Role of the Spatzle Pro-domain in the generation of an active toll receptor ligand

The cytokine Sp?tzle is the ligand for Drosophila Toll, the prototype of an important family of membrane receptors that function in embryonic patterning and innate immunity. A dimeric precursor of Sp?tzle is processed by an endoprotease to produce a form (C-106) that cross-links Toll receptor ectodomains and establishes signaling. Here we show that before processing the pro-domain of Sp?tzle is required for correct biosynthesis and secretion. We mapped two loss-of-function mutations of Sp?tzle to a discrete site in the pro-domain and showed that the phenotype arises because of a defect in biosynthesis rather than signaling. We also report that the pro-domain and C-106 remain associated after cleavage and that this processed complex signals with the same characteristics as the C-terminal fragment. These results suggest that before activation the determinants on C-106 that bind specifically to Toll are sequestered by the pro-domain and that proteolytic processing causes conformational rearrangements that expose these determinants and enables binding to Toll. Furthermore, we show that the pro-domain is released when the Toll extracellular domain binds to the complex, a finding that has implications for the generation of a signaling-competent Toll dimer.     

Cofilin-mediated F-actin severing is regulated by the Rap GTPase and controls the cytoskeletal dynamics that drive lymphocyte spreading and BCR microcluster formation

When lymphocytes encounter APCs bearing cognate Ag, they spread across the surface of the APC to scan for additional Ags. This is followed by membrane contraction and the formation of Ag receptor microclusters that initiate the signaling reactions that lead to lymphocyte activation. Breakdown of the submembrane cytoskeleton is likely to be required for the cytoskeleton reorganization that drives cell spreading and for removing physical barriers that limit Ag receptor mobility. In this report, we show that Ag receptor signaling via the Rap GTPases promotes the dephosphorylation and activation of the actin-severing protein cofilin and that this results in increased severing of cellular actin filaments. Moreover, we show that this cofilin-mediated actin severing is critical for the changes in actin dynamics that drive B and T cell spreading, for the formation of BCR microclusters, and for the increased mobility of BCR microclusters within the plasma membrane after BCR engagement. Finally, using a model APC, we show that activation of this Rap-cofilin signaling module controls the amount of Ag that is gathered into BCR microclusters and that this is directly related to the magnitude of the resulting BCR signaling that is initiated during B cell-APC interactions. Thus, Rap-dependent activation of cofilin is critical for the early cytoskeletal changes and BCR reorganization that are involved in APC-dependent lymphocyte activation.     

Progress toward a general species concept

New insights in the speciation process and the nature of "species" that accumulated in the past decade demand adjustments of the species concept. The standing of some of the most broadly accepted or most innovative species concepts in the light of the growing evidence that reproductive barriers are semipermeable to gene flow, that species can differentiate despite ongoing interbreeding, that a single species can originate polyphyletically by parallel evolution, and that uniparental organisms are organised in units that resemble species of biparental organisms is discussed. As a synthesis of ideas in existing concepts and the new insights, a generalization of the genic concept is proposed that defines species as groups of individuals that are reciprocally characterized by features that would have negative fitness effects in other groups and that cannot be regularly exchanged between groups upon contact. The benefits of this differential fitness species concept are that it classifies groups that keep differentiated and keep on differentiating despite interbreeding as species, that it is not restricted to specific mutations or mechanisms causing speciation, and that it can be applied to the whole spectrum of organisms from uni- to biparentals.     

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

Previous studies have estimated that, in angiosperms, the synonymous substitution rate of chloroplast genes is three times higher than that of mitochondrial genes and that of nuclear genes is twelve times higher than that of mitochondrial genes. Here we used 12 genes in 27 seed plant species to investigate whether these relative rates of substitutions are common to diverse seed plant groups. We find that the overall relative rate of synonymous substitutions of mitochondrial, chloroplast and nuclear genes of all seed plants is 1:3:10, that these ratios are 1:2:4 in gymnosperms but 1:3:16 in angiosperms and that they go up to 1:3:20 in basal angiosperms. Our results show that the mitochondrial, chloroplast and nuclear genomes of seed plant groups have different synonymous substitutions rates, that these rates are different in different seed plant groups and that gymnosperms have smaller ratios than angiosperms.     

