Effect of fibroblast growth factors 1, 2, 4, 5, 6, 7, 8, 9, and 10 on avian chondrocyte proliferation.

It has been demonstrated that fibroblast growth factor receptors are key regulators of endochondral bone growth. However, it has not been determined what fibroblast growth factor ligand(s) (FGFs) are important in this process. This study sought to determine whether FGFs 1, 2, 4, 5, 6, 7, 8, 9, and 10 were capable of stimulating avian chondrocyte proliferation in vitro. We have found that FGFs 2, 4, and 9 strongly stimulate avian chondrocyte proliferation while FGFs 6 and 8 stimulate proliferation to a lesser extent. RT-PCR indicates that FGF-2 and FGF-4 are expressed in the postnatal avian epiphyseal growth plate (EGP) while FGF-8 and FGF-9 are not. Thus, FGF-2 and FGF-4 stimulate chondrocyte proliferation and are both present in the EGP. This suggests that FGF-2 and FGF-4 may be important ligands, in vivo, for the regulation of endochondral bone growth. These observations coupled with our observation that multiple avian FGF receptors (Cek1, Cek2, Cek3, and FREK) are expressed in proliferative chondrocytes highlights the complexity of FGF signaling pathways in postnatal endochondral bone growth.     

Comparative floral structure and systematics in Oxalidales (Oxalidaceae, Connaraceae, Brunelliaceae, Cephalotaceae, Cunoniaceae, Elaeocarpaceae, Tremandraceae)

Floral morphology, anatomy and histology were studied in representatives of all families of current Oxalidales, which were recently constituted as a result of molecular systematic studies by other authors, and are composed of families of different positions in traditional classifications (Oxalidaceae, Connaraceae, Brunelliaceae, Cephalotaceae, Cunoniaceae, Elaeocarpaceae, Tremandraceae). Two of the three pairs of sister (or nested) families that come out in molecular analyses are highly supported by floral structure: Oxalidaceae/Connaraceae and Elaeocarpaceae/Tremandraceae, whereas Cephalotaceae/Cunoniaceae are not especially similar at the level of Oxalidales. Oxalidaceae and Connaraceae share petals that are postgenitally united into a basal tube (although they are imbricate in both) but free at the insertion zone, stamens that are congenitally united at the base, uniseriate glandular hairs on the stamen filaments, and ovules that are hemianatropous to almost orthotropous. The sharing of a special type of sieve-tube plastids and of trimorphic heterostyly, studied by other authors, should also be mentioned. With Brunelliaceae, the two families share an androgynophore and nectaries at the base of the stamens in alternisepalous sectors. Elaeocarpaceae and Tremandraceae share buzz-pollinated flowers and a syndrome of features functionally connected with it. In addition, petals are larger than sepals in advanced bud, they are valvate, involute and enwrap part of the adjacent stamens, they have three vascular traces. Lignified hairs are common on the anthers and are found in the ovary locules and on the ovules (not lignified) of representatives of both families. Ovules have a chalazal appendage, and the inner integument is much thicker than the outer.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 321–381.     

Robustness, evolvability, and neutrality

Biological systems, from macromolecules to whole organisms, are robust if they continue to function, survive, or reproduce when faced with mutations, environmental change, and internal noise. I focus here on biological systems that are robust to mutations and ask whether such systems are more or less evolvable, in the sense that they can acquire novel properties. The more robust a system is, the more mutations in it are neutral, that is, without phenotypic effect. I argue here that such neutral change--and thus robustness--can be a key to future evolutionary innovation, if one accepts that neutrality is not an essential feature of a mutation. That is, a once neutral mutation may cause phenotypic effects in a changed environment or genetic background. I argue that most, if not all, neutral mutations are of this sort, and that the essentialist notion of neutrality should be abandoned. This perspective reconciles two opposing views on the forces dominating organismal evolution, natural selection and random drift: neutral mutations occur and are especially abundant in robust systems, but they do not remain neutral indefinitely, and eventually become visible to natural selection, where some of them lead to evolutionary innovations.     

