Subcellular localization, oligomerization, and ATP-binding of Caenorhabditis elegans CED-4.

Caspase family cell death proteases are activated during apoptosis through the oligomerization of caspase-binding "adapter" proteins. In the nematode Caenorhabditis elegans one adapter protein, CED-4, exists. Here we report an analysis of CED-4 protein expressed in insect Sf9 cells by infection with recombinant baculovirus. During expression, CED-4 assumed a perinuclear spherical or reticular localization where it was partly resistant to extraction with nonionic detergents. Both purified FLAG-CED-4 and GST-FLAG-CED-4 proteins were present in solution as large complexes. FLAG-CED-4 complexes were estimated by gel filtration to have a molecular weight of approximately 500 kDa to >1.2 MDa, while GST-FLAG-CED-4 complexes appeared somewhat smaller. Unlike its mammalian homologue Apaf-1, CED-4 exhibited a marked preference for ATP over dATP in filter binding studies and in competition experiments. ATP hydrolysis was required neither for complex stability nor for binding of CED-3. These features are likely to be relevant for CED-4's function as a caspase adapter.     

Species diversity of the genus Osmundea (Ceramiales,Rhodophyta) in the Macaronesian region

Species diversity within the genus Osmundea in the Macaronesian region was explored by conducting a comprehensive sampling in the Azores, the Canary, and the Madeira archipelagos. Toward identification, all specimens were first observed alive to verify the absence of corps en cerise, a diagnostic character for the genus and morphometric data were measured (thallus length and width, first‐order branches length and width, branchlets length and width, cortical cell length and width in surface view, cortical cell length and width in transverse section). Specimens were sequenced for COI‐5P (39 specimens) and three species delimitation methods (Generalized Mixed Yule Coalescent, Automatic Barcode Gap Discovery method, and Poisson Tree Processes) were used to assess the threshold between infra‐ and interspecific relationships. Subsequently, one or several sequences of plastid‐encoded large subunit of RuBisCO (21 specimens) per delimited species were generated to assess the phylogenetic relationships among Macaronesian Osmundea. Moreover, for each delineated species, vegetative and reproductive anatomy was thoroughly documented and, when possible, specimens were either assigned to existing taxa or described as novel species. This integrative approach has provided data for (i) the presence of O. oederi, O. pinnatifida, and O. truncata in Macaronesia; (ii) the proposal of two novel species, O. prudhommevanreinei sp. nov. and O. silvae sp. nov.; and (iii) evidence of an additional species referred as “Osmundea sp.1,” which is a sister taxon of O. hybrida.     

MHC Class I Immunopeptidome: Past,Present, and Future

In the 35 years since the revelation that short peptides bound to major histocompatibility complex class I and II molecules are the secret of the major histocompatibility complex–restricted nature of T-cell recognition, there has been enormous progress in characterizing the immunopeptidome, the repertoire of peptide presented for immunosurveillance. Here, the major milestones in the journey are marked, the contribution of proteasome-mediated splicing to the immunopeptidome is discussed, and exciting recent findings relating the immunopeptidome to the translatome revealed by ribosome profiling (RiboSeq) is detailed. Finally, what is needed for continued progress is opined about, which includes the infusion of talented young scientists into the antigen-processing field, currently undergoing a renaissance; thanks in part to the astounding success of T-cell–based cancer immunotherapy.     

Strategy for fluorescent labeling of human acidic fibroblast growth factor without impairment of mitogenic activity: A bona fide tracer

Here we describe, for the first time, the design and characterization of a bona fide fluorescently labeled mutant of the human acidic fibroblast growth factor (aFGF). The aFGF–Cys2 mutant was recombinantly synthesized by substituting the second amino acid with a reactive cysteine whose sulfhydryl group’s side chain reactivity facilitated the covalent binding of a fluorescent probe as a thiolyte monobromobimane. Using a combination of biophysical and functional assays, we found that the fluorescently labeled mutant aFGF is characterized by essentially the same global folding, mitogenic activity, and association behavior with heparin, its physiological activator, as the unlabeled wild-type protein. We used this new tracer protein mutant to determine the association behavior of aFGF with heparin in the presence of high concentrations of albumin that mimicked more closely the plasma medium in which aFGF is naturally located and in which it has evolved to function. By exposing the aFGF–Cys2–heparin complex to increasing concentrations of albumin up to physiological plasma levels, we were able to demonstrate that macromolecular crowding does not affect the stoichiometry of the interaction. In summary, the dimeric aFGF–Cys2–heparin complex might represent a biologically relevant complex in physiological media.     

