Bayesian estimation of concordance among gene trees

Multigene sequence data have great potential for elucidating important and interesting evolutionary processes, but statistical methods for extracting information from such data remain limited. Although various biological processes may cause different genes to have different genealogical histories (and hence different tree topologies), we also may expect that the number of distinct topologies among a set of genes is relatively small compared with the number of possible topologies. Therefore evidence about the tree topology for one gene should influence our inferences of the tree topology on a different gene, but to what extent? In this paper, we present a new approach for modeling and estimating concordance among a set of gene trees given aligned molecular sequence data. Our approach introduces a one-parameter probability distribution to describe the prior distribution of concordance among gene trees. We describe a novel 2-stage Markov chain Monte Carlo (MCMC) method that first obtains independent Bayesian posterior probability distributions for individual genes using standard methods. These posterior distributions are then used as input for a second MCMC procedure that estimates a posterior distribution of gene-to-tree maps (GTMs). The posterior distribution of GTMs can then be summarized to provide revised posterior probability distributions for each gene (taking account of concordance) and to allow estimation of the proportion of the sampled genes for which any given clade is true (the sample-wide concordance factor). Further, under the assumption that the sampled genes are drawn randomly from a genome of known size, we show how one can obtain an estimate, with credibility intervals, on the proportion of the entire genome for which a clade is true (the genome-wide concordance factor). We demonstrate the method on a set of 106 genes from 8 yeast species.     

Optimisation of an extraction procedure and chemical characterisation of Croatian propolis tinctures

Three spectrophotometric methods for the quantitative determination of different flavonoid groups and total phenolics in Croatian propolis samples were optimised and validated. The assay based on the formation of aluminium chloride complex (with galangin as a standard) was applied to the quantification of flavones and flavonols, while the 2,4-dinitrophenylhydrazine method (with pinocembrine as a reference) was used for the quantification of flavanones. Total phenolic content was measured by the Folin-Ciocalteau method using reference solution of caffeic acid:galangin:pinocembrine (1:1:1). Through analytical validation, the most suitable extraction conditions (with respect to time, temperature and concentration of extraction solvent) were determined, and final conditions for the extraction were established (80% ethanol, 1 h at the room temperature). The appropriate ratio between the mass of raw propolis and the extraction solvent volume was also established. By the application of the optimised method of extraction, 10 propolis tinctures were prepared and subjected to the analysis of general pharmacopoeial parameters, which are fundamental for the creation of quality specification (relative density, dry residue of extract, content of ethanol, methanol and 2-propanol). Additionally, the content of waxes as the main inactive constituents was determined in order to observe the level of their migration from crude propolis to the prepared tinctures.     

DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile

Dividing protein structures into domains is proven useful for more accurate structural and functional characterization of proteins. Here, we develop a method, called DDOMAIN, that divides structure into DOMAINs using a normalized contact-based domain-domain interaction profile. Results of DDOMAIN are compared to AUTHORS annotations (domain definitions are given by the authors who solved protein structures), as well as to popular SCOP and CATH annotations by human experts and automatic programs. DDOMAIN's automatic annotations are most consistent with the AUTHORS annotations (90% agreement in number of domains and 88% agreement in both number of domains and at least 85% overlap in domain assignment of residues) if its three adjustable parameters are trained by the AUTHORS annotations. By comparison, the agreement is 83% (81% with at least 85% overlap criterion) between SCOP-trained DDOMAIN and SCOP annotations and 77% (73%) between CATH-trained DDOMAIN and CATH annotations. The agreement between DDOMAIN and AUTHORS annotations goes beyond single-domain proteins (97%, 82%, and 56% for single-, two-, and three-domain proteins, respectively). For an "easy" data set of proteins whose CATH and SCOP annotations agree with each other in number of domains, the agreement is 90% (89%) between "easy-set"-trained DDOMAIN and CATH/SCOP annotations. The consistency between SCOP-trained DDOMAIN and SCOP annotations is superior to two other recently developed, SCOP-trained, automatic methods PDP (protein domain parser), and DomainParser 2. We also tested a simple consensus method made of PDP, DomainParser 2, and DDOMAIN and a different version of DDOMAIN based on a more sophisticated statistical energy function. The DDOMAIN server and its executable are available in the services section on http://sparks.informatics.iupui.edu.     

Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates

Bayesian methods have become extremely popular in molecular ecology studies because they allow us to estimate demographic parameters of complex demographic scenarios using genetic data. Articles presenting new methods generally include sensitivity studies that evaluate their performance, but they tend to be limited and need to be followed by a more thorough evaluation. Here we evaluate the performance of a recent method, bayesass , which allows the estimation of recent migration rates among populations, as well as the inbreeding coefficient of each local population. We expand the simulation study of the original publication by considering multi-allelic markers and scenarios with varying number of populations. We also investigate the effect of varying migration rates and F _ST more thoroughly in order to identify the region of parameter space where the method is and is not able to provide accurate estimates of migration rate. Results indicate that if the demographic history of the species being studied fits the assumptions of the inference model, and if genetic differentiation is not too low ( F _ST ≥ 0.05), then the method can give fairly accurate estimates of migration rates even when they are fairly high (about 0.1). However, when the assumptions of the inference model are violated, accurate estimates are obtained only if migration rates are very low ( m  = 0.01) and genetic differentiation is high ( F _ST ≥ 0.10). Our results also show that using posterior assignment probabilities as an indication of how much confidence we can place on the assignments is problematical since the posterior probability of assignment can be very high even when the individual assignments are very inaccurate.     

