Systematic identification of gene families for use as markers for phylogenetic and phylogeny- driven ecological studies of bacteria and archaea and their major subgroups

With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as marker genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities. We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology) markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa. We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for all bacteria and archaea, 114 for all bacteria, and much more for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible previously.Comment: 24 pages, 3 figure

BUILDING AN EVALUATION FRAMEWORK OF ENVIRONMENTAL INTERPRETATION FOR CHINESE GEOPARKS---CASE STUDY OF YUNTAISHAN WORLD GEOPARK

Environmental interpretation is a key tool for integrated management of tourism, with potential for greater use in managing visitor numbers, behavior and impacts, and enhancing experience. Evaluation is necessary to determine whether interpretation is achieving its goals. It is vital for park managers to know if their management is effective in order to determine what techniques can be used to address a particular problem. The study first introduces the background of Geoparks, and clarifies the definition of environmental interpretation. Next, the study identifies the context that a comprehensive evaluation framework for environmental interpretation in Geoparks is used in order to help Geopark managers to institute the continuous improvement of environmental interpretation. The detailed objectives include: 1.To build an evaluation indicator framework that can be used by Geoparks to evaluate environmental interpretation; 2.To use the evaluation indicator framework to study Yuntaishan World Geopark; 3. To use the data provided by Yuntaishan World Geopark to identify the perceptions of the visitors; 4. To use the data provided by Yuntaishan World Geopark to identify the perceptions of experts and peers

The positional cloning and expression studies of the IMMUTANS variegation locus of Arabidopsis thaliana

immutans (im), a nuclear gene induced variegation mutation of Arabidopsis, causes green- and white-sectored leaves and is recessive. The green sectors contain cells with normal chloroplasts, whereas the white sectors are heteroplastidic and contain cells with abnormal, pigment-deficient plastids as well as some normal chloroplasts. The white sectors accumulate the carotenoid precursor phytoene. We have cloned IM by chromosome walking and found that the gene encodes a 40.5-kD chloroplast thylakoid membrane protein with sequence motifs characteristic of alternative oxidase, a mitochondrial protein that functions as a terminal oxidase in the respiratory chains of all plants. IM protein functions as a component of a redox. chain responsible for phytoene desaturation. Our research on IM expression at the transcriptional level reveals that IM is expressed ubiquitously and it suggests that IM may play roles in different kinds of plastids including chloroplasts, leucoplasts, chromoplasts and etioplasts. In addition to carotenoid biosynthesis, IM may play a general role in desaturation reactions in plastids

Finite Mixtures of Mean-Parameterized Conway-Maxwell-Poisson Models

For modeling count data, the Conway-Maxwell-Poisson (CMP) distribution is a popular generalization of the Poisson distribution due to its ability to characterize data over- or under-dispersion. While the classic parameterization of the CMP has been well-studied, its main drawback is that it is does not directly model the mean of the counts. This is mitigated by using a mean-parameterized version of the CMP distribution. In this work, we are concerned with the setting where count data may be comprised of subpopulations, each possibly having varying degrees of data dispersion. Thus, we propose a finite mixture of mean-parameterized CMP distributions. An EM algorithm is constructed to perform maximum likelihood estimation of the model, while bootstrapping is employed to obtain estimated standard errors. A simulation study is used to demonstrate the flexibility of the proposed mixture model relative to mixtures of Poissons and mixtures of negative binomials. An analysis of dog mortality data is presented. As a generalization of the Poisson distribution and a common alternative to other discrete distributions, the Conway-Maxwell-Poisson (CMP) distribution has the flexibility to explicitly characterize data over- or under-dispersion. The mean-parameterized version of the CMP has received increasing attention in the literature due to its ability to directly model the data mean. When the mean further depends on covariates, then the mean-parameterized CMP regression model can be treated in a generalized linear models framework. In this work, we propose a mixture of mean-parameterized CMP regressions model to apply on data which are potentially comprised of subpopulations with different conditional means and varying degrees of dispersions. An EM algorithm is constructed to find maximum likelihood estimates of the model. A simulation study is performed to test the proposed mixture of mean-parameterized CMP regressions model, and to compare it to model fits using mixtures of Poisson regressions and mixtures of negative binomial regressions. An analysis of the spread of a viral infection in potato plants is performed using these different mixtures of count regressions models, where we show the mixture of mean-parameterized CMP regressions to be an effective model

From social cognition difficulties to later emotional and behavioural problems: the roles of cortisol and inflammatory markers