Variation in active and passive resource inputs to experimental pools: mechanisms and possible consequences for food webs

1. Cross‐ecosystem movements of resources, including detritus, nutrients and living prey, can strongly influence food web dynamics in recipient habitats. Variation in resource inputs is thought to be driven by factors external to the recipient habitat (e.g. donor habitat productivity and boundary conditions). However, inputs of or by ‘active’ living resources may be strongly influenced by recipient habitat quality when organisms exhibit behavioural habitat selection when crossing ecosystem boundaries. 2. To examine whether behavioural responses to recipient habitat quality alter the relative inputs of ‘active’ living and ‘passive’ detrital resources to recipient food webs, we manipulated the presence of caged predatory fish and measured biomass, energy and organic content of inputs to outdoor experimental pools of adult aquatic insects, frog eggs, terrestrial plant matter and terrestrial arthropods. 3. Caged fish reduced the biomass, energy and organic matter donated to pools by tree frog eggs by ～70%, but did not alter insect colonisation or passive allochthonous inputs of terrestrial arthropods and plant material. Terrestrial plant matter and adult aquatic insects provided the most energy and organic matter inputs to the pools (40–50%), while terrestrial arthropods provided the least (7%). Inputs of frog egg were relatively small but varied considerably among pools and over time (3%, range = 0–20%). Absolute and proportional amounts varied by input type. 4. Aquatic predators can strongly affect the magnitude of active, but not passive, inputs and that the effect of recipient habitat quality on active inputs is variable. Furthermore, some active inputs (i.e. aquatic insect colonists) can provide similar amounts of energy and organic matter as passive inputs of terrestrial plant matter, which are well known to be important. Because inputs differ in quality and the trophic level they subsidise, proportional changes in input type could have strong effects on recipient food webs. 5. Cross‐ecosystem resource inputs have previously been characterised as donor‐controlled. However, control by the recipient food web could lead to greater feedback between resource flow and consumer dynamics than has been appreciated so far.     

A Scribble/Cdep/Rac pathway controls follower-cell crawling and cluster cohesion during collective border-cell migration

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Turing bifurcations with a temporally varying diffusion coefficient

This paper is concerned with the possibility of Turing bifurcations in a reaction-diffusion system in which the diffusion coefficient of one species varies periodically in time. This problem was introduced and investigated numerically by Timm and Okubo (J. Math. Biol. 30, 307, 1992) in the context of predator-prey interactions in plankton populations. Here, I consider the simple case in which the temporal variation in diffusivity has a square-tooth form, alternating between two constant values, with a period that is long compared with the time scale of the kinetics. The analysis is valid for any set of reaction kinetics. I derive explicit expressions for the Floquet multipliers that determine the stability of the steady state, and thereby obtain the conditions for diffusion driven instability to occur. These conditions imply that, depending on the kinetics, the homogeneous equilibrium may be either more or less stable than when the diffusion coefficient is a constant equal to the mean of the variable diffusivity. I go on to consider the form of the solution when diffusion driven instability does occur, and I use perturbation theory to determine the effect of a small temporal variation in the diffusion coefficient on the spatial wavelength of the pattern that results from diffusion driven instability.     

Life history shifts and alterations in the early development of parasitic wasps

Summary

In insects, the regulation of embryonic development has been intensively studied in model species like Drosophila melanogaster. Previous comparative studies have suggested that the developmental processes documented in Drosophila well describe embryogenesis of holometabolous insects generally. However, there have been few attempts to take into account how life history has influenced insect embryogenesis or to characterize early development of species with life histories fundamentally different from flies. Our studies of advanced insects in the order Hymenoptera suggest that punctuated shifts in life history can profoundly influence these events. In particular, alterations associated with the evolution of endoparasitism argue that departures from the fly paradigm may occur commonly among insects that develop under conditions different from typical terrestrial species.