大气有机氮沉降研究进展

大气氮素沉降是全球氮素生物地球化学循环的一个重要部分,包括干?湿沉降两种,以无机态和有机态形式发生沉降。长期以来由于受研究方法的限制,国际上对大气氮素沉降的研究多集中在无机态氮的沉降上,忽视了对有机态氮形式发生的沉降,因而造成了人们对大气氮素沉降总量的低估。在全面总结国内外文献的基础上,综述了大气有机态氮沉降的研究进展,具体包括大气有机氮的来源、种类?雨水有机氮的测定方法?有机氮沉降对大气氮沉降总量(氮沉降总量=无机氮沉降 有机氮沉降)的贡献,以及有机氮沉降可能的生态效应等。最后,指出了今后我国大气有机氮沉降研究需要加强的主要方面。     

施肥对沙打旺根系提水及土壤养分活性的影响

采用上下桶分根法,通过下桶施肥研究施肥对沙打旺根系提水作用能力及上桶土壤养分活性的影响.结果发现：沙打旺根系提水量随施肥量的增加而增加;在上桶不浇水的情况下,高肥处理组上桶伴生的浅根植物早熟禾在干旱胁迫时间较短时较对照组生长正常;根系提水量最大时,高肥和低肥处理的上桶土壤呼吸速率分别比对照增加14.9%和51.4%,有机质含量分别下降17.8%、19.6%,速效磷分别增加13.9%、33.2%,速效钾分别增加20.4%和22.8%.研究表明,施肥促进了沙打旺根系的生长发育,增加了下桶根系吸水和上桶释水量,有效地缓解了上桶土壤的旱情,显著提高了上桶土壤养分的活化程度和有效养分含量.     

一类扩散循环系统正解的存在性与稳定性

利用上下解方法及全藕合线性互惠系统的最大值原理,研究了一类非线性椭圆系统,给出了其正解存在的充分必要条件,同时也得到了其正解局部稳定的某些结果．     

3种纯化重组禽流感病毒NS1抗原方法的比较

目的：摸索出最佳分离纯化和复性重组禽流感病毒NS1抗原的方法,得到高纯度的重组蛋白。方法：将重组质粒pET32a—NS1转染大肠杆菌BL21（DE3）后获得表达,分别以尿素变性、复性,Ni—NTA His．Bind Resin亲和,以及脱氧胆酸钠-N-十二烷基肌氨酸钠（DOC—SKL）洗涤溶解等3种纯化方法从表达产物包涵体中分离纯化NS1蛋白,并进行比较研究。结果：原核表达得到相对分子质量约45000的目的蛋白;3种纯化方法均能分离和纯化出NS1重组蛋白,其中尿素纯化的蛋白纯度为50％～60％,Ni—NTA His．Bind Resin亲和纯化的蛋白纯度为80％-90％,DOC-SKL纯化的蛋白纯度达95％以上;Western blot检测表明,复性后的纯化蛋白具有良好的生物学活性。结论：应用十二烷基肌氨酸钠洗涤纯化是最佳的纯化NS1蛋白的方法,所获得的蛋白可作为包被ELISA的抗原。     

Feeding with speed: prey capture evolution in cichilds

The diversity of both the locomotor and feeding systems in fish is extensive, although little is known about the integrated evolution of the two systems. Virtually, all fish swim to ingest prey and all open their buccal cavity during prey capture, but the relationship between these two ubiquitous components of fish feeding strikes is unknown. We predicted that there should be a positive correlation between ram speed (RS) and maximum gape (MG) because the accuracy of a predatory strike goes down with an increase in RS and fish with larger mouths eat larger, more evasive prey. For 18 species of neotropical cichlids, we used phylogenetic-independent contrasts to study the relationship between the predator closing speed (RS) and mouth size (MG) during prey capture. To provide a robust comparative framework, we augmented existing phylogenetic information available from the mitochondrial cytochrome b gene with sequences from the S7 nuclear ribosomal intron for these species. Then, we captured high-speed (500 images per second), lateral view feeding sequences of each species by using a digital video camera and measured both RS and MG. Uncorrected species values of MG and RS were positively and significantly correlated. When accounting for any of the set of phylogenetic relationships recovered, the independent contrasts of RS and MG remained significantly, and positively, correlated. This tight evolutionary coupling highlights what is likely a common relationship between locomotor behaviour and feeding kinematics in many organisms.