MORPHOMETRIC CORRELATION PATTERNS OF ADULT BIRDS (FRINGILLIDAE: PASSERIFORMES AND COLUMBIFORMES) MIRROR THE EXPRESSION OF DEVELOPMENTAL CONTROL GENES

Stimulated by the rapid progress in developmental genetics, recent approaches to evolutionary theory focus on the interface function of developmental processes in the study of genotype-phenotype mapping. From this viewpoint, the main result of the present analysis is that the expression patterns of developmental control genes are reflected in the infraspecific correlation patterns of phenotypic characters in the adult stage. The study is based on 42 logarithmically scaled skeletal measurements of two avian clades, finches (43 species, n = 313) and pigeons (27 species, n = 219). First, for each clade an “observed correlation matrix” was calculated by computing a bias-reduced pooled-species correlation matrix based on the clade-specific pooled within-species variance-covariance matrix between measurements. Second, the expression domains of diverse developmental control genes, that is, Hox, Msx, Pax, Mhox, Shh, Bmp, and Gdf, in characters were represented by “theoretical matrices.” Finally, the observed and the theoretical matrices were compared by Mantel's test to test hypotheses about pattern similarities between phenotypic correlations and the expression of developmental control genes. Seventeen percent of the single matrix comparisons revealed significant (P ≤ 0.05) pattern correspondences in finches, whereas 63% were significant in pigeons. The multiple comparisons revealed correspondences at the highest significance level (P ≤ 0.001) in both clades and disclosed that 15% of the observed matrix patterns are explained in finches versus 22% in pigeons. Presumably, as finches have less pronounced correspondences between gene expression and phenotypic correlation, they are more derived than pigeons. Out of the significant single matrix comparisons, four correspondences are common to both clades: one of them is connected with the Gdf gene expression concerning limb length relations and also harmonizes with the dominant pattern within the infraspecific correlation matrices. The general implication is that the significant correspondences detected here between observed and theoretical matrices are based on a correspondence between phenotypic and genetic modules. Because the phenotypic modules are potential candidates for a direct impact of selection, the important role of genotype-phenotype mapping in molding the body plan becomes apparent.     

MODELING BRAIN EVOLUTION FROM BEHAVIOR: A PERMUTATIONAL REGRESSION APPROACH

This paper has two complementary purposes: first, to present a method to perform multiple regression on distance matrices, with permutation testing appropriate for path-length matrices representing evolutionary trees, and then, to apply this method to study the joint evolution of brain, behavior and other characteristics in marsupials. To understand the computation method, consider that the dependent matrix is unfolded as a vector y; similarly, consider X to be a table containing the independent matrices, also unfolded as vectors. A multiple regression is computed to express y as a function of X. The parameters of this regression (R² and partial regression coefficients) are tested by permutations, as follows. When the dependent matrix variable y represents a simple distance or similarity matrix, permutations are performed in the same manner as the Mantel permutational test. When it is an ultrametric matrix representing a dendrogram, we use the double-permutation method (Lapointe and Legendre 1990, 1991). When it is a path-length matrix representing an additive tree (cladogram), we use the triple-permutation method (Lapointe and Legendre 1992). The independent matrix variables in X are kept fixed with respect to one another during the permutations. Selection of predictors can be accomplished by forward selection, backward elimination, or a stepwise procedure. A phylogenetic tree, derived from marsupial brain morphology data (28 species), is compared to trees depicting the evolution of diet, sociability, locomotion, and habitat in these animals, as well as their taxonomy and geographical relationships. A model is derived in which brain evolution can be predicted from taxonomy, diet, sociability and locomotion (R² = 0.75). A new tree, derived from the “predicted” data, shows a lot of similarity to the brain evolution tree. The meaning of the taxonomy, diet, sociability, and locomotion predictors are discussed and conclusions are drawn about the evolution of brain and behavior in marsupials.     

The role of marriage rules in the structure of genetic relatedness

In this work, we take a forward in time approach to compute the probabilities of non-identity by descent for a population consisting of n sections obeying one of a class of marriage rules that is invariant under cyclical relabeling of sections. A perturbation method allows for exact asymptotics using the reciprocal of the section population as a small parameter. The analysis yields relatedness measures that generalize Wright's F-statistics.     

Evaluation of support matrices for immobilization of anaerobic consortia for efficient carbon cycling in waste regeneration

