Oxidative stress, antioxidant defenses, and damage removal, repair, and replacement systems

Oxidative stress is an unavoidable consequence of life in an oxygen-rich atmosphere. Oxygen radicals and other activated oxygen species are generated as by-products of aerobic metabolism and exposure to various natural and synthetic toxicants. The "Oxygen Paradox" is that oxygen is dangerous to the very life-forms for which it has become an essential component of energy production. The first defense against oxygen toxicity is the sharp gradient of oxygen tension, seen in all mammals, from the environmental level of 20% to a tissue concentration of only 3-4% oxygen. These relatively low tissue levels of oxygen prevent most oxidative damage from ever occurring. Cells, tissues, organs, and organisms utilize multiple layers of antioxidant defenses and damage removal, and replacement or repair systems in order to cope with the remaining stress and damage that oxygen engenders. The enzymes comprising many of these protective systems are inducible under conditions of oxidative stress adaptation, in which the expression of over 40 mammalian genes is upregulated. Mitotic cells have the additional defensive ability of entering a transient growth-arrested state (in the first stages of adaptation) in which DNA is protected by histone proteins, energy is conserved by diminished expression of nonessential genes, and the expression of shock and stress proteins is greatly increased. Failure to fully cope with an oxidative stress can switch mitotic cells into a permanent growth-arrested, senescence-like state in which they may survive for long periods. Faced with even more severe oxidative stress, or the declining protective enzymes and adaptive capacity associated with aging, cells may "sacrifice themselves" by apoptosis, which protects surrounding healthy tissue from further damage. Only under the most severe oxidative stress conditions will cells undergo a necrotic death, which exposes surrounding tissues to the further vicissitudes of an inflammatory immune response. This remarkable array of systems for defense; damage removal, replacement, and repair; adaptation; growth modulation; and apoptosis make it possible for us to enjoy life in an oxygen-rich environment.     

Life,information theory,probability, and physics

A purely information-theoretical approach to the problem of self-replication of elementary living units implies that pure chance is the determining factor in the formation of the first living unit. The probability of such a spontaneous formation can be calculated from the minimum amount of information which an organism must possess in order to replicate itself. An estimation of this amount of information is made here by two different methods. First by a “paper and pencil experiment” which indicates the minimum amount of information needed on a printed page in order that with given tools the page could be reproduced. Second—by an analytical consideration of some hypothetical molecular mechanisms. A general method for handling such problems is suggested. On the basis of estimated information contents it is shown that under most favorable conditions the probability of a spontaneous generation by pure chance during the lifetime of the earth is vanishingly small. It is concluded that dynamic factors, which may reduce tremendously the information content, must play a role in the genesis of life on earth.     

Earth, sky, wind, and weather

This paper seeks to understand what it means to live 'in the open'. It begins with an account of experiments that test whether children have acquired a scientifically correct understanding of the shape of the earth, according to which people live all around on the outside of a solid sphere. This understanding cannot accommodate the phenomenon of the sky, in relation to which the earth can appear only as the ground of human habitation. James Gibson's ecological approach to perception offers a possible alternative, depicting earth and sky as complementary hemispheres. Yet for Gibson, this earth-sky can be inhabited only insofar as it is furnished with objects. To that extent, it ceases to be open. Drawing on elements of Merleau-Ponty's phenomenology, it is argued that in the open world persons and things relate not as closed forms but by virtue of their common immersion in the generative fluxes of the medium – in wind and weather. Fundamental to life is the process of respiration, by which organisms continually disrupt any boundary between earth and sky, binding substance and medium together in forging their own growth and movement. Thus to inhabit the open is not to be stranded on the outer surface of the earth but to be caught up in the transformations of the weather-world.     

Homophily,Close Friendship,and Life Satisfaction among Gay,Lesbian, Heterosexual,and Bisexual Men and Women

Friends play important roles throughout our lives by providing expressive, instrumental, and companionate support. We examined sexual orientation, gender, and age differences in the number of friends people can rely on for expressive, instrumental, and companionate support. Additionally, we examined the extent to which people relied on same-gender versus cross-gender friends for these types of support. Participants (N = 25,185) completed a survey via a popular news website. Sexual orientation differences in number of same-gender and cross-gender friends were generally small or non-existent, and satisfaction with friends was equally important to overall life satisfaction for all groups. However, the extent to which people’s friendship patterns demonstrated gender-based homophily varied by sexual orientation, gender, and age. Young adult gay and bisexual men, and to some extent bisexual women and older bisexual men, did not conform to gendered expectations that people affiliate primarily with their own gender.     