Endosomal microdomains: Formation and function

It is widely recognized that after endocytosis, internalized cargo is delivered to endosomes that act as sorting stations. The limiting membrane of endosomes contain specialized subregions, or microdomains, that represent distinct functions of the endosome, including regions competing for cargo capture leading to degradation or recycling. Great progress has been made in defining the endosomal protein coats that sort cargo in these domains, including Retromer that recycles transmembrane cargo, and ESCRT (endosomal sorting complex required for transport) that degrades transmembrane cargo. In this review, we discuss recent work that is beginning to unravel how such coat complexes contribute to the creation and maintenance of endosomal microdomains. We highlight data that indicates that adjacent microdomains do not act independently but rather interact to cross-regulate. We posit that these interactions provide an agile means for the cell to adjust sorting in response to extracellular signals and intracellular metabolic cues.     

Energy allocation in the cladoceran Daphnia magna Straus,under starvation and refeeding

Summary Models incorporating the energetics of individual daphnids (Cladocera) have been developed to predict the effect of environmental variables, particularly food availability, on population dynamics. One of them, that of Kooijman (1986), assumes that all assimilated energy enters a storage compartment prior to use in production and metabolism, and that under starvation the stores are used to support maintenance, reproduction and somatic growth, in that order of priority. This predicts that, under starvation, reproduction and growth will continue for a time, and that after they cease death will be immediate. Another model, that of McCauley et al. (1990), assumes that assimilated energy is used directly for maintenance and production, and that stores are accumulated to support maintenance metabolism under starvation. This predicts that growth and reproduction should cease immediately upon starvation and that death will not be immediate. We have carried out laboratory experiments, manipulating starvation time, on Daphnia magna to distinguish between these two models. The results support features of both models in that reproduction, but not growth, ceases upon starvation. We therefore developed a third model in which both maintenance and growth are supported from stores under starvation, with maintenance taking priority over growth under these conditions.     

microRNA-34a is tumor suppressive in brain tumors and glioma stem cells

We recently found that microRNA-34a (miR-34a) is downregulated in human glioma tumors as compared to normal brain, and that miR-34a levels in mutant-p53 gliomas were lower than in wildtype-p53 tumors. We showed that miR-34a expression in glioma and medulloblastoma cells inhibits cell proliferation, G1/S cell cycle progression, cell survival, cell migration and cell invasion, but that miR-34a expression in human astrocytes does not affect cell survival and cell cycle. We uncovered the oncogenes c-Met, Notch-1 and Notch-2 as direct targets of miR-34a that are inhibited by miR-34a transfection. We found that c-Met levels in human glioma specimens inversely correlate with miR-34a levels. We showed that c-Met and Notch partially mediate the inhibitory effects of miR-34a on cell proliferation and cell death. We also found that mir-34a expression inhibits in vivo glioma xenograft growth. We concluded that miR-34a is a potential tumor suppressor in brain tumors that acts by targeting multiple oncogenes. In this extra view, we briefly review and discuss the implications of these findings and present new data on the effects of miR-34a in glioma stem cells. The new data show that miR-34a expression inhibits various malignancy endpoints in glioma stem cells. Importantly, they also show for the first time that miR-34a expression induces glioma stem cell differentiation. Altogether, the data suggest that miR-34a is a tumor suppressor and a potential potent therapeutic agent that acts by targeting multiple oncogenic pathways in brain tumors and by inducing the differentiation of cancer stem cells.     

Optimal Information Transfer in the Cortex through Synchronization

In recent experimental work it has been shown that neuronal interactions are modulated by neuronal synchronization and that this modulation depends on phase shifts in neuronal oscillations. This result suggests that connections in a network can be shaped through synchronization. Here, we test and expand this hypothesis using a model network. We use transfer entropy, an information theoretical measure, to quantify the exchanged information. We show that transferred information depends on the phase relation of the signal, that the amount of exchanged information increases as a function of oscillations in the signal and that the speed of the information transfer increases as a function of synchronization. This implies that synchronization makes information transport more efficient. In summary, our results reinforce the hypothesis that synchronization modulates neuronal interactions and provide further evidence that gamma band synchronization has behavioral relevance.     

Functional specialization of ribosomes?

