Mitochondrial sequence data and Dipsacales phylogeny: mixed models, partitioned Bayesian analyses, and model selection

Phylogenetic analyses of chloroplast DNA sequences, morphology, and combined data have provided consistent support for many of the major branches within the angiosperm clade Dipsacales. Here we use sequences from three mitochondrial loci to test the existing broad scale phylogeny and in an attempt to resolve several relationships that have remained uncertain. Parsimony, maximum likelihood, and Bayesian analyses of a combined mitochondrial data set recover trees broadly consistent with previous studies, although resolution and support are lower than in the largest chloroplast analyses. Combining chloroplast and mitochondrial data results in a generally well-resolved and very strongly supported topology but the previously recognized problem areas remain. To investigate why these relationships have been difficult to resolve we conducted a series of experiments using different data partitions and heterogeneous substitution models. Usually more complex modeling schemes are favored regardless of the partitions recognized but model choice had little effect on topology or support values. In contrast there are consistent but weakly supported differences in the topologies recovered from coding and non-coding matrices. These conflicts directly correspond to relationships that were poorly resolved in analyses of the full combined chloroplast-mitochondrial data set. We suggest incongruent signal has contributed to our inability to confidently resolve these problem areas.     

COI序列:影响动物分类学与生态学的DNA barcode

DNA barcode是一段特殊的、可用于物种鉴定的DNA序列.目前在动物中最常用的DNA barcode是细胞色素C氧化酶1号基因(COI)的部分序列.随着标准数据库的建立,基于COI基因的DNA barcode在动物分类学和生态学中得到了广泛应用.但是,采用COI基因作为DNA barcode所隐含的涉及线粒体的进化历史、遗传特性和物种成种时间的默认前提,并非完全成立,由此引发了许多问题.本文阐述了基于COI基因的DNA barcode对分类学和生态学的影响,目前存在的问题,以及可能的研究方向.     

Characterizing complex mixed-species bird flocks using an objective method for determining species participation

We developed sampling methods to characterize the participation of bird species in foraging flocks led by the Eastern Tufted Titmouse (Baeolophus bicolor) in North-central Florida during winter, because standard field methods, developed primarily for permanent resident Neotropical flocks, were intractable in our system. During January–February 2004 and November 2004–March 2005, we observed 55 mixed-species flocks, recorded 40 potential flocking species [mean of 12.4 species (SD = 3.8; range 3–20), 26.3 individuals (SD = 12.2; range 8–60), and 3.1 titmice (SD = 1.4; range 1–7), per flock]. Twenty-six species were observed frequently enough (>10% of observations) to be included in analyses. We paired 60-min flock observations with 10-min point counts conducted in locations used by flocks, but after flocks had moved more than 100 m away. This method yielded a measure of flocking propensity: the ratio of the number of individuals observed in the flock versus during the point count for each species. We used regression tree (RT) analysis to classify species into groupings according to their levels of flock participation, and to investigate relationships between flocking propensity and various environmental and social factors that we measured. Our analysis identified three clear species groups; “Nuclear/Regular Associate” (12 spp.; high/moderate), “Occasional Associate” (four spp.; moderate/low), and “Non-joiner/Accidental” (ten spp.; low/no flocking propensity). Groupings were similar to schemes produced via more time-intensive field methods. In order to contextualize grouping categories, we conducted a review of flocking group definitions and relevant autecological information (e.g., interspecific sociality) about our study species. We found this method to be useful for geographically extensive sampling of species’ participation in mixed-species flocks, despite high inter-flock variability in species composition and limited labor.     

Nonparametric functional mapping of quantitative trait loci

Summary .  Functional mapping is a useful tool for mapping quantitative trait loci (QTL) that control dynamic traits. It incorporates mathematical aspects of biological processes into the mixture model-based likelihood setting for QTL mapping, thus increasing the power of QTL detection and the precision of parameter estimation. However, in many situations there is no obvious functional form and, in such cases, this strategy will not be optimal. Here we propose to use nonparametric function estimation, typically implemented with B-splines, to estimate the underlying functional form of phenotypic trajectories, and then construct a nonparametric test to find evidence of existing QTL. Using the representation of a nonparametric regression as a mixed model, the final test statistic is a likelihood ratio test. We consider two types of genetic maps: dense maps and general maps, and the power of nonparametric functional mapping is investigated through simulation studies and demonstrated by examples.     

Cluster detection based on spatial associations and iterated residuals in generalized linear mixed models

Summary .  Spatial clustering is commonly modeled by a Bayesian method under the framework of generalized linear mixed effect models (GLMMs). Spatial clusters are commonly detected by a frequentist method through hypothesis testing. In this article, we provide a frequentist method for assessing spatial properties of GLMMs. We propose a strategy that detects spatial clusters through parameter estimates of spatial associations, and assesses spatial aspects of model improvement through iterated residuals. Simulations and a case study show that the proposed method is able to consistently and efficiently detect the locations and magnitudes of spatial clusters.     

