The role of ‘soaking’ in spiteful toxin production in Pseudomonas aeruginosa

The ubiquitous production of antibacterial toxins, such as bacteriocins, is an ecologically significant class of interbacterial interactions that have primarily evolved through their indirect fitness benefits to the producer. Bacteria release bacteriocins into the environment at a cost to individual cell, but individual bacteriocin-producing cells are unlikely to gain any direct benefit from their own toxin; indeed, cell lysis is required in many species. There is a growing body of research describing the ecological conditions that can favour the evolution of bacteriocin production. However, an important aspect of many bacteriocins has yet to be investigated: the ability of bacteriocin-producing cells to neutralize toxin (‘soaking’) produced by other clonemates. By competing Pseudomonas aeruginosa bacteriocin-producing wild-type and ‘non-soaking’ strains against a bacteriocin-susceptible strain, we find that soaking markedly reduces the fitness of a bacteriocin-producing strain at both high and low frequencies.     

The inductive role of Wnt-β-Catenin signaling in the formation of oral apparatus

Proper patterning and growth of oral structures including teeth, tongue, and palate rely on epithelial–mesenchymal interactions involving coordinated regulation of signal transduction. Understanding molecular mechanisms underpinning oral–facial development will provide novel insights into the etiology of common congenital defects such as cleft palate. In this study, we report that ablating Wnt signaling in the oral epithelium blocks the formation of palatal rugae, which are a set of specialized ectodermal appendages serving as Shh signaling centers during development and niches for sensory cells and possibly neural crest related stem cells in adults. Lack of rugae is also associated with retarded anteroposterior extension of the hard palate and precocious mid-line fusion. These data implicate an obligatory role for canonical Wnt signaling in rugae development. Based on this complex phenotype, we propose that the sequential addition of rugae and its morphogen Shh, is intrinsically coupled to the elongation of the hard palate, and is critical for modulating the growth orientation of palatal shelves. In addition, we observe a unique cleft palate phenotype at the anterior end of the secondary palate, which is likely caused by the severely underdeveloped primary palate in these mutants. Last but not least, we also discover that both Wnt and Shh signalings are essential for tongue development. We provide genetic evidence that disruption of either signaling pathway results in severe microglossia. Altogether, we demonstrate a dynamic role for Wnt-β-Catenin signaling in the development of the oral apparatus.     

The role of Schmidt ‘Antonovka’ in apple scab resistance breeding

??Antonovka?? has long been recognised as a major source of scab (Venturia inaequalis) resistance useful for apple breeding worldwide. Both major gene resistances in the form of the Rvi10 and Rvi17 and quantitative resistance, collectively identified as VA, have been identified in different accessions of ??Antonovka??. Most of the ??Antonovka?? scab resistance used in apple-breeding programmes around the world can be traced back to Schmidt ??Antonovka?? and predominantly its B VIII progenies 33,25 (PI 172623), 34,6 (PI 172633), 33,8 (PI 172612) and 34,5 (PI 172632). Using genetic profile reconstruction, we have identified ??common ??Antonovka?? ?? as the progenitor of the B VIII family, which is consistent with it having been a commercial cultivar in Poland and the single source of scab resistance used by Dr. Martin Schmidt. The major ??Antonovka?? scab resistance genes mapped to date are located either very close to Rvi6, or about 20?C25?cM above it, but their identities need further elucidation. The presence of the 139?bp allele of the CH-Vf1 microsatellite marker known to be associated with Rvi17 (Va1) in most of the ??Antonovka?? germplasm used in breeding suggests that it plays a central role in the resistance. The nature and the genetic relationships of the scab resistance in these accessions as well as a number of apple cultivars derived from ??Antonovka??, such as, ??Freedom??, ??Burgundy?? and ??Angold??, are discussed. The parentage of ??Reglindis?? is unclear, but the cultivar commercialised as ??Reglindis?? was confirmed to be an Rvi6 cultivar.     

The Fate of the Method of ‘Paradigms’ in Paleobiology

An earlier article described the mid-twentieth century origins of the method of “paradigms” in paleobiology, as a way of making testable hypotheses about the functional morphology of extinct organisms. The present article describes the use of “paradigms” through the 1970s and, briefly, to the end of the century. After I had proposed the paradigm method to help interpret the ecological history of brachiopods, my students developed it in relation to that and other invertebrate phyla, notably in Euan Clarkson’s analysis of vision in trilobites. David Raup’s computer-aided “theoretical morphology” was then combined with my functional or adaptive emphasis, in Adolf Seilacher’s tripartite “constructional morphology.” Stephen Jay Gould, who had strongly endorsed the method, later switched to criticizing the “adaptationist program” he claimed it embodied. Although the explicit use of paradigms in paleobiology had declined by the end of the century, the method was tacitly subsumed into functional morphology as “biomechanics.”     

The nature of ‘slow’ and ‘fast’ contractions in the coxal muscles of the cockroach

An investigation was carried out to examine in detail the mechanical responses of the coxal muscles of the cockroach using an isometric recording technique, and at the same time attempts were made to correlate these responses with the electrical events of neuromuscular transmission. It has been possible to show that the different mechanical responses are not due to intrinsic properties of the muscle fibres as suggested by Becht and Dresden, but appear to be related to differences in motor nerve innervation of the different muscles.     