Lightness, illumination, and gradients

The illumination interpretation approach claims that lightness illusions can be explained as misapplications of lightness constancy mechanisms, processes which usually enable veridical extraction of surface reflectance from luminance distributions by discounting illumination. In particular, luminance gradients are thought to provide cues about the interactions of light and surfaces. Several examples of strong lightness illusions are discussed for which explanations based on illumination interpretation can be proposed. In criticisms of this approach, a variety of demonstrations of similarly structured control displays are presented, which involve equivalent lightness effects that cannot readily be accounted for by illumination interpretation mechanisms. Furthermore, a number of known and novel displays are presented that demonstrate effects of gradients on the qualitative appearance of uniform regions. Finally, some simple simulations of neural effects of luminance distributions are discussed.     

Neanderthals: Names, Hypotheses, and Scientific Method

The Neanderthal "problem" is less likely to be solved by hypotheses which are broad and inclusive, with respect to late Pleistocene hominids, than by more limited ones for which existing data are suitable and which conform in as many dimensions as possible to evolutionary theory. Specifically, the Brose-Wolpoff hypothesis (1971) fails to use a "population" understanding of Upper Pleistocene hominid variation and argues a universal model of Middle Paleolithic-Upper Paleolithic cultural and physical transition unsuitable for southern Africa or Southeast Asia.     

Metabolomics, pathway regulation, and pathway discovery

Metabolomics is a data-based research strategy, the aims of which are to identify biomarker pictures of metabolic systems and metabolic perturbations and to formulate hypotheses to be tested. It involves the assay by mass spectrometry or NMR of many metabolites present in the biological system investigated. In this minireview, we outline studies in which metabolomics led to useful biomarkers of metabolic processes. We also illustrate how the discovery potential of metabolomics is enhanced by associating it with stable isotopic techniques.     

Programmed longevity,youthspan, and juventology

The identification of conserved genes and pathways that regulate lifespan but also healthspan has resulted in an improved understanding of the link between nutrients, signal transduction proteins, and aging but has also provided evidence for the existence of multiple “longevity programs,” which are selected based on the availability of nutrients. Periodic fasting and other dietary restrictions can promote entry into a long‐lasting longevity program characterized by cellular protection and optimal function but can also activate regenerative processes that lead to rejuvenation, which are independent of the aging rate preceding the restricted period. Thus, a “juventology”‐based strategy can complement the traditional gerontology approach by focusing not on aging but on the longevity program affecting the life history period in which mortality is very low and organisms remain youthful, healthy, and fully functional.     

Myxobacteria, Polarity, and Multicellular Morphogenesis

Myxobacteria are renowned for the ability to sporulate within fruiting bodies whose shapes are species-specific. The capacity to build those multicellular structures arises from the ability of M. xanthus to organize high cell-density swarms, in which the cells tend to be aligned with each other while constantly in motion. The intrinsic polarity of rod-shaped cells lays the foundation, and each cell uses two polar engines for gliding on surfaces. It sprouts retractile type IV pili from the leading cell pole and secretes capsular polysaccharide through nozzles from the trailing pole. Regularly periodic reversal of the gliding direction was found to be required for swarming. Those reversals are generated by a G-protein switch which is driven by a sharply tuned oscillator. Starvation induces fruiting body development, and systematic reductions in the reversal frequency are necessary for the cells to aggregate rather than continue to swarm. Developmental gene expression is regulated by a network that is connected to the suppression of reversals.     

