral processes (such as mutation and drift) as well as by selection. Up to now, a systematic examination of the codon usage for the chicken genome has not been performed. Here, we carried out a whole genome analysis of the chicken genome by the use of the relative synonymous codon usage (RSCU) method and identified 11 putative optimal codons, all of them ending with uracil (U), which is significantly departing from the pattern observed in other eukaryotes. Optimal codons in the chicken genome are most likely the ones corresponding to highly expressed transfer RNA (tRNAs) or tRNA gene copy numbers in the cell. Codon bias, measured as the frequency of optimal codons (Fop), is negatively correlated with the G + C content, recombination rate, but positively correlated with gene expression, protein length, gene length and intron length. The positive correlation between codon bias and protein, gene and intron length is quite different from other multi-cellular organism, as this trend has been only found in unicellular organisms. Our data displayed that regional G + C content explains a large proportion of the variance of codon bias in chicken. Stepwise selection model analyses indicate that G + C content of coding sequence is the most important factor for codon bias. It appears that variation in the G + C content of CDSs accounts for over 60% of the variation of codon bias. This study suggests that both mutation bias and selection contribute to codon bias. However, mutation bias is the driving force of the codon usage in the Gallus gallus genome. Our data also provide evidence that the negative correlation between codon bias and recombination rates in G. gallus is determined mostly by recombination-dependent mutational patterns.     

Interspecific and Intragenic Differences in Codon Usage Bias Among Vertebrate Myosin Heavy-Chain Genes

Synonymous codon usage bias is a broadly observed phenomenon in bacteria, plants, and invertebrates and may result from selection. However, the role of selective pressures in shaping codon bias is still controversial in vertebrates, particularly for mammals. The myosin heavy-chain (MyHC) gene family comprises multiple isoforms of the major force-producing contractile protein in cardiac and skeletal muscles. Slow and fast genes are tandemly arrayed on separate chromosomes, and have distinct patterns of functionality and expression in muscle. We analyze both full-length MyHC genes (~5400?bp) and a larger collection of partial sequences at the 3' end (~500?bp). The MyHC isoforms are an interesting system in which to study codon usage bias because of their length, expression, and critical importance to organismal mobility. Codon bias and GC content differs among MyHC genes with regards to functional type, isoform, and position within the gene. Codon bias even varies by isoform within a species. We find evidence in favor of both chromosomal influences on nucleotide composition and selection against nonsense errors (SANE) acting on codon usage in MyHC genes. Intragenic variation in codon bias and elongation rate is significant, with a strong trend for increasing codon bias and elongation rate towards the 3' end of the gene, although the trend is dependent upon the degeneracy class of the codons. Therefore, patterns of codon usage in MyHC genes are consistent with models supporting SANE as a major force shaping codon usage.     

Unanticipated ankle inversions are significantly different from anticipated ankle inversions during drop landings: overcoming anticipation bias

Few ankle inversion studies have taken anticipation bias into account or collected data with an experimental design that mimics actual injury mechanisms. Twenty-three participants performed randomized single-leg vertical drop landings from 20 cm. Subjects were blinded to the landing surface (a flat force plate or 30° inversion wedge on the force plate). After each trial, participants reported whether they anticipated the landing surface. Participant responses were validated with EMG data. The protocol was repeated until four anticipated and four unanticipated landings onto the inversion wedge were recorded. Results revealed a significant main effect for landing condition. Normalized vertical ground reaction force (% body weights), maximum ankle inversion (degrees), inversion velocity (degrees/second), and time from contact to peak muscle activation (seconds) were significantly greater in unanticipated landings, and the time from peak muscle activation to maximum VGRF (second) was shorter. Unanticipated landings presented different muscle activation patterns than landings onto anticipated surfaces, which calls into question the usefulness of clinical studies that have not controlled for anticipation bias.