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.     

Primary amphipathic cell-penetrating peptides: structural requirements and interactions with model membranes

To identify rules for the design of efficient cell-penetrating peptides that deliver therapeutic agents into subcellular compartments, we compared the properties of two closely related primary amphipathic peptides that mainly differ by their conformational state. On the basis of a peptide Pbeta that is nonstructured in water and that promotes efficient cellular uptake of nucleic acids through noncovalent association, we have designed a peptide [Palpha] that is predicted to adopt a helical conformation. We show that [Pbeta] undergoes a lipid-induced conformational transition into a sheet structure, while [Palpha] remains helical. Penetration experiments show that both peptides can spontaneously insert into phospholipid membranes. Analysis of compression isotherms indicates that both peptides interact with phospholipids in the liquid expanded and liquid condensed states. AFM observations reveal that the peptides strongly disrupt the lipid organization of the monolayers and that the conformational state can influence the uptake by model membranes.     

Domain structure of secretin PulD revealed by limited proteolysis and electron microscopy

Secretins, a superfamily of multimeric outer membrane proteins, mediate the transport of large macromolecules across the outer membrane of Gram-negative bacteria. Limited proteolysis of secretin PulD from the Klebsiella oxytoca pullulanase secretion pathway showed that it consists of an N-terminal domain and a protease-resistant C-terminal domain that remains multimeric after proteolysis. The stable C-terminal domain starts just before the region in PulD that is highly conserved in the secretin superfamily and apparently lacks the region at the C-terminal end to which the secretin-specific pilot protein PulS binds. Electron microscopy showed that the stable fragment produced by proteolysis is composed of two stacked rings that encircle a central channel and that it lacks the peripheral radial spokes that are seen in the native complex. Moreover, the electron microscopic images suggest that the N-terminal domain folds back into the large cavity of the channel that is formed by the C-terminal domain of the native complex, thereby occluding the channel, consistent with previous electrophysiological studies showing that the channel is normally closed.     

Phosphorylation of the porcine reproductive and respiratory syndrome virus nucleocapsid protein

Porcine reproductive and respiratory syndrome virus (PRRSV) is a cytoplasmic RNA virus with the unique or unusual feature of having a nucleocapsid (N) protein that is specifically transported to the nucleolus of virus-infected cells. In this communication, we show that the N protein is a phosphoprotein. Phosphoamino acid analysis of authentic and recombinant N proteins demonstrated that serine residues were exclusively phosphorylated. The pattern of phosphorylated N protein cellular distribution in comparison with that of [(35)S]methionine-labeled N protein suggested that phosphorylation does not influence subcellular localization of the protein. Time course studies showed that phosphorylation occurred during, or shortly after, synthesis of the N protein and that the protein remained stably phosphorylated throughout the life cycle of the virus to the extent that phosphorylated N protein was found in the mature virion. Two-dimensional electrophoresis and acid-urea gel electrophoresis showed that one species of the N protein is predominant in virus-infected cells, suggesting that multiple phosphorylated isoforms of N do not exist.     

Breaking the ties: epistemic significance, bacilli, and underdetermination

One premise of the underdetermination argument is that entailment of evidence is the only epistemic constraint on theory-choice. I argue that methodological rules can be epistemically significant, both with respect to observables and unobservables. Using an example from the history of medicine -- Koch's 1882 discovery of tuberculosis bacteria -- I argue that even anti-realists ought to accept that these rules can break the tie between theories that are allegedly underdetermined. I then distinguish two types of underdetermination and argue that anti-realists, in order to maintain the underdetermination argument, need to do more than show that theories are empirically equivalent: they need to show that a certain kind of underdetermination obtains.     

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.     

Effects of pore mutations and permeant ion concentration on the spontaneous gating activity of OmpC porin

Porins are trimers of beta-barrels that form channels for ions and other hydrophilic solutes in the outer membrane of Gram-negative bacteria. The X-ray structures of OmpF and PhoE show that each monomeric pore is constricted by an extracellular loop that folds into the channel vestibule, a motif that is highly conserved among bacterial porins. Electrostatic calculations have suggested that the distribution of ionizable groups at the constriction zone (or eyelet) may establish an intrinsic transverse electrostatic field across the pore, that is perpendicular to the pore axis. In order to study the role that electrostatic interactions between pore residues may have in porin function, we used spontaneous mutants and engineered site-directed mutants that have an altered charge distribution at the eyelet and compared their electrophysiological behavior with that of wild-type OmpC. We found that some mutations lead to changes in the spontaneous gating activity of OmpC porin channels. Changes in the concentration of permeant ions also altered this activity. These results suggest that the ionic interactions that exist between charged residues at the constriction zone of porin may play a role in the transitions between the channel's closed and open states.     