Manipulation,salience, and nudges

Cass Sunstein and Richard Thaler recommend helping people make better decisions by employing ‘nudges’, which they define as noncoercive methods of influencing choice for the better. Not surprisingly, healthcare practitioners and public policy professionals have become interested in whether nudges might be a promising method of improving health‐related behaviors without resorting to heavy‐handed methods such as coercion, deception, or government regulation. Many nudges seem unobjectionable as they merely improve the quality and quantity available for the decision‐maker. However, other nudges influence decision‐making in ways that do not involve providing more and better information. Nudges of this sort raise concerns about manipulation. This paper will focus on noninformational nudges that operate by changing the salience of various options. It will survey two approaches to understanding manipulation, one which sees manipulation as a kind of pressure, and one that sees it as a kind of trickery. On the pressure view, salience nudges do not appear to be manipulative. However, on the trickery view (which the author favors), salience nudges will be manipulative if they increase the salience so that it is disproportionate to that fact's true relevance and importance for the decision at hand. By contrast, salience nudges will not be manipulative if they merely highlight some fact that is true and important for the decision at hand. The paper concludes by providing examples of both manipulative and nonmanipulative salience nudges.     

Mimicry and mutualism in carnivorous pitcher plants (Sarraceniaceae, Nepenthaceae, Cephalotaceae, Bromeliaceae)

The carnivorous pitcher plants of the Sarraceniaceae, Nepenthaceae and Cephalotaceae seem to have developed attraction and rewarding systems which resemble those of many flowers. Contrary to a previous view, Batcsian mimicry does not appear to apply to pitcher traps because: (a) there is no evidence of insects visiting traps by mistake, (b) no model is known for any one of the traps, (c) the duration of the trap activity and the structure of the plant community are not compatible with a deceptive mimetic status, (d) nectar which is a real reward is provided to visiting insects by the pitcher plants. It is suggested that these plants perform mutual rather than deceptive relations with the insect communities in their habitats. Insects benefit from nectar which is provided by pitchers and which serves for their nutrition in habitats where sources of floral nectar might be either uncommon or absent. At the same time the insects pay the plants in a small portion of their community which is 'sacrificed' as prey and consumed by the plants, which grow in nutrient deficient soils.     

Melanins, metals, and mate quality

Many animals display large patches of black or brown color in their integument, which contain melanin pigments and function as important sexually selected indicators of mate quality. To date, however, the particular means by which melanin-based color ornaments are costly to produce and serve as honest advertisements have remained elusive. Here, I propose a novel biochemical mechanism by which melanin-based coloration may serve as a reliable indicator of quality, involving the interplay of metal ions. In animals and other biochemical systems, a series of scarce macro- and microminerals (e.g. Ca, Zn, Cu, Fe) obtained from the diet act as critical regulatory factors in the biosynthesis of eumelanin and phaeomelanin pigments, but can also be toxic to the body when accumulated in high concentrations. As large polymers with many functional (carboxyl) groups, melanin granules also bind these metals and store them in pigmented cells. Thus, by sequestering large deposits of melanin, often in dead tissue (as in hair or feathers), animals may directly reveal dietary access to these rare elements and the physiological protection they have afforded themselves from initially beneficial, but eventually damaging, high mineral concentrations .     

Ferritin,iron homeostasis,and oxidative damage

Ferritin is one of the major proteins of iron metabolism. It is almost ubiquitous and tightly regulated by the metal. Biochemical and structural properties of the ferritins are largely conserved from bacteria to man, although the role in the regulation of iron trafficking varies in the different organisms. Recent studies have clarified some of the major aspects of the reaction between iron and ferritin, which results in the formation of the iron core and production of hydrogen peroxide. The characterization of cellular models in which ferritin expression is modulated has shown that the ferroxidase catalytic site on the H-chain has a central role in regulating iron availability. In turn, this has secondary effects on a number of cellular activities, which include proliferation and resistance to oxidative damage. Moreover, the response to apoptotic stimuli is affected by H-ferritin expression. Altered ferritin L-chain expression has been found in at least two types of genetic disorders, although its role in the determination of the pathology has not been fully clarified. The recent discovery of a new ferritin specific for the mitochondria, which is functionally similar to the H-ferritin, opens new perspectives in the study of the relationships between iron, oxidative damage and free radicals.     