Objective: Deficits in social cognition are associated with a variety of emotional and behavioural problems in youth. It has been suggested that stress may be one of the mechanisms underlying these associations. Therefore, the overall aim of this PhD project is to examine the relationships between social cognition abilities, physiological stress, and mental health problems. Specifically, this project aims to evaluate the associations between different domains of social cognition and stress, investigate the link between stress and various emotional and behavioural problems, and explore the role of stress in the longitudinal association between childhood social cognition deficits and mental health problems in late adolescence. The thesis focused on two indicators of physiological stress, hypothalamic-pituitary-adrenal (HPA) axis activities (i.e., diurnal cortisol patterns) and systemic inflammation. Method: A systematic review and meta-analysis was first conducted to examine the association between social cognition and cortisol in the general population, followed by three empirical studies. The statistical analyses of the empirical studies were based on the secondary data from the Avon Longitudinal Study of Parents and Children (ALSPAC), a UK population-based birth cohort. In the first empirical study, multiple regression models were fitted to investigate the predictive effect of cortisol and inflammation on emotional and behavioural problems at 17 years old, with the adjustment of the mental health problems at 4 years old and covariates. The second study assessed if chronicity and severity of hyperactivity/inattention problems could predict abnormal cortisol profile in adolescence. Growth mixture models were used to identify classes with distinct developmental trajectories of hyperactivity/inattention symptoms from ages 4 to 13 years. In the third study, Bayesian structural equation modelling was used to investigate the mediating effects of cortisol and inflammation on the links between childhood social cognition abilities and emotional or behavioural problems at 17 years. Results: The meta-analyses showed that emotion control was positively associated with basal cortisol levels, while emotion recognition or theory of mind was not associated with cortisol. The empirical studies found that social communication deficits, but not emotion recognition abilities, were linked with later emotional and behavioural problems. Flattened diurnal cortisol slope and lower morning cortisol levels were associated with hyperactivity/inattention problems two years later. Adolescents with persistently high levels of hyperactivity/inattention symptoms since childhood showed lower total morning cortisol and a smaller diurnal decline. Lower morning cortisol partially mediated the direct association between social communication deficits at 8 years and hyperactivity/inattention and conduct problems at 17 years, even after adjustments for inflammation and confounders. There was no significant association between systemic inflammation and social cognition difficulties, emotional problems, or behavioural problems. Conclusion: The findings of this project provided evidence for the hypoactivity of HPA axis among adolescents with chronic hyperactivity/inattention problems since childhood in the general population. Adolescents with childhood social communication deficits were also at risk of blunted HPA axis activity in the morning. However, as the indirect effect of morning cortisol on the association between social cognition and behavioural problems is very small in magnitude, it may not be clinically or practically significant

Finite Element Analysis of Residual Stress in the Diffusion Zone of Mg/Al Alloys

In this study, the finite element method was applied for analyzing the effect of annealing temperatures on residual stress in the diffusion zone of AZ31 Mg and 6061 Al alloys. The microstructure and mechanical behavior of the diffusion zone were also investigated. Simulations on the annealing of the welded specimens at 200°C, 250°C, and 300°C were conducted. Moreover, experiments such as diffusion bonding and annealing, analysis of residual stress by X-ray diffraction, elemental analysis using an electron probe microanalyzer, and microstructure investigation via scanning electron microscopy were performed for further investigation of the diffusion layers. According to the results of the simulations and experiments, the diffusion layers widen with increasing annealing temperatures, and the results of the simulations are in good agreement with those of the experiments. The microstructure and elemental distribution were the most uniform and the residual stress was the least for samples annealed at 250°C. Thus, 250°C was found to be the most appropriate annealing temperature

Endothelium in the pharyngeal arches 3, 4 and 6 is derived from the second heart field.

Oxygenated blood from the heart is directed into the systemic circulation through the aortic arch arteries (AAAs). The AAAs arise by remodeling of three symmetrical pairs of pharyngeal arch arteries (PAAs), which connect the heart with the paired dorsal aortae at mid-gestation. Aberrant PAA formation results in defects frequently observed in patients with lethal congenital heart disease. How the PAAs form in mammals is not understood. The work presented in this manuscript shows that the second heart field (SHF) is the major source of progenitors giving rise to the endothelium of the pharyngeal arches 3 - 6, while the endothelium in the pharyngeal arches 1 and 2 is derived from a different source. During the formation of the PAAs 3 - 6, endothelial progenitors in the SHF extend cellular processes toward the pharyngeal endoderm, migrate from the SHF and assemble into a uniform vascular plexus. This plexus then undergoes remodeling, whereby plexus endothelial cells coalesce into a large PAA in each pharyngeal arch. Taken together, our studies establish a platform for investigating cellular and molecular mechanisms regulating PAA formation and alterations that lead to disease