Dissociation of conditioned taste avoidance from conditioned disgust reactions induced by wheel running in rats

It is well established that wheel running in rats produces conditioned taste avoidance; that is, rats that run in wheels after consuming a novel-tasting solution later consume less of that solution than rats that do not run. In experiment 1, we found that wheel running also produces conditioned disgust reactions, indicated by gapes elicited by both the taste and context that were experienced before running. Experiment 2 showed that the conditioned disgust reactions were likely not due to running itself but to a by-product of running, the rocking of the wheel that occurs when the running stops. When rocking was reduced, the disgust reactions were also reduced, but consumption of the taste solution was not changed, showing dissociation of conditioned taste avoidance and disgust. These findings indicate that the taste avoidance induced by wheel running itself is more like the taste avoidance produced by rewarding drugs than that produced by nausea-inducing drugs.     

A Quantitative Measure of the Mitotic Pairing of Alleles in Drosophila Melanogaster and the Influence of Structural Heterozygosity

In Drosophila there exist several examples of gene expression that can be modified by an interaction between alleles; this effect is known as transvection. The inference that alleles interact comes from the observations that homologous chromosomes pair in mitotically dividing cells, and that chromosome rearrangements can alter the phenotype produced by a pair of alleles. It is thought that heterozygous rearrangements impede the ability of alleles to pair and interact. However, because the existing data are inconsistent, this issue is not fully settled. By measuring the frequency of site-specific recombination between homologous chromosomes, we show that structural heterozygosity inhibits the pairing of alleles that lie distal to a rearrangement breakpoint. We suggest that some of the apparent conflicts may owe to variations in cell-cycle lengths in the tissues where the relevant allelic interactions occur. Cells with a longer cell cycle have more time to establish the normal pairing relationships that have been disturbed by rearrangements. In support, we show that Minute mutations, which slow the rate of cell division, partially restore a transvection effect that is disrupted by inversion heterozygosity.     

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.     

Reconsidering cochlear implants: the lessons of Martha's Vineyard

I distinguish and assess three separate arguments utilized by the opponents of cochlear implants: that treating deafness as a medical condition is inappropriate since it is not a disability; that so treating it sends a message to the Deaf that they are of lesser worth; and that the use of such implants would signal the end of Deaf culture. I give some qualified support to the first and second claim, but find that the principal weight of the argument must be borne by the third argument: that use of the cochlear implants is impermissible because Deaf culture is intrinsically valuable. I show that this claim is, in practice, incompatible with the claim that deafness is not a disability: that the significant disadvantages suffered by the hearing impaired can only be corrected by measures that would end Deaf culture. Since the potential recipients of cochlear implants are, in the main, the prelingually deaf children of hearing parents, the burden of banning the implants would be borne by people who are not members of Deaf culture, and who owe that culture nothing over and above what we all owe cultures in general. I conclude that we cannot ask the parents of these children to sacrifice the interests of their children for the sake of Deaf culture.     

Isoform-specific interaction of C-RAF with mitochondria

The proteins of the RAF family (A-RAF, B-RAF, and C-RAF) are serine/threonine kinases that play important roles in development, mature cell regulation, and cancer. Although it is widely held that their localization on membranes is an important aspect of their function, there are few data that address this aspect of their mode of action. Here, we report that each member of the RAF family exhibits a specific distribution at the level of cellular membranes and that C-RAF is the only isoform that directly targets mitochondria. We found that the RAF kinases exhibit intrinsic differences in terms of mitochondrial affinity and that C-RAF is the only isoform that binds this organelle efficiently. This affinity is conferred by the C-RAF amino-terminal domain and does not depend on the presence of RAS GTPases on the surface of mitochondria. Finally, we analyzed the consequences of C-RAF activation on mitochondria and observed that this event dramatically changes their morphology and their subcellular distribution. Our observations indicate that: (i) RAF kinases exhibit different localizations at the level of cellular membranes; (ii) C-RAF is the only isoform that directly binds mitochondria; and (iii) through its functional coupling with MEK, C-RAF regulates the shape and the cellular distribution of mitochondria.     

Surface changes of the mechanosensitive channel MscS upon its activation, inactivation, and closing

MscS is a bacterial mechanosensitive channel that shows voltage dependence. The crystal structure of MscS revealed that the channel is a homoheptamer with a large chamber on the intracellular site. Our previous experiments indicated that the cytoplasmic chamber of the channel is not a rigid structure and changes its conformation upon the channel activation. In this study, we have applied various sized cosolvents that are excluded from protein surfaces. It is well known that such cosolvents induce compaction of proteins and prevent thermal fluctuations. It is also known that they shift channel equilibrium to the state of lower volume. We have found that large cosolvents that cannot enter the channel interior accelerate channel inactivation when applied from the cytoplasmic side, but they slow down inactivation when applied from the extracellular side. We have also found that small cosolvents that can enter the channel cytoplasmic chamber prevent the channel from opening, unlike the large ones. These data support our idea that the channel cytoplasmic chamber shrinks upon inactivation but also give new clues about conformational changes of the channel upon transitions between its functional states.     

S-laminin expression in adult and developing retinae: a potential cue for photoreceptor morphogenesis.

