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PubMed1988

Permanency of response to selection for quantitative characters in finite populations.

To study the permanency of response to selection for a quantitative character in finite populations and the nature of the genetic effects that contribute to this response, we have used the covariance between ancestors and descendents within populations. Effects and variances are defined for an initial equilibrium random mating monoecious population that gives rise to replicate finite populations. After a prescribed history of restricted population size, the replicate populations are expanded, and the covariance between ancestors and descendents is quantified in terms of descent measures and genetic components in the initial population as a means of determining the additive variance within populations. Several dominance components including joint dominance effects of loci contribute to the additive variance, some of which can be negative. There is always a positive contribution of additive by additive variance to the additive variance within populations, which can be large. With the new definitions of components of genetic variance within populations, selection response is formulated in the same manner as for the initial random mating population, but the components have been modified considerably by the restricted population size.

Biological Evolution↗
PubMed1993

Early Cretaceous mammal from North America and the evolution of marsupial dental characters.

A mammal from the Early Cretaceous of the western United States, represented by a lower jaw exceptional in its completeness, presents unambiguous evidence of postcanine dental formula in an Early Cretaceous marsupial-like mammal, and prompts a reconsideration of the early evolution of marsupial dental characters. A marsupial postcanine dental formula (three premolars and four molars) and several marsupial-like features of the lower molars are present in the new taxon, but a hallmark specialization of marsupials (twinning of the hypoconulid and entoconid on lower molars) is lacking. This, coupled with recent evidence from the Late Cretaceous of the western United States, suggests that the distinctive marsupial dental formula evolved prior to the most characteristic specialization of lower molars and that apomorphies presumed to be diagnostic of the upper molars (such as auxiliary stylar cusps) were relatively more recent developments in marsupial history. Dental evidence supports the monophyly of higher (tribosphenic) mammals and suggests that the predominantly Old World Deltatheroida, recently proposed as a sister taxon to marsupials, represents a primitive and unrelated group of higher mammals; by this interpretation, early marsupials and their presumed close relatives are restricted to North America. This, together with the hypothesized relationships of South American/Australian marsupials (in the context of the North American Cretaceous radiation) and evidence from the fossil record of South America, in turn supports a North American origin for the group.

Animals↗
PubMed2000

Changes in mitochondrial genetic codes as phylogenetic characters: two examples from the flatworms.

Shared molecular genetic characteristics other than DNA and protein sequences can provide excellent sources of phylogenetic information, particularly if they are complex and rare and are consequently unlikely to have arisen by chance convergence. We have used two such characters, arising from changes in mitochondrial genetic code, to define a clade within the Platyhelminthes (flatworms), the Rhabditophora. We have sampled 10 distinct classes within the Rhabditophora and find that all have the codon AAA coding for the amino acid Asn rather than the usual Lys and AUA for Ile rather than the usual Met. We find no evidence to support claims that the codon UAA codes for Tyr in the Platyhelminthes rather than the standard stop codon. The Rhabditophora are a very diverse group comprising the majority of the free-living turbellarian taxa and the parasitic Neodermata. In contrast, three other classes of turbellarian flatworm, the Acoela, Nemertodermatida, and Catenulida, have the standard invertebrate assignments for these codons and so are convincingly excluded from the rhabditophoran clade. We have developed a rapid computerized method for analyzing genetic codes and demonstrate the wide phylogenetic distribution of the standard invertebrate code as well as confirming already known metazoan deviations from it (ascidian, vertebrate, echinoderm/hemichordate).

Amino Acid Sequence↗
PubMed1995

X-ray absorption near edge studies of cytochrome P-450-CAM, chloroperoxidase, and myoglobin. Direct evidence for the electron releasing character of a cysteine thiolate proximal ligand.

