Robustness: predicting the effects of life history perturbations on stage-structured population dynamics

Matrix-based models lie at the core of many applications across the physical, engineering and life sciences. In ecology, matrix models arise naturally via population projection matrices (PPM). The eigendata of PPMs provide detailed quantitative and qualitative information on the dynamic behaviour of model populations, especially their asymptotic rates of growth or decline. A fundamental task in modern ecology is to assess the effect that perturbations to life-cycle transition rates of individuals have on such eigendata. The prevailing assessment tools in ecological applications of PPMs are direct matrix simulations of eigendata and linearised extrapolations to the typically non-linear relationship between perturbation magnitude and the resulting matrix eigenvalues. In recent years, mathematical systems theory has developed an analytical framework, called 'Robustness Analysis and Robust Control', encompassing also algorithms and numerical tools. This framework provides a systematic and precise approach to studying perturbations and uncertainty in systems represented by matrices. Here we lay down the foundations and concepts for a 'robustness' inspired approach to predictive analyses in population ecology. We treat a number of application-specific perturbation problems and show how they can be formulated and analysed using these robustness methodologies.     

Substitution analog peptide derived from HER-2 can efficiently induce HER-2-specific, HLA-A24 restricted CTLs

In order to broaden the possibility for anti-HER-2/neu (HER-2) immune targeting, it is important to identify HLA-A24 restricted peptide epitopes derived from HER-2, since HLA-A24 is one of the most common alleles in Japanese and Asian people. In the present study, we have screened HER-2-derived, HLA-A24 binding peptides for cytotoxic T lymphocyte (CTL) epitopes. A panel of HER-2-derived peptides with HLA-A24 binding motifs and the corresponding analogs designed to enhance HLA-A24 binding affinity were selected. Identification of HER-2-reactive and HLA-A24 restricted CTL epitopes were performed by a reverse immunology approach. To induce HER-2-reactive and HLA-A24 restricted CTLs, PBMCs from healthy donors were repeatedly stimulated with monocytes-derived, mature DCs pulsed with HER-2 peptide. Subsequent peptide-induced T cells were tested for the specificity by enzyme linked immunospot, cytotoxicity and tetramer assays. CTL clones were then obtained from the CTL lines by limiting dilution. Of the peptides containing HLA-A24 binding motifs, 16 peptides (nine mers) including wild type peptides (IC₅₀<1,000 nM) and substituted analog peptides (IC₅₀<50 nM) were selected for the present study. Our studies show that an analog peptide, HER-2(905AA), derived from HER-2(905) could efficiently induce HER-2-reactive and HLA-A24 restricted CTLs. The reactivity of the HER-2(905AA)-induced CTL (CTL905AA) was confirmed by different CTL assays. The CTL905AA clones also were able to lyse HER-2(+), HLA-A24(+) tumor cells and cytotoxicity could be significantly reduced in cold target inhibition assays using cold targets pulsed with the HER-2(905) wild type peptide as well as the inducing HER-2(905AA) analog peptide. A newly identified HER-2(905) peptide epitope is naturally processed and presented as a CTL epitope on HER-2 overexpressing tumor cells, and an MHC anchor-substituted analog, HER-2(905AA), can efficiently induce HER-2-specific, HLA-A24 restricted CTLs.     

A Novel Approach to Phylogeny Reconstruction from Protein Sequences

The reliable reconstruction of tree topology from a set of homologous sequences is one of the main goals in the study of molecular evolution. If consistent estimators of distances from a multiple sequence alignment are known, the distance method is attractive because the tree reconstruction is consistent. To obtain a distance estimate d, the observed proportion of differences p (p-distance) is usually ``corrected' for multiple and back substitutions by means of a functional relationship d=f(p). In this paper the conditions under which this correction of p-distances will not alter the selection of the tree topology are specified. When these conditions are not fulfilled the selection of the tree topology may depend on the correction function applied. A novel method which includes estimates of distances not only between sequence pairs, but between triplets, quadruplets, etc., is proposed to strengthen the proper selection of correction function and tree topology. A ``super' tree that includes all tree topologies as special cases is introduced. Received: 17 February 1998 / Accepted: 20 July 1998     

Modulation of prostate cancer growth in bone microenvironments

Bone remains one of the major sites, and most lethal host organs, for prostate cancer metastasis. Prostate cell spread and establishment in bone depends on multiple reciprocal modifications of bone stromal and epithelial cancer cell behaviors. This review focuses on recent advances in the characterization of cell-cell and cell-matrix interplay, effects on cell growth, adhesion and invasion, and several therapeutic possibilities for co-targeting prostate cancer cells and bone stroma. We address the topic from three main perspectives: (1) the normal and aging bone stromal environment, (2) the "reactive" bone stromal environment, and (3) the cancerous prostate epithelial cells themselves. First, normal, and especially aging, bones provide uniquely rich and "fertile soil" for roaming cancer cells. The interactions between prostate cancer cells and insoluble extracellular matrices, soluble growth factors, and/or sex steroid hormones trigger bone remodeling, through increased osteoclastogenesis and furthur matrix metalloproteinase activity. Second, after cancer cell arrival and establishment in the bone, host stromal cells respond, becoming "reactive" in a process again involving extracellular matrix remodeling, together with growth factor and steroid receptor signaling this process ultimately enhances cancer cell migration, stromal transdifferentiation, and invasion of the cancer tissues by stromal, inflammatory, and immune-responsive cells. Third, prostate cancer cells also respond to supportive bone microenvironments, where soluble and matrix-associated molecules affect cancer cell growth and gene expression, especially altering cancer cell surface receptor and integrin-mediated cell signaling. We discuss both integrin cell-matrix and gap junctional cell-cell communication between cancer cells and their microenvironments during prostate cancer progression.     

