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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

NORMAL PSYCHOLOGICAL CHANGES IN ADOLESCENCE

It behooves physicians to be aware that adolescents are different people, that they have a vast capacity for change, that they often exhibit the sickest kind of behavior, which may be very frightening to us and to them.Physicians have to be able to wait and not become panicked by the turbulences, confusions, and contradictions that mark the adolescent''s behavior; to keep in mind at all times that much of what is going on is relatively normal behavior in the drive toward maturation and adulthood; that the adolescent has to cope with his sexual drive which is continually frustrated, that he has to cope with the problems of emancipation from parental authority, that he has to cope with an aggressive drive to achieve and to dominate.Parents, too, have to be understanding and ready to render unselfish support, for they continue to be the source of strength and security, and even the source of healthy restrictions. Adults must be aware that the adolescent struggles with his conscience and its dictates, and we should look upon cliques, groups and clubs as a healthy assistance in the preservation of standards, ethics, and mores.     

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.     

ENHANCING EVOLUTION AND ENHANCING EVOLUTION

It has been claimed in several places that the new genetic technologies allow humanity to achieve in a generation or two what might take natural selection hundreds of millennia in respect of the elimination of certain diseases and an increase in traits such as intelligence. More radically, it has been suggested that those same technologies could be used to instil characteristics that we might reasonably expect never to appear due to natural selection alone. John Harris, a proponent of this genomic optimism, claims in his book Enhancing Evolution that we not only have it in our power to enhance evolution, but that we also have a duty to do so. In this paper, I claim that Harris' hand is strong but that he overplays it nevertheless. He is correct to dismiss the arguments of the anti‐enhancement lobby and correct to say that enhancement is permissible; but ‘good’ is different from ‘permissible’ and his argument for the goodness of enhancement is less convincing. Moreover, he is simply wrong to claim that it generates a duty to enhance.     

Human organisms begin to exist at fertilization

Eugene Mills has recently argued that human organisms cannot begin to exist at fertilization because the evidence suggests that egg cells persist through fertilization and simply turn into zygotes. He offers two main arguments for this conclusion: that ‘fertilized egg’ commits no conceptual fallacy, and that on the face of it, it looks as though egg cells survive fertilization when the process is watched through a microscope. We refute these arguments and offer several reasons of our own to think that egg cells do not survive fertilization, appealing to various forms of essentialism regarding persons, fission cases, and a detailed discussion of the biological facts relevant to fertilization and genetics. We conclude that it is plausible, therefore, that human organisms begin to exist at fertilization – or, at the very least, that there are grounds for thinking that they existed as zygotes which do not apply to the prior egg cells. While this does not entail that human persons begin to exist at this point, it nevertheless has considerable significance for this latter question.     

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.     

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.     

Social cognition

Social cognition concerns the various psychological processes that enable individuals to take advantage of being part of a social group. Of major importance to social cognition are the various social signals that enable us to learn about the world. Such signals include facial expressions, such as fear and disgust, which warn us of danger, and eye gaze direction, which indicate where interesting things can be found. Such signals are particularly important in infant development. Social referencing, for example, refers to the phenomenon in which infants refer to their mothers' facial expressions to determine whether or not to approach a novel object. We can learn a great deal simply by observing others. Much of this signalling seems to happen automatically and unconsciously on the part of both the sender and the receiver. We can learn to fear a stimulus by observing the response of another, in the absence of awareness of that stimulus. By contrast, learning by instruction, rather than observation, does seem to depend upon awareness of the stimulus, since such learning does not generalize to situations where the stimulus is presented subliminally. Learning by instruction depends upon a meta-cognitive process through which both the sender and the receiver recognize that signals are intended to be signals. An example would be the 'ostensive' signals that indicate that what follows are intentional communications. Infants learn more from signals that they recognize to be instructive. I speculate that it is this ability to recognize and learn from instructions rather than mere observation which permitted that advanced ability to benefit from cultural learning that seems to be unique to the human race.     

Cell Budding from Normal Appearing Epithelia: A Predictor of Colorectal Cancer Metastasis?

Background: Colorectal carcinogenesis is believed to be a multi-stage process that originates with a localized adenoma, which linearly progresses to an intra-mucosal carcinoma, to an invasive lesion, and finally to metastatic cancer. This progression model is supported by tissue culture and animal model studies, but it is difficult to reconcile with several well-established observations, principally among these are that up to 25% of early stage (Stage I/II), node-negative colorectal cancer (CRC) develop distant metastasis, and that circulating CRC cells are undetectable in peripheral blood samples of up to 50% of patients with confirmed metastasis, but more than 30% of patients with no detectable metastasis exhibit such cells. The mechanism responsible for this diverse behavior is unknown, and there are no effective means to identify patients with pending, or who are at high risk for, developing metastatic CRC.Novel findings: Our previous studies of human breast and prostate cancer have shown that cancer invasion arises from the convergence of a tissue injury, the innate immune response to that injury, and the presence of tumor stem cells within tumor capsules at the site of the injury. Focal degeneration of a capsule due to age or disease attracts lymphocyte infiltration that degrades the degenerating capsules resulting in the formation of a focal disruption in the capsule, which selectively favors proliferating or “budding” of the underlying tumor stem cells. Our recent studies suggest that lymphocyte infiltration also triggers metastasis by disrupting the intercellular junctions and surface adhesion molecules within the proliferating cell buds causing their dissociation. Then, lymphocytes and tumor cells are conjoined through membrane fusion to form tumor-lymphocyte chimeras (TLCs) that allows the tumor stem cell to avail itself of the lymphocyte''s natural ability to migrate and breach cell barriers in order to intravasate and to travel to distant organs. Our most recent studies of human CRC have detected nearly identical focal capsule disruptions, lymphocyte infiltration, budding cells, and the formation of TLCs. Our studies have further shown that age- and type-matched node-positive and -negative CRC have a significantly different morphological and immunohistochemical profile and that the majority of lymphatic ducts with disseminated cells are located within the mucosa adjacent to morphologically normal appearing epithelial structures that express a stem cell-related marker.New hypothesis: Based on these findings and the growth patterns of budding cells revealed by double immunohistochemistry, we further hypothesize that metastatic spread is an early event of carcinogenesis and that budding cells overlying focal capsule disruptions represent invasion- and metastasis-initiating cells that follow one of four pathways to progress: (1) to undergo extensive in situ proliferation leading to the formation of tumor nests that subsequently invade the submucosa, (2) to migrate with associated lymphocytes functioning as “seeds” to grow in new sites, (3) to migrate and intravasate into pre-existing vascular structures by forming TLCs, or (4) to intravasate into vascular structures that are generated by the budding cells themselves. We also propose that only node-positive cases harbor stem cells with the potential for multi-lineage differentiation and unique surface markers that permit intravasation.     