The low spin ferric and low and high spin ferrous forms of myoglobin, bacterial cytochrome P-450-CAM, and chloroperoxidase have been examined by Fe-K x-ray absorption edge spectroscopy. The positions of the absorption edge and the shapes of preedge and edge regions of imidazole adducts of ferric P-450-CAM and chloroperoxidase are essentially the same when compared with thiolate-ligated ferric myoglobin. As these three protein derivatives all have six-coordinate, low spin, ferric hemes with axial imidazole and thiolate ligands, the superposition of x-ray absorption edge spectral properties demonstrates that the protein environment does not effect the spectra, provided one compares heme iron centers with identical coordination numbers, spin and oxidation states, and ligand sets. In contrast, a 0.96 eV difference is observed in the energy of the absorption edge for imidazole- and thiolate-ligated ferric myoglobin with the latter shifted to lower energy as observed for ferrous myoglobin states. Similarly, in the low spin ferric-imidazole and ferrous-CO states, the energies of the absorption edge for chloroperoxidase and P-450-CAM are shifted in the direction of the ferrous state (to lower energy) when compared with those for analogous myoglobin derivatives. In the deoxyferrous high spin state, comparison of the edge spectra of chloroperoxidase with analogous data for cytochrome P-450-CAM suggests that the electron density at the iron is similar for these two protein states. The shifts observed in the energies of the x-ray absorption edge for the thiolate-ligated states of these proteins relative to derivatives lacking a thiolate ligand provide a direct measure of the electron releasing character of a thiolate axial ligand. These results therefore support the suggested role of the cysteinate proximal ligand of P-450 as a strong internal electron donor to promote O-O bond cleavage in the putative ferric-peroxide intermediate to generate the proposed ferryl-oxo "active oxygen" state of the reaction cycle.

Camphor 5-Monooxygenase↗
PubMed1994

The armature in the genital atrium as a new taxonomic character distinguishing females of Phlebotomus papatasi and P. duboscqi (Diptera: Psychodidae).

Descriptions are given of armatures in the genital atria of females of the two morphologically similar sandfly species, Phlebotomus papatasi and P. duboscqi. The species are distinguishable by the size and shape of the armature, the grouping of the spines in the armature and the length and shape of the spines. These characters have been shown to separate females of other closely related species of phlebotomine sandflies.

Animals↗
PubMed1999

Aliveness in the work of the group: a subjective guide to creative character change.

The subjective response of aliveness in the work of the group may be a valuable signal on the journey toward creative character change in group therapy. In order to promote change in others, the group therapist must engage deeply and use internal responses as guides during interactions with group members as well as in relation to the group as a whole. Subjective awareness of increased aliveness that is linked with a sense of the work of the group may guide both therapist and group participants in the midst of inevitable anxieties and passions aroused during this quest for new vitality and freedom in relationships in the group. Winnicott's concept of potential space as well as group-relations theory about the primary task provide a conceptual foundation for this approach not only on the level of the individual member within the group but also on the level of the group as a whole.

Adult↗
PubMed2000

Hope and the inclination to be troublesome: Winnicott and the treatment of character disorder in group therapy.

While some group participants communicate about the problems in their lives by patterns of troublesome behavior, others may accommodate superficially to the needs of the group but feel an inner sense of futility and quiet desperation. Through use of Winnicott's paradoxical emphasis on the hope that is expressed within the "antisocial inclination" in all character disorders, the group may negotiate an adequate alliance for the discovery, containment, and exploration of the inclination to be troublesome in group in all participants. It may also provide supportive holding during the experience of affects that formerly were overwhelming, such as shame and unresolved guilty anxiety. This approach is applicable to the group as a whole as well as to individuals.

Adult↗
PubMedDate not supplied

Effect of the lipophilic/hydrophilic character of cationic triarylmethane dyes on their selective phototoxicity toward tumor cells.