Ribosomes are highly conserved macromolecular machines that are responsible for protein synthesis in all living organisms. Work published in the past year has shown that changes to the ribosome core can affect the mechanism of translation initiation that is favored in the cell, which potentially leads to specific changes in the relative efficiencies with which different proteins are made. Here, I examine recent data from expression and proteomic studies that suggest that cells make slightly different ribosomes under different growth conditions, and discuss genetic evidence that such differences are functional. In particular, I argue that eukaryotic cells probably produce ribosomes that lack one or more core ribosomal proteins (RPs) under some conditions, and that core RPs contribute differentially to translation of distinct subpopulations of mRNAs.     

The anarchist's guide to ecological theory. Or, we don't need no stinkin' laws

Several ecologists have recently suggested that ecology has several laws. This conclusion contrasts with the views of some philosophers of science, who have suggested that biology cannot have laws. I argue that the debate has been confused because two very different types of law can be recognised: correlative and causal laws. Once we recognise that there is a difference, the argument against causal laws becomes stronger, and instead I suggest that ecologists should recognise that they can and do produce generalisations that are used to build models – nomological machines – that describe the ecological systems they are studying.     

Inner-membrane proteins PMI/TMEM11 regulate mitochondrial morphogenesis independently of the DRP1/MFN fission/fusion pathways

Mitochondria are highly dynamic organelles that can change in number and morphology during cell cycle, development or in response to extracellular stimuli. These morphological dynamics are controlled by a tight balance between two antagonistic pathways that promote fusion and fission. Genetic approaches have identified a cohort of conserved proteins that form the core of mitochondrial remodelling machineries. Mitofusins (MFNs) and OPA1 proteins are dynamin-related GTPases that are required for outer- and inner-mitochondrial membrane fusion respectively whereas dynamin-related protein 1 (DRP1) is the master regulator of mitochondrial fission. We demonstrate here that the Drosophila PMI gene and its human orthologue TMEM11 encode mitochondrial inner-membrane proteins that regulate mitochondrial morphogenesis. PMI-mutant cells contain a highly condensed mitochondrial network, suggesting that PMI has either a pro-fission or an anti-fusion function. Surprisingly, however, epistatic experiments indicate that PMI shapes the mitochondria through a mechanism that is independent of drp1 and mfn. This shows that mitochondrial networks can be shaped in higher eukaryotes by at least two separate pathways: one PMI-dependent and one DRP1/MFN-dependent.     

FtsZ ring: the eubacterial division apparatus conserved in archaebacteria

FtsZ is a tubulin-like protein that is essential for cell division in eubacteria. It functions by forming a ring at the division site that directs septation. The archaebacteria constitute a kingdom of life separate from eubacteria and eukaryotes. Like eubacteria, archaebacteria are prokaryotes, although they are phylogenetically closer to eukaryotes. Here it is shown that archaebacteria also possess FtsZ and that it is biochemically similar to eubacterial FtsZs. Significantly, FtsZ from the archaebacterium Haloferax volcanii is a GTPase that is localized to a ring that coincides with the division constriction. These results indicate that the FtsZ ring was part of the division apparatus of a common prokaryotic ancestor that was retained by both eubacteria and archaebacteria.     

GABA and “neuro-cardiovascular” mechanisms

One has only to recall that GABA appears to be a major inhibitory neurotransmitter in the vertebrate central nervous system (CNS), that it exerts a hypotensive action upon systemic administration, that it is present in the blood, that its actions are antagonized by bicuculline and picrotoxin and facilitated by benzodiazepines, and that receptors for GABA exist in cerebral blood vessels, to consider that GABA is somehow involved in cardiovascular regulation. One might even postulate that influences upon GABA-ergic mechanisms are involved in that dangerous sequence of biological activities: environmental stress → anxiety → atherosclerosis and hypertension, the latter of which represent major health problems of man. Herein, some evidence that appears to support this view will be presented.     

Reliable sampling method for analysis of the ecology of the human alimentary tract.

An intubation method has been developed that allows removal of a sample of human intestinal fluid within a short period of time, that avoids contamination, and that minimizes exposure of the sample to air. Preliminary results obtained with this method have shown that the stomach and duodenum are essentially sterile and that the bacterial population present in the remainder of the small intestine is similar to that described by previous workers except that Veillonella species were encountered frequently and Haemophilus species were also detected in the lower jejunum and ileum of some individuals.     