Population viability analysis of Saxifraga cotyledon,a perennial plant with semelparous rosettes

The aim with this study was to analyse the population dynamics ofSaxifraga cotyledon, a rare, long lived herb, withsemelparous rosettes. In Sweden, S. cotyledon grows infragmented habitats at high altitude and is classified as vulnerable accordingto the IUCN system. From a five year demographical study we estimatedpopulationgrowth rates and extinction risks for one small and one large subpopulation. Inthe small subpopulation deterministic matrix simulations showed largevariation,with two transitions projecting negative and two projecting positive populationgrowth. The large subpopulation also showed large variation, but all yearlytransitions projected positive population growth. In both subpopulationssurvival and growth contributed more than twice as much to population growthrates than did sexual reproduction, vegetative reproduction and the seed bankall taken together. In stochastic simulations the maximum likelihood growthestimator waslarger than 1 for both subpopulations. None of the two subpopulations sufferfrom high extinction rates and although the effect of demographic stochasticityincrease extinction risk in small populations it is enough with 70 individualsfor a viable population of S. cotyledon. Hence, for thestudied population of S. cotyledon, rareness per se is nota good indicator of vulnerability.     

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.     

Modulation by extracellular matrices of monooxygenase and CYP1A1 induction in Hep G2 cells in serum-free culture

The in vitro cellular functions of differentiated cells are influenced by culture conditions. Effects of several extracellular matrices (ECMs) on cytochrome P450-dependent monooxygenases (MFOs) induction and cytochrome P4501A1 (CYP1A1) gene expression were estimated in Hep G2 cells cultured in a serum-free medium. The cells were cultured on collagen type I- and II-, fibronectin-, and matrigel-coated dishes and MFO activities were induced by the addition of 3-methylcholanthrene (MC). The induction of ethoxycoumarin O-deethylase (ECOD) and alkoxyresorufin O-dealkylase activities as well as the expression of CYP1A1 mRNA were also determined. ECOD and methoxy- and ethoxyresorufin O-dealkylase activities in Hep G2 cells were enhanced by culturing the cells using a serum-free medium on fibronectin- or matrigel-coated dishes. ECOD activity on fibronectin-coated dishes was about 3-fold higher than that using a serum-supplemented medium on untreated dishes. Furthermore, both immobilized and soluble fibronectin enhanced the induction of MFOs. The expression of CYP1A1 mRNA using fibronectin-coated dishes was about 2-fold higher than that using a serum-supplemented medium on untreated dishes. These findings suggest that the gene expression in cultured cells is greatly influenced by ECMs. By using fibronectin-coated dishes to cell culture in a serum-free medium, reproducible and highly sensitive results can be obtained in experiments using cultured cells. This revised version was published online in August 2006 with corrections to the Cover Date.     

Models of natural mutations including site heterogeneity

New computational models of natural site mutations are developed that account for the different selective pressures acting on different locations in the protein. The number of adjustable parameters is greatly reduced by basing the models on the underlying physical-chemical properties of the amino acids. This allows us to use our method on small data sets built of specific protein types. We demonstrate that with this approach we can represent the evolutionary patterns in HIV envelope proteins far better than with more traditional methods. Proteins 32:289–295, 1998. © 1998 Wiley-Liss, Inc.     

Estimating the pattern of nucleotide substitution

Knowledge of the pattern of nucleotide substitution is important both to our understanding of molecular sequence evolution and to reliable estimation of phylogenetic relationships. The method of parsimony analysis, which has been used to estimate substitution patterns in real sequences, has serious drawbacks and leads to results difficult to interpret. In this paper a model-based maximum likelihood approach is proposed for estimating substitution patterns in real sequences. Nucleotide substitution is assumed to follow a homogeneous Markov process, and the general reversible process model (REV) and the unrestricted model without the reversibility assumption are used. These models are also applied to examine the adequacy of the model of Hasegawa et al. (J. Mol. Evol. 1985;22:160–174) (HKY85). Two data sets are analyzed. For the -globin pseudogenes of six primate species, the REV model fits the data much better than HKY85, while, for a segment of mtDNA sequences from nine primates, REV cannot provide a significantly better fit than HKY85 when rate variation over sites is taken into account in the models. It is concluded that the use of the REV model in phylogenetic analysis can be recommended, especially for large data sets or for sequences with extreme substitution patterns, while HKY85 may be expected to provide a good approximation. The use of the unrestricted model does not appear to be worthwhile.