The observation that enhanced mitochondrial transmembrane potential is a prevalent tumor cell phenotype has provided the conceptual basis for the development of mitochondrial targeting as a novel therapeutic strategy for both chemo- and photochemotherapy of neoplastic diseases. Because the plasma transmembrane potential is negative on the inner side of the cell and the mitochondrial transmembrane potential is negative on the inner side of this organelle, extensively conjugated cationic molecules (dyes) displaying appropriate structural features are driven electrophoretically through these membranes and tend to accumulate inside energized mitochondria. As a result of the higher mitochondrial transmembrane potential typical of tumor cells, a number of cationic dyes preferentially accrue and are retained for longer periods in the mitochondria of these cells compared to normal cells. This differential in both drug loading and retention brings about the opportunity to attack and destroy tumor cells with a high degree of selectivity. Only a small subset of the cationic dyes known to accumulate in energized mitochondria mediate the destruction of tumor cells with a high degree of selectivity, and the lack of a reliable model to describe the structural determinants of this tumor specificity has prevented mitochondrial targeting from becoming a more reliable therapeutic strategy. We describe here a systematic study of how the molecular structure of closely related cationic triarylmethanes affects the selectivity with which these dyes mediate the photochemical destruction of tumor cells. Based on our observations of how the lipophilic/hydrophilic character of these dyes affects tumor selectivity, we propose a simple model to assist in the design of new drugs tailored specifically for imaging and selective destruction of neoplastic tissue via mitochondrial targeting.

Animals↗
PubMed2002

The inorganic and organic characters for predicting bioconcentration on wide variety of chemicals in fish.

The applicability of Fujita's inorganic (i) and organic (o) characters as descriptors for predicting bioconcentration factor (BCF) in fish was investigated with a wide variety of organic chemicals. Among 612 BCF data recently released by National Institute of Technology and Evaluation (NITE), the values for the chemicals with a molecular weight of less than 600 and the 1-octanol/water partition coefficient (log P) of less than six were extracted and analyzed. By applying theoretically derived model equation, a good relationship between these BCF and each Fujita's sigma i: sigma o was established. Statistical analyses and model validations revealed that the estimations of our approach were very excellent. More precise predictions were attained than those by using other published models, especially, for chemicals such as disperse dye having hetero atoms.

Animals↗
PubMed2004

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data.

We describe a general likelihood-based 'mixture model' for inferring phylogenetic trees from gene-sequence or other character-state data. The model accommodates cases in which different sites in the alignment evolve in qualitatively distinct ways, but does not require prior knowledge of these patterns or partitioning of the data. We call this qualitative variability in the pattern of evolution across sites "pattern-heterogeneity" to distinguish it from both a homogenous process of evolution and from one characterized principally by differences in rates of evolution. We present studies to show that the model correctly retrieves the signals of pattern-heterogeneity from simulated gene-sequence data, and we apply the method to protein-coding genes and to a ribosomal 12S data set. The mixture model outperforms conventional partitioning in both these data sets. We implement the mixture model such that it can simultaneously detect rate- and pattern-heterogeneity. The model simplifies to a homogeneous model or a rate-variability model as special cases, and therefore always performs at least as well as these two approaches, and often considerably improves upon them. We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program.

Base Sequence↗
PubMed2004

Bayesian estimation of ancestral character states on phylogenies.

Biologists frequently attempt to infer the character states at ancestral nodes of a phylogeny from the distribution of traits observed in contemporary organisms. Because phylogenies are normally inferences from data, it is desirable to account for the uncertainty in estimates of the tree and its branch lengths when making inferences about ancestral states or other comparative parameters. Here we present a general Bayesian approach for testing comparative hypotheses across statistically justified samples of phylogenies, focusing on the specific issue of reconstructing ancestral states. The method uses Markov chain Monte Carlo techniques for sampling phylogenetic trees and for investigating the parameters of a statistical model of trait evolution. We describe how to combine information about the uncertainty of the phylogeny with uncertainty in the estimate of the ancestral state. Our approach does not constrain the sample of trees only to those that contain the ancestral node or nodes of interest, and we show how to reconstruct ancestral states of uncertain nodes using a most-recent-common-ancestor approach. We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods (BayesMultiState) is available from the authors.

Animals↗
PubMed2006

Medusozoan phylogeny and character evolution clarified by new large and small subunit rDNA data and an assessment of the utility of phylogenetic mixture models.