Desiccation risk drives the spatial ecology of an invasive anuran (Rhinella marina) in the Australian semi-desert

Some invasive species flourish in places that impose challenges very different from those faced in their native geographic ranges. Cane toads (Rhinella marina) are native to tropical and subtropical habitats of South and Central America, but have colonised extremely arid regions over the course of their Australian invasion. We radio-tracked 44 adult cane toads at a semi-arid invasion front to investigate how this invasive anuran has managed to expand its geographic range into arid areas that lie outside of its native climatic niche. As predicted from their low physiological control over rates of evaporative water loss, toads selected diurnal shelter sites that were consistently cooler and damper (and thus, conferred lower water loss rates) than nearby random sites. Desiccation risk also had a profound influence on rates of daily movement. Under wet conditions, toads that were far from water moved further between shelter sites than did conspecifics that remained close to water, presumably in an attempt to reach permanent water sources. However, this relationship was reversed under dry conditions, such that only toads that were close to permanent water bodies made substantial daily movements. Toads that were far from water bodies also travelled along straighter paths than did conspecifics that generally remained close to water. Thus, behavioural flexibility--in particular, an ability to exploit spatial and temporal heterogeneity in the availability of moist conditions--has allowed this invasive anuran to successfully colonize arid habitats in Australia. This finding illustrates that risk assessment protocols need to recognise that under some circumstances an introduced species may be able to thrive in conditions far removed from any that it experiences in its native range.     

Are insects flower constant because they use search images to find flowers?

Many insects which gather nectar or pollen exhibit flower constancy, a learned fidelity to a particular species of plant. Recent studies suggest that foraging insects may use a perceptual mechanism akin to a search image to detect flowers, in a manner analogous to the way that predators search for prey. This has emerged as an alternative (but not mutually exclusive) explanation for flower constancy to that proposed by Darwin, who suggested that it may result from a limited ability to learning or remember the handling skills appropriate for particular flowers. However, search images are thought to be a mechanism for locating cryptic prey. Plants which are pollinated by animals have evolved brightly coloured flowers to attract the attention of their pollinators. It thus seems implausible to argue that flowers may actually be cryptic. One possible explanation for this apparent contradiction is that flowers are effectively cryptic when viewed against a background which contains many other flowers of similar colour. I present experimental evidence which suggests that a background of flowers of similar colour does reduce foraging efficiency of bumblebees, but that a background of dissimilarly coloured flowers has no effect. This I interpret as evidence that flowers may be cryptic, suggesting that pollinators may indeed use a search image in location of flowers. However, the relative importance of constraints on foragers' abilities to locate flowers versus their abilities to handle them as causes of flower constancy remain to be elucidated.     

Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.     

Mammalian target of rapamycin promotes vincristine resistance through multiple mechanisms independent of maintained glycolytic rate

Deregulation of the phosphoinositide 3-kinase-Akt pathway is a major contributor to oncogenesis and resistance to cancer therapy. Recent work has shown mammalian target of rapamycin (mTOR) to be a major target downstream of Akt that contributes to both transformation and therapeutic resistance. Although inhibitors of Akt are not yet clinically available, rapamycin, a mTOR-specific inhibitor, has long been used as an immunosuppressant, and several rapamycin analogues are now in clinical trials in oncology. Recent data indicate that a mTOR complex phosphorylates Akt, and this complex is insensitive to rapamycin. We show that dominant-negative mTOR diminishes phosphorylation of endogenous Akt and exogenous myristoylated Akt (mAkt), that prolonged exposure to rapamycin also inhibits Akt activation, and that this inhibition is dependent on new protein synthesis. These data suggest that mTOR facilitates Akt activation through mechanisms other than direct phosphorylation. A constitutively active mTOR mutant that fails to enhance Akt phosphorylation nevertheless promotes resistance to multiple antimicrotubule agents, indicating that mTOR also mediates survival independent of Akt. Although Akt- and mTOR-mediated survival has been linked to regulation of cellular metabolism, we also show that survival and metabolic control are separable. The hexokinase inhibitor 5-thioglucose markedly inhibits glycolytic rate but does not diminish vincristine resistance mediated by mAkt or mTOR, and it has only a minor effect on mTOR- or mAkt-mediated resistance to growth factor withdrawal, suggesting that Akt-mTOR-mediated resistance is largely independent of maintenance of glycolytic rate. We conclude that mTOR activity can promote resistance through multiple mechanisms independent of maintained glycolytic rate.