The role of nodal roots in prostrate clonal herbs: ‘phalanx’ versus ‘guerrilla’

The influence of nodal rooting on branching was studied in three evolutionarily and morphologically diverse species of prostrate clonal herbs: Tradescantia fluminensis (a monocotyledonous extreme ‘phalanx’ species), Calystegia silvatica (a dicotyledonous extreme ‘guerrilla’ species) and Trifolium repens (a dicotyledonous intermediate species). In all three, branch development from axillary buds is regulated by a positive signal produced by roots together with inhibitory influences from both pre-existing branches and shoot apical buds (apical dominance). Responses to nodal roots are cumulative and increased root activity leads to more vigorous bud outgrowth. In the absence of nodal roots, a single basal root system is unable to maintain continued extension growth of the shoot. We suggest that as individual nodal roots and stem internodes are both short-lived in these nodally-rooting clonal species, the plants’ investment in them is minimal. Thus, in contrast to perennial species lacking nodal roots, individual root systems in prostrate clonal herbs are small and stems have little secondary thickening and development of long-distance transport tissues. Hence the decline in extension growth of the shoot in the absence of nodal roots could be linked to the weak development of long-distance transport tissues in their relatively thin horizontal stems and to resource sharing between primary stems and lateral branches (as suggested by the greater retardation of primary stem growth in the more profusely branched ‘phalanx’ species (Trifolium and Tradescantia) than in the weakly branched ‘guerrilla’ species, Calystegia). These findings are consistent with the view that the long-term persistence of genotypes of nodally-rooting prostrate species is dependent upon them encountering the moist conditions required to facilitate the continual development of new young nodal root systems.     

The potamoplankton of the Middle Loire and the role of the ’moving littoral‘ in downstream transfer of algae and rotifers

The seasonal succession of the potamoplankton of the Middel Loire was studied fortnightly from June to October 1995, a period of low water flow. The increase in dissolved oxygen, suspended matter, BOD₅ and chlorophyll a, associated with the decrease in nutrients downstream, are typical of eutrophic rivers. Algae were the principal components of the suspended matter flux in the river. Their density increased from the upper site of Dampierre-en-Burly to the lower site of Saint-Laurent des Eaux, with respective maxima of 68 ×10⁶ cells l^-1 and 106 × 10⁶cells l^-1. A large rotifer community developed in association with the algal growth, with densities up to 3700 ind l^-1 at Dampierre-en-Burly and up to 5800 ind l^-1 at Saint-Laurent des Eaux. They had a high Shannon-Weaver diversity, while grazing appeared to control the algae. As the year progressed to the warmer season, the biomass of the β and β α mesosaprobic rotifer species increased parallel with algae. The water theoretically transported potamoplankton at 0.2 ms^-1 during mid-summer, which meant that the biomass of the algae doubled in minimum 17 km and that of the rotifers in 34 km. From these values and the distances between sampling stations, we deduce that inoculation points were located in areas which could be as short as a hundred meters. Not only algae, but also rotifers are capable of restoring an inoculum of organisms from place to place. Summer hydrodynamics, close to localised lentic areas, were responsible for an increase in plankton abundance in the stream. These movements had an ecotone effect at the boundary between standing and running water, creating pulses. The lower regions were progressively enriched by successive inoculates, dilution and seeding inputs, which did not prevent the growth of algae and of parthenogenetic species in the river. Such processes, which occur in years of low flow, are responsible for the large variations in plankton density observed between years. This revised version was published online in August 2006 with corrections to the Cover Date.     

A cyto-biochemical study of the ‘canal’ formation in the yeast cell wall

Summary A distinction between the chemical composition of ultrastructurally modified regions and the rest of the cell wall (canals) of the yeast Schwanniomyces occidentalis was shown by cytochemical staining of cell wall polysaccharides. The formation of canals was induced by cultivation of yeasts on hydrocarbons and was parallelled by the enhancement of -glucosidase, -glucanase and -mannosidase activities which were all capable of degrading cell wall polysaccharides. The presence of cycloheximide prevented canal formation. We assume that these hydrolases modified definite cell wall regions transforming them into canals.     

‘Us’ and ‘Them’: The role of religion in mediating and challenging the ‘model minority’ and other civic boundaries

This article examines how Korean Americans use the cultural resources of religious communities to mediate race, ethnic, and socio-economic boundaries that have consequences for civic life. Specifically, I compare involvement of Korean Americans in second-generation Korean congregations to those in multiethnic churches. I find Korean Americans who participate in second-generation Korean churches use religion to largely reproduce images of Korean Americans as model minorities, and implicitly distance themselves from those whom they perceive as less financially successful. In contrast, Korean Americans in multiethnic congregations use religion to emphasize the commonality Korean Americans have with other minorities. By using a cultural framework that allows for the agency of individuals in identity and group boundary construction, this work more generally shows the potential for new Americans to use the cultural resources of local organizations to change existing ethnic and racial boundaries in the United States.     