A newly compiled data set of nearly complete sequences of the large subunit of the nuclear ribosome (LSU or 28S) sampled from 31 diverse medusozoans greatly clarifies the phylogenetic history of Cnidaria. These data have substantial power to discern among many of the competing hypotheses of relationship derived from prior work. Moreover, LSU data provide strong support at key nodes that were equivocal based on other molecular markers. Combining LSU sequences with those of the small subunit of the nuclear ribosome (SSU or 18S), we present a detailed working hypothesis of medusozoan relationships and discuss character evolution within this diverse clade. Stauromedusae, comprising the benthic, so-called stalked jellyfish, appears to be the sister group of all other medusozoans, implying that the free-swimming medusa stage, the motor nerve net, and statocysts of ecto-endodermal origin are features derived within Medusozoa. Cubozoans, which have had uncertain phylogenetic affinities since the elucidation of their life cycles, form a clade-named Acraspeda-with the scyphozoan groups Coronatae, Rhizostomeae, and Semaeostomeae. The polyps of both cubozoans and hydrozoans appear to be secondarily simplified. Hydrozoa is comprised by two well-supported clades, Trachylina and Hydroidolina. The position of Limnomedusae within Trachylina indicates that the ancestral hydrozoan had a biphasic life cycle and that the medusa was formed via an entocodon. Recently hypothesized homologies between the entocodon and bilaterian mesoderm are therefore suspect. Laingiomedusae, which has often been viewed as a close ally of the trachyline group Narcomedusae, is instead shown to be unambiguously a member of Hydroidolina. The important model organisms of the Hydra species complex are part of a clade, Aplanulata, with other hydrozoans possessing direct development not involving a ciliated planula stage. Finally, applying phylogenetic mixture models to our data proved to be of little additional value over a more traditional phylogenetic approach involving explicit hypothesis testing and bootstrap analyses under multiple optimality criteria. [18S; 28S; Cubozoa; Hydrozoa; medusa; molecular systematics; polyp; Scyphozoa; Staurozoa.].

Animals↗
PubMed1998

Reassessment of homology of morphological characters in tetractinellid sponges based on molecular data.

In sponges, as in other taxa with simple organization, the evaluation and use of morphological characters is difficult. Phylogenetic analysis of the first 850 nucleotides from the 5' end of the 28S rRNA gene is used here to assess the homology of spicules used in the classification of the subclass Tetractinellida. A single well-supported MP tree was obtained. The monophyly of the nine Tetractinellida species studied confirms the tetraxon megasclere as a morphological synapomorphy for the Tetractinellida. Two species are reallocated, Penares helleri as a Geodiidae, now thought to have lost sterraster microscleres, and Stryphnus mucronatus to the Streptosclerophorida. SEM micrographs of Stryphnus microscleres show that the morphology of the sanidasters is compatible with the hypothesis that they are homologous with streptoscleres and confirm this reallocation. Two other synapomorphies are confirmed within the tetractinellid clade, the simultaneous presence of tetraxon megasclere and aster-type microsclere (Astrophorida) and the loss of the streptosclere and persistence of the euaster s.s. microscleres (Euastrophorida) evidenced by the reallocation of Stryphnus mucronatus. The streptosclere microscleres cannot be evaluated in terms of homology because Streptosclerophorida may be paraphyletic (although these nodes are not supported by reliable bootstrap proportions) contrary to the currently accepted classification.

Animals↗
PubMed1998

Data sets, partitions, and characters: philosophies and procedures for analyzing multiple data sets.

We compared four approaches for analyzing three data sets derived from staphylinoid beetles, a superfamily whose known species diversity is roughly comparable to that of vertebrates. One data set is derived from adult morphology and the two molecular data sets are from 12S ribosomal RNA and cytochrome b mitochondrial DNA. We found that taxonomic congruence following conditional data combination, herein called compatible evidence (CE), resolved more nodes compatible with an initial conservative hypothesis than did total evidence (TE), conditional data combination (CDC), or taxonomic congruence (TC). CE sets a base of nodes obtained by CDC analysis and then investigates what further agreement may arise in a universe where these nodes are accepted as given. We suggest that CE75-75 may be appropriate for future studies that aim to both generate a well-corroborated tree and investigate conflicts between data sets, partitions, and characters. CE75-75 is a 75% bootstrap consensus CDC tree followed by combinable-component consensus of a 75% bootstrap consensus of each homogeneous set of partitions having hierarchical structure.