Scaling of differentiation in networks: nervous systems,organisms, ant colonies,ecosystems, businesses,universities, cities,electronic circuits,and Legos

Nodes in networks are often of different types, and in this sense networks are differentiated. Here we examine the relationship between network differentiation and network size in networks under economic or natural selective pressure, such as electronic circuits (networks of electronic components), Legos (networks of Lego pieces), businesses (networks of employees), universities (networks of faculty), organisms (networks of cells), ant colonies (networks of ants), and nervous systems (networks of neurons). For each of these we find that (i) differentiation increases with network size, and (ii) the relationship is consistent with a power law. These results are explained by a hypothesis that, because nodes are costly to build and maintain in such "selected networks", network size is optimized, and from this the power-law relationship may be derived. The scaling exponent depends on the particular kind of network, and is determined by the degree to which nodes are used in a combinatorial fashion to carry out network-level functions. We find that networks under natural selection (organisms, ant colonies, and nervous systems) have much higher combinatorial abilities than the networks for which human ingenuity is involved (electronic circuits, Legos, businesses, and universities). A distinct but related optimization hypothesis may be used to explain scaling of differentiation in competitive networks (networks where the nodes themselves, rather than the entire network, are under selective pressure) such as ecosystems (networks of organisms).     

Information,Representation, Biology

Biosemiotics contains at its core fundamental issues of naturalism: are normative properties, such as meaning, referent, and others, part of the natural world, or are they part of a second, intentional and normative, metaphysical realm — one that might be analogically applied to natural phenomena, such as within biological cells — but a realm that nevertheless remains metaphysically distinct? Such issues are manifestations of a fundamental metaphysical split between a “natural” realm and a realm of normativity and intentionality. This problematic metaphysical split derives from conceptual problems originating with the Pre-Socratics; transcending that split requires correcting those problems. In particular, transcending that split requires a model of metaphysical emergence, and, in particular, normative emergence. This paper will limn that argument regarding metaphysical emergence, but focus most strongly on an overview of a model of normative, representational emergence that overcomes that metaphysical diremption.     

Lightness, illumination, and gradients

The illumination interpretation approach claims that lightness illusions can be explained as misapplications of lightness constancy mechanisms, processes which usually enable veridical extraction of surface reflectance from luminance distributions by discounting illumination. In particular, luminance gradients are thought to provide cues about the interactions of light and surfaces. Several examples of strong lightness illusions are discussed for which explanations based on illumination interpretation can be proposed. In criticisms of this approach, a variety of demonstrations of similarly structured control displays are presented, which involve equivalent lightness effects that cannot readily be accounted for by illumination interpretation mechanisms. Furthermore, a number of known and novel displays are presented that demonstrate effects of gradients on the qualitative appearance of uniform regions. Finally, some simple simulations of neural effects of luminance distributions are discussed.     

Iron, infection, and neoplasia

In nearly all forms of life, the number and diversity of enzymes that contain iron or that depend on the presence of this metal for activity are impressive. Not surprisingly, chemical mechanisms have been evolved by many organisms that permit them to solubilize and acquire iron while at the same time depriving their competitors or their pathogens of this element. Proteins such as transferrin and lactoferrin that are employed by vertebrate hosts for iron transport and acquisition can, to some extent, withhold the metal from the siderophores of invading bacteria and fungi. Attempts also are made by animal hosts to withhold iron from protozoa and neoplastic cells. Unfortunately, pathogenic microorganisms have developed a variety of counter measures that are especially dangerous in hosts stressed by iron overload in specific fluids, tissues, or cells. In recent years, however, a number of possible methods and agents for strengthening iron-withholding defense have become apparent. Nearly 3,000 papers on various aspects of iron withholding are contained in the 18-year Medline Database and numerous reviews have been published since 1966. The present paper will focus on developments that have been reported within the past 2 1/2 years.     

Arginyltransferase, its specificity, putative substrates, bidirectional promoter, and splicing-derived isoforms

