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.     

On the Specificity of Adaptive Mutations

Adaptive mutations are mutations that occur in nondividing or slowly dividing cells during prolonged nonlethal selection, and that appear to be specific to the challenge of the selection in the sense that the only mutations that arise are those that provide a growth advantage to the cell. The issue of the specificity has been controversial because it violates our most basic assumptions about the randomness of mutations with respect to their effect on the cell. Although a variety of experiments in several systems in both bacteria and yeast have claimed to demonstrate that specificity, those experiments have been subjected to a variety of technical criticisms suggesting that the specificity may not be real. Here I use the ebg system to provide evidence that when selection is applied to one specific nucleotide site within a gene, mutation occurs at that site but not at an alternative and equally mutable site within the same gene.     

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.     

Review of the specific effects of microwave radiation on bacterial cells

The aim of the present review was to evaluate the literature suggesting that consideration be given to the existence of specific microwave (MW) effects on prokaryotic microorganisms; that is, effects on organisms that cannot be explained by virtue of temperature increases alone. This review considered a range of the reported effects on cellular components; including membranes, proteins, enzyme activity as well as cell death. It is concluded that the attribution of such effects to non-thermal mechanisms is not justified due to poor control protocols and because of the possibility that an unmeasurable thermal force, relating to instantaneous temperature (T (i)) that occurs during MW processing, has not been taken into account. However, due to this lack of control over T (i), it also follows that it cannot be concluded that these effects are not 'non-thermal'. Due to this ambiguity, it is proposed that internal 'micro'-thermal effects may occur that are specific to MW radiation, given its inherent unusual energy deposition patterning.     

Absence of Spatial Tuning in the Orbitofrontal Cortex

There is limited data in the literature to explicitly support the notion that neurons in OFC are truly action-independent in their coding. We set out to specifically test the hypothesis that OFC value-related neurons in area 13 m of the monkey do not carry information about the action required to obtain that reward – that activity in this area represents reward values in an abstract and action-independent manner. To accomplish that goal we had two monkeys select and execute saccadic eye movements to 81 locations in the visual field for three different kinds of juice rewards. Our detailed analysis of the response fields indicates that these neurons are insensitive to the amplitude or direction of the saccade required to obtain these rewards. Our data thus validate earlier proposals that neurons of 13 m in the OFC encode subjective value independent of the saccadic action required to obtain that reward.     

The role of variant surface antigens on malaria-infected red blood cells.

It has been proposed that the primary role of variant antigens appearing on the surface of red blood cells infected with malaria parasites is to mediate cytoadherence, and that the antigenic variation they display is an adaptation to avoid immune attack. Here, Allan Saul proposes that their role is the opposite: that their primary purpose is to generate an immune response, which regulates their growth and thereby establishes a chronic infection, and that the role of cytoadherence is to ensure that parasites failing to express this flag to the immune system are destroyed by the spleen.     

Impacts of global change on plant diversity and vice versa: Old and new challenges for vegetation scientists

Abstract. The desire to stop the current dramatic loss of biodiversity has been a major stimulus for many vegetation ecologists to unravel the mechanisms responsible for the coexistence of species. After the Rio Janeiro Convention many ecologists were convinced that nature conservation would gain strong societal support if they could prove that the loss of species would have important negative effects on the ecosystem functions that are relevant to society. I conclude that in order to understand such possible effects, it is necessary to analyse the effects of individual species on those ecosystem processes that we consider to be relevant in the context of specific questions. The great challenge for the near future is to scale the effects of plant species on their local environment up to the level of the whole planet, so that we learn about possible feedbacks that might regulate or destabilize those characteristics of the globe that are essential to our society.     

Site of graviperception in roots: a re-examination

Two lines of evidence have been cited to support the assertion that the root cap is the sole site of graviperception in the root. The first evidence is based on surgical removal of the cap, which abolishes the response to gravity. This is sufficient to conclude that the cap is involved in gravitropism, but not to conclude that the cap is the site of graviperception. The second is based on the results of centrifugation experiments, in which different parts of the plant are subjected to different centrifugal forces. The data from such experiments have been cited to support the conclusion that the perception of gravity is limited to the rootcap. However, these data actually support the conclusion that gravity is perceived throughout the root tip, and not only in the root cap. We believe that the data support the conclusion that the root cap is involved in root gravitropism, but that there is inadequate evidence to conclude that the cap is the sole site of graviperception.     