Protein that induces cell differentiation causes nicks in double-stranded DNA

The growth and differentiation of myeloid hematopoietic cells are regulated by different macrophage and granulocyte inducing proteins, those that induce growth and others that induce differentiation. The proteins that induce differentiation but not those that induce growth bind to double-stranded DNA. We now report that purified myeloid cell differentiation-inducing protein causes single strand breaks (nicks) in double-stranded DNA. This DNA nicking may initiate the changes in gene expression that are required for differentiation.     

Bioethics and conflicts of interest

Bioethics has been subject to considerable social criticism in recent years. One criticism that has caused particular discomfort in the bioethics community is that bioethicists, because of the way their work is funded, are involved in profound conflicts of interest that undermine their title to be considered independent moral commentators on developments in biomedicine and biotechnology. This criticism draws its force from the assumption that bioethics is, or ought to be, a type of normative social criticism. Versions of this criticism come from both the political left and right. For instance, such criticisms include allegations that bioethics is inherently socially conservative, that it is inherently “pro-technology”, that it lays spurious claims to moral and social authority and expertise, that its focus on autonomy links it to neoliberal theories of choice, and that it is an ideological mystification of real social relationships and political power. This commentary paper analyses the problem of bioethical conflict of interest, and argues that the types of conflict of interest facing bioethics are inherent to the role of “public intellectual” that bioethicists generally wish to assume. The paper defends this conception of the role of the bioethicist, arguing that bioethicists should be interested and openly so.     

Vasoactive intestinal polypeptide and glucagon: stimulation of adenylate cyclase activity via distinct receptors in liver and fat cell membranes

Vasoactive intestinal polypeptide (VIP), a peptide hormone that is chemically and biologically related to glucagon and secretin, stimulates the activity of adenylate cyclase in liver and fat cell membranes. Effects of combinations of VIP with glucagon and secretin at concentrations that maximally activate adenylate cyclase suggest that in adipose tissue, the three hormones act on the same enzyme, whereas in liver, VIP and secretin activate a common enzyme that is distinct from that responding to glucagon. Studies with radioiodinated derivatives of VIP and glucagon indicate that these hormones interact with separate receptors. Secretin, which gives a maximal stimulation of adenylate cyclase activity virtually identical to that elicited by VIP, inhibits the binding of the latter to its receptor. However, the apparent affinity of secretin for adenylate cyclase and for the VIP receptor is about two order of magnitude lower than that of VIP. It is suggested that VIP and secretin may activate adenylate cyclase via a common receptor.     

Comparative analysis of the subventricular zone in rat, ferret and macaque: evidence for an outer subventricular zone in rodents

The mammalian cerebral cortex arises from precursor cells that reside in a proliferative region surrounding the lateral ventricles of the developing brain. Recent work has shown that precursor cells in the subventricular zone (SVZ) provide a major contribution to prenatal cortical neurogenesis, and that the SVZ is significantly thicker in gyrencephalic mammals such as primates than it is in lissencephalic mammals including rodents. Identifying characteristics that are shared by or that distinguish cortical precursor cells across mammalian species will shed light on factors that regulate cortical neurogenesis and may point toward mechanisms that underlie the evolutionary expansion of the neocortex in gyrencephalic mammals. We immunostained sections of the developing cerebral cortex from lissencephalic rats, and from gyrencephalic ferrets and macaques to compare the distribution of precursor cell types in each species. We also performed time-lapse imaging of precursor cells in the developing rat neocortex. We show that the distribution of Pax6+ and Tbr2+ precursor cells is similar in lissencephalic rat and gyrencephalic ferret, and different in the gyrencephalic cortex of macaque. We show that mitotic Pax6+ translocating radial glial cells (tRG) are present in the cerebral cortex of each species during and after neurogenesis, demonstrating that the function of Pax6+ tRG cells is not restricted to neurogenesis. Furthermore, we show that Olig2 expression distinguishes two distinct subtypes of Pax6+ tRG cells. Finally we present a novel method for discriminating the inner and outer SVZ across mammalian species and show that the key cytoarchitectural features and cell types that define the outer SVZ in developing primates are present in the developing rat neocortex. Our data demonstrate that the developing rat cerebral cortex possesses an outer subventricular zone during late stages of cortical neurogenesis and that the developing rodent cortex shares important features with that of primates.