Substrates of the N-end rule pathway include proteins with destabilizing N-terminal residues. Three of them, Asp, Glu, and (oxidized) Cys, function through their conjugation to Arg, one of destabilizing N-terminal residues that are recognized directly by the pathway's ubiquitin ligases. The conjugation of Arg is mediated by arginyltransferase, encoded by ATE1. Through its regulated degradation of specific proteins, the arginylation branch of the N-end rule pathway mediates, in particular, the cardiovascular development, the fidelity of chromosome segregation, and the control of signaling by nitric oxide. We show that mouse ATE1 specifies at least six mRNA isoforms, which are produced through alternative splicing, encode enzymatically active arginyltransferases, and are expressed at varying levels in mouse tissues. We also show that the ATE1 promoter is bidirectional, mediating the expression of both ATE1 and an oppositely oriented, previously uncharacterized gene. In addition, we identified GRP78 (glucose-regulated protein 78) and protein-disulfide isomerase as putative physiological substrates of arginyltransferase. Purified isoforms of arginyltransferase that contain the alternative first exons differentially arginylate these proteins in extract from ATE1(-/-) embryos, suggesting that specific isoforms may have distinct functions. Although the N-end rule pathway is apparently confined to the cytosol and the nucleus, and although GRP78 and protein-disulfide isomerase are located largely in the endoplasmic reticulum, recent evidence suggests that these proteins are also present in the cytosol and other compartments in vivo, where they may become N-end rule substrates.     

Modularity, noise, and natural selection

Most biological systems are formed by component parts that are to some degree interrelated. Groups of parts that are more associated among themselves and are relatively autonomous from others are called modules. One of the consequences of modularity is that biological systems usually present an unequal distribution of the genetic variation among traits. Estimating the covariance matrix that describes these systems is a difficult problem due to a number of factors such as poor sample sizes and measurement errors. We show that this problem will be exacerbated whenever matrix inversion is required, as in directional selection reconstruction analysis. We explore the consequences of varying degrees of modularity and signal-to-noise ratio on selection reconstruction. We then present and test the efficiency of available methods for controlling noise in matrix estimates. In our simulations, controlling matrices for noise vastly improves the reconstruction of selection gradients. We also perform an analysis of selection gradients reconstruction over a New World Monkeys skull database to illustrate the impact of noise on such analyses. Noise-controlled estimates render far more plausible interpretations that are in full agreement with previous results.     

Molecules, Morphology, Fossils, and the Relationship of Angiosperms and Gnetales

Morphological analyses of seed plant phylogeny agree that Gnetales are the closest living relatives of angiosperms, but some studies indicate that both groups are monophyletic, while others indicate that angiosperms are nested within Gnetales. Molecular analyses of several genes agree that both groups are monophyletic, but differ on whether they are related. Conflicts among morphological trees depend on the interpretation of certain characters; when these are analyzed critically, both groups are found to be monophyletic. Conflicts among molecular trees may reflect the rapid Paleozoic radiation of seed plant lines, aggravated by the long branches leading to extant taxa. Trees in which angiosperms are not related to Gnetales conflict more with the stratigraphic record. Even if molecular data resolve the relationships among living seed plant groups, understanding of the origin of angiosperm organs will require integration of fossil taxa, necessarily using morphology.     

Count data, detection probabilities, and the demography, dynamics, distribution, and decline of amphibians

The evidence for amphibian population declines is based on count data that were not adjusted for detection probabilities. Such data are not reliable even when collected using standard methods. The formula C = Np (where C is a count, N the true parameter value, and p is a detection probability) relates count data to demography, population size, or distributions. With unadjusted count data, one assumes a linear relationship between C and N and that p is constant. These assumptions are unlikely to be met in studies of amphibian populations. Amphibian population data should be based on methods that account for detection probabilities.     

New Coleoptera records from New Brunswick, Canada: Anthribidae, Brentidae, Dryophthoridae, Brachyceridae, and Curculionidae, with additions to the fauna of Quebec, Nova Scotia and Prince Edward Island

We report 63 species of Curculionoidea that are new to New Brunswick (three species of Anthribidae, four species of Brentidae, three species of Dryophthoridae, three species of Brachyceridae, 50 species of Curculionidae). Among these are 27 species (two Anthribidae, two Brenthidae, one Brachyceridae, 22 Curculionidae) that are also newly recorded for the Maritime provinces, and one species, Plesiobaris disjuncta Casey (Curculionidae) that is newly recorded for Canada from New Brunswick and Quebec. Bagous planatus LeConte is reinstated to the faunal list of New Brunswick. Two species of Curculionidae are newly recorded from Nova Scotia and the Maritime provinces, and two others are reported for the first time for Prince Edward Island.     