Animals↗
PubMed1965

Studies on a cytoplasmic character in Neurospora crassa.

Two morphologically distinctive slow growing strains of Neurospora crassa have been isolated and studied. These, abn-1 and abn-2, differ from wild type in that their growth rates are greatly reduced and often irregular, aerial hyphae are absent, conidia are extremely rare, and no protoperithecia are formed. Growth was not improved by addition of any nutrients tested, oxygen consumption was similar to that of wild type, and cytochrome c appeared abnormally high, and b low or absent. Both abn strains gave rise only to normal progeny in crosses with normal strains. The abn characteristics appear in heterocaryons, and have been transmitted to other genetic strains by means of heterocaryosis followed by plating of conidia. Conidia formed by such heterocaryons typically showed low viability, and gave rise to cultures with great variability in growth rate, morphology, and survival. Even apparently normal derived cultures often later became abnormal or died. It is concluded that the abnormal characteristics are determined primarily by cytoplasmic factors. This conclusion was strengthened by the transmission of the typical characteristics to normal strains by microinjection of cytoplasm from abn cultures, even without demonstrable transfer of nuclei. This constitutes the first time microinjection techniques have been successfully applied to the analysis of a cytoplasmic character in Neurospora.

Culture Media↗
PubMed1965

A cytoplasmic character in Neurospora crassa. The role of nuclei and mitochondria.

Nuclear fractions isolated from mutants of Neurospora produced no effect when microinjected into mutants with complementary biochemical requirements. DNA isolated from the nuclear fractions similarly injected also had no effect. Mitochondrial fractions isolated from an abnormal inositolless strain (abn-1) produced drastic changes in the rate of growth, morphology, reproductive characteristics, and cytochrome spectra of normal inositolless strains when single hyphal compartments were microinjected and isolated, whereas the mitochondrial fractions of the wild type produced no effect. These results provide evidence for the transmission of biochemical and biological characters when mitochondria are transferred to new nucleocytoplasmic environments.

Cell Nucleus↗
PubMed1974

Changes in the ribosome content, principal microsomal protein composition, and secretory character of mammary epithelial rough endoplasmic reticulum during differentiation. Evidence that messenger RNAs specific for milk proteins are incorporated into rough endoplasmic reticulum formed de novo after parturition.

The equilibrium density distribution, protein composition, and secretory character of mouse mammary epithelial rough microsomes have been determined during differentiation. The density range exhibited by the rough microsomes broadens during mammary development; rough microsomes within the 1.25-1.29 g/ml density range appear soon after conception and then within the 1.30-1.34 range after the onset of lactation. The appearance of these denser microsomes represents the progressive increase of the average ribosome content of the rough endoplasmic reticulum (ER) during gestation and lactation. Fractionation of rough microsomal proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis reveals that two proteins, having molecular weights of 57,000 and 76,000, occur to a significant extent only during lactation and are then most prominent in the very dense rough microsomes of the 1.30-1.34 range. Nascent polypeptide chains discharged (by incubation with puromycin) from 17-days lactation rough microsomes in either the 1.21-1.29 or 1.30-1.34 density range are distributed equally between the intra- and extravesicular compartments. Whereas 36% of the chains are discharged intravesicularly from 1-day lactation rough microsomes in the 1.30-1.34 range, only 25% are so discharged from those in the 1.21-1.29 range. The results indicate (a) that there is no correlation between the relative levels in lactation rough microsomes of the two microsomal proteins which become prominent during lactation and the extent of secretory activity and (b) that for a short period after parturition the rough ER elements bearing high surface densities of ribosomes have a greater proportion of ribosomes synthesizing milk proteins than the rough ER elements with moderate ribosome densities.

Animals↗