The development of the neural retina follows a stereotyped time course that begins with an undifferentiated neuroepithelium populated by multipotential progenitor cells and ends with a highly differentiated tissue containing diverse cell types. The identities of the factors that guide this differentiation have remained elusive; a likely location for such factors, however, is the extracellular environment. Here, we show that the extracellular matrix component s-laminin is present in the neural retina, that s-laminin expression parallels the differentiation of rod photoreceptors, that photoreceptors interact with s-laminin in vitro, and that antibodies to s-laminin profoundly reduce the appearance of cells that express rhodopsin in vitro. These data suggest that s-laminin plays a role in the differentiation of the neural retina and provide evidence that the composition of the extracellular matrix may be an important determinant of retinal differentiation.     

The neural and cognitive correlates of aimed throwing in chimpanzees: a magnetic resonance image and behavioural study on a unique form of social tool use

It has been hypothesized that neurological adaptations associated with evolutionary selection for throwing may have served as a precursor for the emergence of language and speech in early hominins. Although there are reports of individual differences in aimed throwing in wild and captive apes, to date there has not been a single study that has examined the potential neuroanatomical correlates of this very unique tool-use behaviour in non-human primates. In this study, we examined whether differences in the ratio of white (WM) to grey matter (GM) were evident in the homologue to Broca's area as well as the motor-hand area of the precentral gyrus (termed the KNOB) in chimpanzees that reliably throw compared with those that do not. We found that the proportion of WM in Broca's homologue and the KNOB was significantly higher in subjects that reliably throw compared with those that do not. We further found that asymmetries in WM within both brain regions were larger in the hemisphere contralateral to the chimpanzee's preferred throwing hand. We also found that chimpanzees that reliably throw show significantly better communication abilities than chimpanzees that do not. These results suggest that chimpanzees that have learned to throw have developed greater cortical connectivity between primary motor cortex and the Broca's area homologue. It is suggested that during hominin evolution, after the split between the lines leading to chimpanzees and humans, there was intense selection on increased motor skills associated with throwing and that this potentially formed the foundation for left hemisphere specialization associated with language and speech found in modern humans.     

Adaptation of prey and predators between patches

Mathematical models are proposed to simulate migrations of prey and predators between patches. In the absence of predators, it is shown that the adaptation of prey leads to an ideal spatial distribution in the sense that the maximal capacity of each patch is achieved. With the introduction of co-adaptation of predators, it is proved that both prey and predators achieve ideal spatial distributions when the adaptations are weak. Further, it is shown that the adaptation of prey and predators increases the survival probability of predators from the extinction in both patches to the persistence in one patch. It is also demonstrated that there exists a pattern that prey and predators cooperate well through adaptations such that predators are permanent in every patch in the case that predators become extinct in each patch in the absence of adaptations. For strong adaptations, it is proved that the model admits periodic cycles and multiple stability transitions.     

The Purity of Spirit and the Power of Blood: A Comparative Perspective on Nation, Gender and Kinship in Cyprus

This article argues that the kinship relations of the national 'family' are not simply a direct appropriation of 'natural' kinship relations but involve a transformation of those relations that also takes into account some gendered image of the land as a member of that family. Using comparative research in the Turkish and Greek communities of Cyprus, I propose that what is centrally important in images of national kinship is the common substance that land and people are imagined to share. Moreover, this common substance is regarded as so 'natural' that it constitutes an important axiom that is central to understanding the logic of nationalisms.     

Feature-based attention: it is all bottom-up priming

Feature-based attention (FBA) enhances the representation of image characteristics throughout the visual field, a mechanism that is particularly useful when searching for a specific stimulus feature. Even though most theories of visual search implicitly or explicitly assume that FBA is under top-down control, we argue that the role of top-down processing in FBA may be limited. Our review of the literature indicates that all behavioural and neuro-imaging studies investigating FBA suffer from the shortcoming that they cannot rule out an effect of priming. The mere attending to a feature enhances the mandatory processing of that feature across the visual field, an effect that is likely to occur in an automatic, bottom-up way. Studies that have investigated the feasibility of FBA by means of cueing paradigms suggest that the role of top-down processing in FBA is limited (e.g. prepare for red). Instead, the actual processing of the stimulus is needed to cause the mandatory tuning of responses throughout the visual field. We conclude that it is likely that all FBA effects reported previously are the result of bottom-up priming.     

Reasoning in bioethics

It is striking that some arguments in the bioethical literature seem implausible, counterintuitive, and even ridiculous when reported to competent moral agents. When examined, these arguments bear uncanny resemblances to the discourse of patients with debilitating mental disorders. I examine the kinds of irrationality involved, and discuss the fact that such irrationality is worrying in a discipline that purports to serve as a guide for real-life practical reasoning. I offer some thoughts about correctives that we might use to temper some of the odd opinions that bedevil our subject in the name of ethical analysis. It seems that one ought to be suspicious of neatly rational arguments that produce counterintuitive conclusions, but the alternative seems to be that we explore new constructions of old problems in Bioethics such that our discussion of them does justice to what we regard as of fundamental significance to our lives together as human beings.