Landscape, flux, correlation, resonance, coherence, stability, and key network wirings of stochastic circadian oscillation

Circadian rhythms with a period of ∼24 h, are natural timing machines. They are broadly distributed in living organisms, such as Neurospora, Drosophila, and mammals. The underlying natures of the rhythmic behavior have been explored by experimental and theoretical approaches. However, the global and physical natures of the oscillation under fluctuations are still not very clear. We developed a landscape and flux framework to explore the global stability and robustness of a circadian oscillation system. The potential landscape of the network is uncovered and has a global Mexican-hat shape. The height of the Mexican-hat provides a quantitative measure to evaluate the robustness and coherence of the oscillation. We found that in nonequilibrium dynamic systems, not only the potential landscape but also the probability flux are important to the dynamics of the system under intrinsic noise. Landscape attracts the systems down to the oscillation ring while flux drives the coherent oscillation on the ring. We also investigated the phase coherence and the entropy production rate of the system at different fluctuations and found that dissipations are less and the coherence is higher for larger number of molecules. We also found that the power spectrum of autocorrelation functions show resonance peak at the frequency of coherent oscillations. The peak is less prominent for smaller number of molecules and less barrier height and therefore can be used as another measure of stability of oscillations. As a consequence of nonzero probability flux, we show that the three-point correlations from the time traces show irreversibility, providing a possible way to explore the flux from the observations. Furthermore, we explored the escape time from the oscillation ring to outside at different molecular number. We found that when barrier height is higher, escape time is longer and phase coherence of oscillation is higher. Finally, we performed the global sensitivity analysis of the underlying parameters to find the key network wirings responsible for the stability of the oscillation system.     

Seed coats: Structure,development, composition,and biotechnology

Summary Although seeds have been the subject of extensive studies for many years, their seed coats are just beginning to be examined from the perspective of molecular genetics and control of development. The seed coat, plays a vital role in the life cycle of plants by controlling the development of the embryo and determining seed dormancy and germination. Within the seed coat are a number of unique tissues that undergo differentiation to serve specific functions in the seed. A large number of genes are known to be specifically expressed within the seed coat tissues; however, very few of them are understood functionally. The seed coat synthesizes a wide range of novel compounds that may serve the plant in diverse ways, including defense and control of development. Many of the compounds are sources of industrial products and are components of food and feeds. The use of seed coat biotechnology to enhance seed quality and yield, or to generate novel components has not been exploited, largely because of lack of knowledge of the genetic systems that govern seed coat development and composition. In this review, we will examine the recent advances in seed coat, biology from the perspective of structure, composition and molecular genetics. We will consider the diverse avenues that are possible for seed coat biotechnology in the future. This review will focus principally on the seed coats of the Brassicaceae and Fabaceae as they allow us to merge the areas of molecular biology, physiology and structure to gain a perspective on the possibilities for seed coat modifications in the future. The authors have contributed equally and are considered first authors.     

The parasitic chytrid, Zygorhizidium, facilitates the growth of the cladoceran zooplankter, Daphnia, in cultures of the inedible alga, Asterionella

In food-web studies, parasites are often ignored owing to their insignificant biomass. We provide evidence that parasites may affect trophic transfer in aquatic food webs. Many phytoplankton species are susceptible to parasitic fungi (chytrids). Chytrid infections of diatoms in lakes may reach epidemic proportions during diatom spring blooms, so that numerous free-swimming fungal zoospores (2-3 microm in diameter) are produced. Analysis shows that these zoospores are rich in polyunsaturated fatty acids and sterols (particularly cholesterol), which indicates that they provide excellent food for zooplankters such as Daphnia. In life-table experiments using the large diatom Asterionella formosa as food, Daphnia growth increased significantly in treatments where a parasite was present. By grazing on the zoospores, Daphnia acquired important supplementary nutrients and were able to grow. When large inedible algae are infected by parasites, nutrients within the algal cells are consumed by these chytrids, some of which, in turn, are grazed by Daphnia. Thus, chytrids transfer energy and nutrients from their hosts to zooplankton. This study suggests that parasitic fungi alter trophic relationships in freshwater ecosystems and may be the important components in shaping the community and the food-web dynamics of lakes.     