Efficient metabolism of fatty acids during anaerobic waste digestion requires development of consortia that include "fatty acid consuming H(2) producing bacteria" and methanogenic bacteria. The objective of this research was to optimize methanogenesis from fatty acids by evaluating a variety of support matrices for use in maintaining efficient syntrophic-methanogenic consortia. Tested matrices included clays (montmorillonite and bentonite), glass beads (106 and 425-600mum), microcarriers (cytopore, cytodex, cytoline, and cultispher; conventionally employed for cultivation of mammalian cell lines), BioSep beads (powdered activated carbon), and membranes (hydrophilic; nylon, polysulfone, and hydrophobic; teflon, polypropylene). Data obtained from headspace methane (CH(4)) analyses as an indicator of anaerobic carbon cycling efficiency indicated that material surface properties were important in maintenance and functioning of the anaerobic consortia. Cytoline yielded significantly higher CH(4) than other matrices as early as in the first week of incubation. 16S rRNA gene sequence analysis from crushed cytoline matrix showed the presence of Syntrophomonas spp. (butyrate oxidizing syntrophs) and Syntrophobacter spp. (propionate oxidizing syntrophs), with Methanosaeta spp. (acetate utilizing methanogen), and Methanospirillum spp. (hydrogen utilizing methanogen) cells. It is likely that the more hydrophobic surfaces provided a suitable surface for adherence of cells of syntrophic-methanogenic consortia. Cytoline also appeared to protect entrapped consortia from air, resulting in rapid methanogenesis after aerial exposure. Our study suggests that support matrices can be used in anaerobic digestors, pre-seeded with immobilized or entrapped consortia on support matrices, and may be of value as inoculant-adsorbents to rapidly initiate or recover proper system functioning following perturbation.     

Database searching with DNA and protein sequences: an introduction

This review of sequence database searching aims to set out current practice in the area, in order to give practical guidelines to the experimental biologist. It describes the basic principles behind the programs and enumerates the range of databases available in the public domain. Of these, the most important are the equivalent DNA databases European Molecular Biology Laboratory (EMBL), GenBank and DNA Databank of Japan (DDBJ), and the protein databases Swiss-Prot and TrEMBL. The commonly used BLAST and FASTA algorithms are described in detail and alternative approaches mentioned briefly. Scoring matrices used to compare amino acid types during protein database searches are compared, with an emphasis on the PAM and BLOSUM series of observed substitution matrices.     

Global analysis of competition for perfectly substitutable resources with linear response

We study a model of the chemostat with two species competing for two perfectly substitutable resources in the case of linear functional response. Lyapunov methods are used to provide sufficient conditions for the global asymptotic stability of the coexistence equilibrium. Then, using compound matrix techniques, we provide a global analysis in a subset of parameter space. In particular, we show that each solution converges to an equilibrium, even in the case that the coexistence equilibrium is a saddle. Finally, we provide a bifurcation analysis based on the dilution rate. In this context, we are able to provide a geometric interpretation that gives insight into the role of the other parameters in the bifurcation sequence. Funding was provided by the National Science Foundation-funded ADVANCE Institutional Transformation Program at New Mexico State University, fund # NSF0123690. Research partially supported by the Natural Science and Engineering Research Council of Canada.     

Fibroblastic cells from human periapical granulation tissue preferentially form calcified matrices in decalcified boiled rat bone

We have been studying the potential of human fibroblastic cells (HFC) from periapical granulation tissue to form a calcified matrix. Recently, we reported that inflamed periapical granulation tissue contains osteogenic cells. In the present study, we tested the hypothesis that HFC, cultured with decalcified bone (DB) of rat, might form much greater calcified matrices than with rat decalcified boiled bone (DBB), which was originally prepared as a negative control. HFC were cultured with DB or DBB in the presence or absence of 2 mM -glycerophosphate (-GP) and 50 g/ml ascorbic acid. After six weeks of culture, a number of von Kossa-positive globular structures were unexpectedly observed inside DBB, but not DB. Without HFC, such structures were never seen in DBB incubated with 2 mM -GP and 50 g/ml ascorbic acid. DB cultured with HFC under the same conditions did not show these structures. Electron-microscopic observation revealed that matrix vesicles aggregated on collagen fibrils around globular structures in DBB. Energy dispersive X-ray microanalysis confirmed that these structures were calcified matrices composed of calcium and phosphate. These results suggest that human periapical granulation tissue contains cells responsible for the formation of calcified matrices in DBB, and that DBB could serve as an excellent scaffold for the calcification of HFC, rather than DB.This work was supported by grant-in-aid (project 15689024) for scientific research from the Ministry of Education, Culture, Sports, Science and Technology, Japan.     

Stereoselective histidine sensor based on molecularly imprinted sol-gel films

A piezoelectric sensor coated with a thin molecularly imprinted sol-gel film has been developed for the determination of L-histidine in the liquid phase. Without preprotection, L-histidine was imprinted directly into silica sol-gel films that consisted of a hybrid mixture of functionalized organosilicon precursors (phenyltrimethoxysilane and methyltrimethoxysolane). The viscoelasticity of the film in the air and in buffer solution has been studied by the piezoelectric quartz crystal impedance technique. The binding of L-histidine to the imprinted film in the liquid phase was investigated by the piezoelectric microgravimetry and electrochemical impedance technique. Scatchard analysis showed that the maximum binding site (Qmax) of the L-histidine imprinted sol-gel film is about 23.7 micromol/g. A linear range from 5.0x10(-8) to 1.0x10(-4) M for a detection of L-histidine has been observed with a detection limit of 2.5x10(-8) M for S/N=3. The proposed imprinted sol-gel sensor exhibits good stability, high specificity, and excellent stereoselectivity.