Modelling Thrombin Generation in Human Ovarian Follicular Fluid

A mathematical model is constructed to study thrombin production in human ovarian follicular fluid. The model results show that the amount of thrombin that can be produced in ovarian follicular fluid is much lower than that in blood plasma, failing to reach the level required for fibrin formation, and thereby supporting the hypothesis that in follicular fluid thrombin functions to initiate cellular activities via intracellular signalling receptors. It is also concluded that the absence of the amplification pathway to thrombin production in follicular fluid is a major factor in restricting the amount of thrombin that can be produced. Titration of the initial concentrations of the various reactants in the model lead to predictions for the amount of tissue factor and phospholipid that is required to maintain thrombin production in the follicle, as well as to the conclusion that tissue factor pathway inhibitor has little effect on the time that thrombin generation is sustained. Numerical experiments to determine the effect of factor V, which is at a much reduced level in follicular fluid compared to plasma, and thrombomodulin, illustrate the importance for further experimental work to determine values for several parameters that have yet to be reported in the literature.     

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.     

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.     

CONSPIRATORIAL WHISPERS AND CONSPICUOUS DISPLAYS: GAMES OF SIGNAL DETECTION

Recent models of signaling have assumed that the expenditure required to ensure detection of a display is negligible and have concentrated instead on the costs that may be necessary to maintain honesty. Such models predict that individuals who share the same interests are likely to communicate using “conspiratorial whispers,” signals that are cheap and inconspicuous. Here, I present a game-theoretical model of signal detection (in a noisy environment, in the presence of potential eavesdroppers), which demonstrates that the idea of conspiratorial whispers is far too simplistic. It is true that in “cooperative” signaling systems (where signalers attempt to elicit responses that are beneficial for receivers), signal cost is not required to maintain honesty. However, some level of expenditure is still needed to ensure that a signal is reliably detected. Moreover, there exists a conflict of interest between signalers and receivers over the division of this expenditure. To predict the stable level of display in such cases, one needs to know how this conflict of interest will be resolved. The model reveals that the outcome may range from a whisper to a conspicuous and costly (though still conspiratorial) display. The more closely related the receiver is to the signaler, the greater the level of signal exaggeration that is expected—the opposite prediction to that of honest signaling models.     

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.     

LexA-independent expression of a mutant mucAB operon.

pKM101 is a naturally occurring plasmid that carries mucAB, an analog of the umuDC operon, the gene products of which are required for the SOS-dependent processing of damaged DNA necessary for most mutagenesis. Genetic studies have indicated that mucAB expression is controlled by the SOS regulatory circuit, with LexA acting as a direct repressor. pGW16 is a pKM101 derivative obtained by N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis that was originally identified on the basis of its ability to cause a modest increase in spontaneous mutation rate. In this report, we show that pGW16 differs from pKM101 in being able to enhance methyl methanesulfonate mutagenesis and to confer substantial resistance to UV killing in a lexA3 host. The mutation carried by pGW16 is dominant and was localized to a 2.4-kb region of pGW16 that includes the mucAB coding region and approximately 0.6 kb of the 5'-flanking region. We determined the sequence of a 119-bp fragment containing the region upstream of mucAB and identified a single-base-pair change in that region, a G.C-to-A.T transition that alters a sequence homologous to known LexA-binding sites. DNA gel shift experiments indicate that LexA protein binds poorly to a 125-bp fragment containing this mutation, whereas a fragment containing the wild-type sequence is efficiently bound by LexA. This mutation also alters an overlapping sequence that is homologous to the -10 region of Escherichia coli promoters, moving it closer to the consensus sequence. The observation that the synthesis of pGW16-encoded mucAB proteins in maxicells is increased relative to that of pKM101-encoded mucAB proteins even in the absence of a lexA+ plasmid suggests that this mutation also increases the activity of the mucAB promoter.     