Sperm,Clinics, and Parenthood

In this article I examine a recent approach to regulating assisted reproduction, whereby use of some kind of medical intervention ‘triggers’ laws governing legal parenthood that are more favourable to intending parents and sperm providers. I argue that although perhaps an improvement on the previous legal framework, these laws are problematic for three important reasons. First, they are prone to violating parental rights and unjustly imposing substantial burdens on individuals. Second, they are discriminatory. Third, even if we take a pragmatic approach to the question of parenthood in these cases, these laws fail to properly consider the welfare interests of children. Finally, I conclude by showing that my argument does not entail adopting a laissez‐fair attitude to conception using third‐party sperm.     

Bioethics, vulnerability, and protection

What makes individuals, groups, or even entire countries vulnerable? And why is vulnerability a concern in bioethics? A simple answer to both questions is that vulnerable individuals and groups are subject to exploitation, and exploitation is morally wrong. This analysis is limited to two areas. First is the context of multinational research, in which vulnerable people can be exploited even if they are not harmed, and harmed even if they are not exploited. The type of multinational research likely to raise the most ethical concerns is that in which the investigators or sponsors are from a powerful industrialised country or a giant pharmaceutical company and the research is conducted in a developing country. Second is the situation of women, who are made vulnerable in cultural settings or in entire countries in which they are oppressed and powerless. In the face of cultural values and practices, or governmental policies, these women suffer serious consequences for their health and even lives. Examples are provided, and it is suggested that in some cases vulnerable individuals can be harmed but not exploited. On the positive side, recent developments reveal a new awareness of exploitation and efforts to enhance the ability of developing countries to protect themselves and their citizens from exploitation at the hands of powerful sponsors of research. In addition, human rights principles are increasingly being used to monitor the actions (or inaction) of governments regarding women's reproductive rights and vulnerability with respect to HIV/AIDS, and to take remedial actions.     

Values,Errors, and Precautions

In the environmental health literature, errors in interpreting studies or data are not infrequent. Many are of the Type II variety. Common solecisms of this type are: treating the criterion of p < 0.05 as a sacrament; demanding complete confounder control; arguing for the existence of phantom confounders; arguing that the effect size is trivial; building nonveridical models; arguing for no effect from inadequate sample size; demanding causal proof; arguing that causality is reversed; conducting a ballot of published studies. These are examined in this paper.     

Conjugates of abscisic acid, brassinosteroids, ethylene, gibberellins, and jasmonates

Phytohormones, including auxins, abscisic acid, brassinosteroids, cytokinins, ethylene, gibberellins, and jasmonates, are involved in all aspects of plant growth, and developmental processes as well as environmental responses. However, our understanding of hormonal homeostasis is far from complete. Phytohormone conjugation is considered as a part of the mechanism to control cellular levels of these compounds. Active phytohormones are changed into multiple forms by acylation, esterification or glycosylation, for example. It seems that conjugated compounds could serve as pool of inactive phytohormones that can be converted to active forms by de-conjugation reactions. Some conjugates are thought to be temporary storage forms, from which free active hormones can be released after hydrolysis. It is also believed that conjugation serves functions, such as irreversible inactivation, transport, compartmentalization, and protection against degradation. The nature of abscisic acid, brassinosteroid, ethylene, gibberellin, and jasmonate conjugates is discussed.     

Fossil sedges, macroplants, and roots from Olduvai Gorge, Tanzania

A variety of macroplants has been recorded and collected from the eastern paleolake margin of Olduvai Gorge, Tanzania, from Upper Bed I and Lower Bed II, dated at ∼1.7-1.85 Ma. The plant groups represented are sedges, grasses, and woody and herbaceous dicotyledons. Most of these plants are fragmented, but the roots are in situ. The modes and quality of preservation, however, are very variable. Silicification is the dominant type of preservation; it ranges from high quality faithful replacement of cells resulting in silicified wood and sedge culms that are identifiable on the basis of their internal anatomy, to poor quality biotubes lacking internal anatomy or external features that prevent assignment to a specific plant or invertebrate origin. In between this range are silicified roots and grass culms identified by their external anatomy, and leaf and stem impressions. Interpretation of the paleoecology is limited by the quality of preservation. The in situ root horizons are useful for recognizing paleo-surfaces. The best quality preservation where internal anatomy is preserved occurs at HWK E and MCK, localities that are in the middle of the fault compartments so the vegetation can be reconstructed for these sites. Some sedge culms are described, illustrated, and identified as possible species of Cyperus, Fuirena, and Schoenoplectus.