Phase behaviour of oleanolic acid/stearyl stearate binary mixtures in bulk and at the air-water interface

The solid-liquid phase behaviour of oleanolic acid (OLA)/stearyl stearate (SS) was investigated by differential scanning calorimetry and polarizing optical microscopy. A eutectic type diagram, with the eutectic composition close to pure SS was obtained. Complementary studies by NMR, X-ray diffraction (XRD) and diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy were performed. A mutual influence was detected in mixtures: the low melting form of SS is favoured at low OLA molar fractions (X_OLA) and spherulitic structures appear at high X_OLA and high temperature. Additionally, H-bonding between OLA carbonyl groups increases in the presence of SS. The study of OLA/SS by the Langmuir method and Brewster angle microscopy revealed the organization at the air-water interface: OLA interacts with water in the first layer, while SS is completely segregated to the upper layer for X_OLA > 0.3, and it distributes in the first and upper layers for X_OLA < 0.3.     

Self-assembly of 2D zinc metal-organic frameworks based on mixed organic ligands

Self-assembly of Zn(NO₃)₂·6H₂O, 5-amino-2,4,6-triiodoisophthalic acid (H₂atiip) and 4,4′-bipyridine (bpy) or 1,3-di(4-pyridyl)propane (dpp) gave rise to three unusual zinc metal-organic frameworks, Zn₂(bpy)₂(atiip)₂·3H₂O·2dmf (1), Zn₈(dpp)₈(atiip)₈·4H₂O (2), Zn(dpp)(atiip)·(dmf)·(H₂O) (3). All complexes possess 2D layer frameworks constructed from 1D Zn-carboxylate tubular unit for 1, 1D Zn-carboxylate helical chain for 2 and 3. In 1 and 2, the bpy or dpp act as both bridging and blocking ligands and the blocking ligands play an important role in the formation of the 2D layer frameworks. Both 2 and 3 contain two different large metallomacrocycles. Photoluminescence measurements of 1-3 in the solid state at room temperature show that all complexes exhibit luminescence, which can be assigned to an intraligand π → π^∗ transition or ligand-to-metal charge transfer (LMCT).     

Asymmetric lipid bilayer formation stabilized by DNA at the air/water interface

The lipid bis(guanidinium)-tren-cholesterol (BGTC) is a cationic cholesterol derivative bearing guanidinium polar headgroups used for gene transfection either alone or formulated as liposomes with the zwitterionic lipid 1,2-di-[cis-9-octadecenoyl]-sn-glycero-3-phosphoethanolamine (DOPE). Previous investigations have shown its ability to strongly interact with DNA and form asymmetric lipid bilayers at the air/water interface when mixed with DOPE. Here, with a view to further investigate its physicochemical behavior, we studied the interactions of mixtures of BGTC with another zwitterionic lipid, 1,2-Dimyristoyl-sn-Glycero-3-Phosphocholine, (DMPC), with DNA at the air/water interface by using the Langmuir monolayer technique coupled with Brewster Angle Microscopy (BAM) and Polarization Modulation Infra Red Reflexion Absorption (PMIRRAS) spectroscopy and we investigate DNA–BGTC/DMPC interactions. We demonstrate that when DNA is injected into the subphase in excess compared to the positive charges of BGTC, it adsorbs to BGTC/DMPC monolayers at 20 mN/m whatever the lipid monolayer composition (1/5, 2/3 or 3/2 BGTC/DMPC molar ratio) and forms an incomplete monolayer of either isotropic or anisotropic double strands depending on the BGTC content in the monolayer. Compression beyond the collapse of some mixed DNA–BGTC/DMPC (2/3 and 3/2 molar ratio) systems leads to the formation of DNA monolayers underneath asymmetric lipid bilayers characterized by a bottom layer of BGTC in contact with DNA and a top layer mainly constituted of DMPC.     

Mixed fermentation for natural product drug discovery

Natural products continue to play a major role in drug discovery and development. However, chemical redundancy is an ongoing problem. Genomic studies indicate that certain groups of bacteria and fungi have dozens of secondary metabolite pathways that are not expressed under standard laboratory growth conditions. One approach to more fully access the metabolic potential of cultivatable microbes is mixed fermentation, where the presence of neighboring microbes may induce secondary metabolite synthesis. Research to date indicates that mixed fermentation can result in increased antibiotic activity in crude extracts, increased yields of previously described metabolites, increased yields of previously undetected metabolites, analogues of known metabolites resulting from combined pathways and, importantly, induction of previously unexpressed pathways for bioactive constituents.