Information giving in clinical trials: the views of medical researchers

It is both an ethical and a legal requirement that patients who participate in clinical trials must generally give their consent. As part of this process, patients must be provided with adequate information to enable them to decide whether or not to take part. In the UK, the pharmaceutical companies that sponsor such research, as well as Local Research Ethics Committees, specify in detail the information that must be given to trial participants. The researchers who conduct clinical trials inevitably form views on the amount of information they are required to provide, and about patients' comprehension of that information. The literature in this area suggests that some medical researchers may be unhappy with the amount of information that they must give patient participants. There have been, however, few systematic attempts to determine their views. This paper reports a study that explored researchers' views as to (i) the amount of information provided to trial participants, and (ii) participants' understanding of that information. Researchers generally felt that they were required to give trial participants an appropriate amount of information, and that most patients had at least a reasonable understanding of key aspects of the clinical trials' process. However, there were differing views as to the level of information that they felt patients themselves wanted. The researchers did not generally feel that the patients' inability to comprehend information rendered the process of obtaining 'informed consent' a waste of time. However, some did believe that they were required to burden patients with excessive information.     

The evolution of resistance through costly acquired immunity

We examine the evolutionary dynamics of resistance to parasites through acquired immunity. Resistance can be achieved through the innate mechanisms of avoidance of infection and reduced pathogenicity once infected, through recovery from infection and through remaining immune to infection: acquired immunity. We assume that each of these mechanisms is costly to the host and find that the evolutionary dynamics of innate immunity in hosts that also have acquired immunity are quantitatively the same as in hosts that possess only innate immunity. However, compared with resistance through avoidance or recovery, there is less likely to be polymorphism in the length of acquired immunity within populations. Long-lived organisms that can recover at intermediate rates faced with fast-transmitting pathogens that cause intermediate pathogenicity (mortality of infected individuals) are most likely to evolve long-lived acquired immunity. Our work emphasizes that because whether or not acquired immunity is beneficial depends on the characteristics of the disease, organisms may be selected to only develop acquired immunity to some of the diseases that they encounter.     

Endocytic routes to Notch activation

It is well established that Notch signalling is activated in response to ligand binding through a series of proteolytic cleavages that release the Notch intracellular domain, allowing it to translocate to the nucleus to regulate downstream target gene expression. However there is still much to learn about the mechanisms that can bring about these proteolytic events in the numerous physiological contexts in which signal activation occurs. A number of studies have suggested that endocytosis of Notch contributes to the signal activation process, but the molecular details are unclear and controversial. There is conflicting data as to whether endocytosis of the receptor is essential for ligand-induced signalling or supplements it. Other studies have revealed that Notch can be activated in the endosomal pathway, independently of its ligands, through the activity of Deltex, a Ring-domain Ubiquitin ligase that binds to the Notch intracellular domain. However, it is unclear how the Deltex-activation mechanism relates to that of ligand-induced signalling, or to ectopic Notch signalling brought about by disruption of ESCRT complexes that affect multivesicular body formation. This review will address these issues and argue that the data are best reconciled by proposing distinct activation mechanisms in different cellular locations that contribute to the cellular pool of the soluble Notch intracellular domain. The resulting signalling network may provide developmental robustness to environmental and genetic variation.     

The medium of signs: nominalism, language and the philosophy of mind in the early thought of Dugald Stewart

In 1792 Dugald Stewart published Elements of the philosophy of the human mind. In its section on abstraction he declared himself to be a nominalist. Although a few scholars have made brief reference to this position, no sustained attention has been given to the central role that it played within Stewart's early philosophy of mind. It is therefore the purpose of this essay to unpack Stewart's nominalism and the intellectual context that fostered it. In the first three sections I aver that his nominalism emanated from his belief that objects of the mind--qualities, ideas and words--were signs that bore no necessary relation to the external objects that they were meant to represent. More specifically, it was these signs that were arranged into systems of thought by the 'operations of the mind'. The next three sections suggest that his treatment of words as signs most probably originated in his views on language and medicine and that his nominalistic philosophy of mind could also be extended to systems that sought to classify the natural world. I conclude by suggesting several avenues of enquiry that could be pursued by future scholars interested in excavating Stewart's thought.