The ‘requirement of total evidence’ and its role in phylogenetic systematics

The question of whether or not to partition data for the purposes of inferring phylogenetic hypotheses remains controversial. Opinions have been especially divided since Kluge's (1989, Systematic Zoology 38, 7–25) claim that data partitioning violates the requirement of total evidence (RTE). Unfortunately, advocacy for or against the RTE has not been based on accurate portrayals of the requirement. The RTE is a basic maxim for non-deductive inference, stipulating that evidence must be considered if it has relevance to an inference. Evidence is relevant if it has a positive or negative effect on a given conclusion. In the case of ℈partitioned’ phylogenetic inferences, the RTE is violated, and the basis for rational belief in any conclusion is compromised, unless it is shown that the partitions are evidentially irrelevant to one another. The goal of phylogenetic systematics is to hypothesize past causal conditions to account for observed shared similarities among two or more species. Such inferences are non-deductive, necessitating consideration of the RTE. Some phylogeneticists claim the parsimony criterion as justification for the RTE. There is no relation between the two – parsimony is a relation between a hypothesis and causal question(s). Parsimony does not dictate the content of premises prior to an inference. ℈Taxonomic congruence,’ ℈supertrees,’ and ℈conditional combination’ methods violate the RTE. Taxonomic congruence and supertree methods also fail to achieve the intended goal of phylogenetic inference, such that ℈consensus trees’ and ℈supertrees’ lack an empirical basis. ℈Conditional combination’ is problematic because hypotheses derived from partitioned data cannot be compared – a causal hypothesis inferred to account for a set of effects only has relevance to those effects, not any comparative relevance to other causal hypotheses. A similar problem arises in the comparisons of hypotheses derived from different causal theories.     

Influencing the direct formation of ‘Janus’ particles in molecular dynamics simulations

The binary nucleation of phase-separated Lennard-Jones clusters was analysed under various system conditions using molecular dynamics simulations. The modified potential model provides a simple gateway to observe non-wetting behaviour and imitates the more complex interactions of non-miscible substances. Thus, not only the transition from ideally mixed clusters to so-called ‘Janus’ particles, but also the structural aspects and dynamic formation processes of nanoscopic droplets are directly observable from the gas phase. Various shapes and sizes of these inhomogeneous clusters have been found via simple tuning of system parameters. From this analysis, we gained further insight into the direct formation of ‘Janus’ particles from the gas phase.     

The role of autophagy in endoplasmic reticulum stress-induced pancreatic β cell death

In pancreatic β-cells, the endoplasmic reticulum (ER) is the crucial site for insulin biosynthesis, as this is where the protein-folding machinery for secretory proteins is localized. Perturbations to ER function of the β-cell, such as those caused by high levels of free fatty acid and insulin resistance, can lead to an imbalance in protein homeostasis and ER stress, which has been recognized as an important mechanism for type 2 diabetes. Macroautophagy (hereafter referred to as autophagy) is activated as a novel signaling pathway in response to ER stress. In this review, we outline the mechanism of ER stress-mediated β-cell death and focus on the role of autophagy in ameliorating ER stress. The development of drugs to take advantage of the potential protective effect of autophagy in ER stress, such as glucagon like peptide-1, will be a promising avenue of investigation.     

The role of VDAC in cell death: Friend or foe?

As the voltage-dependent anion channel (VDAC) forms the interface between mitochondria and the cytosol, its importance in metabolism is well understood. However, research on VDAC's role in cell death is a rapidly growing field, unfortunately with much confusing and contradictory results. The fact that VDAC plays a role in outer mitochondrial membrane permeabilization is undeniable, however, the mechanisms behind this remain very poorly understood. In this review, we will summarize the studies that show evidence of VDAC playing a role in cell death. To begin, we will discuss the evidence for and against VDAC's involvement in mitochondrial permeability transition (MPT) and attempt to clarify that VDAC is not an essential component of the MPT pore (MPTP). Next, we will evaluate the remaining literature on VDAC in cell death which can be divided into three models: proapoptotic agents escaping through VDAC, VDAC homo- or hetero-oligomerization, or VDAC closure resulting in outer mitochondrial membrane permeabilization through an unknown pathway. We will then discuss the growing list of modulators of VDAC activity that have been associated with induction/protection against cell death. This article is part of a Special Issue entitled: VDAC structure, function, and regulation of mitochondrial metabolism.     

Effect of procaine on development of ‘ridges’ and ‘domes’ in primary cell cultures from mammary glands of untreated virgin mice: The role of cell density in the occurrence of ‘domes’

Primary cell cultures from mammary glands of virgin mice that were not pretreated with hormones were subjected to: (1) procaine; (2) insulin+ prolactin +hydrocortisone; (3) a combination of (1) and (2). Procaine caused a ‘ridge’ effect similar to that of the hormones. The combination of procaine with the hormones caused a still stronger ‘ridge’ effect as well as the formation of ‘domes’. The formation of ‘domes’ is suggested to be dependent on cell density.