Stress,genomes, and evolution

Evolutionary change, whether in populations of organisms or malignant tumor cells, is contingent on the availability of inherited variation for natural selection to act upon. It is becoming clear that the Hsp90 chaperone, which normally functions to buffer client proteins against the effects of genetic variation, plays a central role in this process. Severe environmental stress can overwhelm the chaperone's buffering capacity, causing previously cryptic genetic variation to be expressed. Recent studies now indicate that in addition to exposing existing variation, Hsp90 can induce novel epigenetic and genetic changes. We discuss key findings that suggest a rich set of pathways by which Hsp90 can mediate the influences of the environment on the genome.     

Bystanders,risks, and consent

This paper considers the moral status of bystanders affected by medical research trials. Recent proposals advocate a very low threshold of permissible risk imposition upon bystanders that is insensitive to the prospective benefits of the trial, in part because we typically lack bystanders' consent. I argue that the correct threshold of permissible risk will be sensitive to the prospective gains of the trial. I further argue that one does not always need a person's consent to expose her to significant risks of even serious harm for the sake of others. That we typically need the consent of participants is explained by the fact that trials risk harmfully using participants, which is very hard to justify without consent. Bystanders, in contrast, are harmed as a side-effect, which is easier to justify. I then consider whether the degree of risk that a trial may impose on a bystander is sensitive to whether she is a prospective beneficiary of that trial.     

Selenium, oxidative stress, and health aspects

Metabolic processes which generate oxidants and antioxidants are governed by genetic disposition as well as environmental factors. Changes in lifestyle, including increased environmental pollution, sun exposure, and dietary habits modify the challenge of the organism by reactive oxygen species. Defense mechanisms are reinforced by increasing dietary intake of antioxidants and micronutrients such as vitamins and selenium (Se). Se deficiency has been recognized to promote some disease states. Epidemiological findings link a lowered Se status to neurodegenerative and cardiovascular diseases as well as to increased cancer risk. While evidence exists to suggest that additional selenocompounds would be beneficial in some health conditions, results from future intervention trials are needed to substantiate the argument for increasing Se intake. Several pieces of the puzzle concerning the molecular mechanisms underlying the reactive oxygen species-triggered disease state and intervention by enzymatic antioxidants have been elucidated. A novel concept of protection of stromal cells against the dominating influence of tumor cells in tumor-stroma interaction by selenocompounds and other antioxidants is presented herein, which may translate into therapeutic strategies in chemoprevention of tumor invasion.     

Radical-driven Fenton reactions: studies with paraquat, adriamycin, and anthraquinone 6-sulfonate and citrate, ATP, ADP, and pyrophosphate iron chelates

Using paraquat, adriamycin, and anthraquinone 6-sulfonate, we have investigated the ability of radical-driven Fenton reactions to oxidize formate or deoxyribose when catalyzed by iron complexed with citrate, ADP, ATP, or pyrophosphate. Radicals were generated either radiolytically or enzymatically with xanthine oxidase or ferredoxin reductase. With each radical source, the citrate, ADP, and ATP complexes were at least 50% as active as Fe(EDTA) at catalyzing deoxyribose oxidation, and slightly less active as catalysts of CO2 formation from formate. Fe(pyrophosphate) was less efficient and in some cases inactive. Although it is not possible to definitively identify the oxidant involved, it behaved more like the hydroxyl radical than the proposed ferryl or peroxoferrous species formed in equivalent reactions catalyzed by nonchelated iron, which can oxidize deoxyribose but not formate. Chelator concentrations of 1-2 mM were required for maximum effect, which implies that the major effect of the chelators is on the reactivity of Fe2+ in the Fenton reaction with H2O2. This also suggests that any iron available physiologically could participate in the Fenton reaction in a nonchelated form, and produce a ferryl species rather than the hydroxyl radical. Reactions of the organic radicals contrast with the equivalent reactions of superoxide (Haber-Weiss reaction) for which the same iron chelates are all very inefficient catalysts. Fenton reactions driven by organic reducing radicals may therefore contribute more to the toxicity of redox cycling compounds than equivalent reactions of superoxide.     

Oligosaccharins, brassinolides, and jasmonates: nontraditional regulators of plant growth, development, and gene expression.

Each of the nontraditional plant hormones reviewed in this article, oligosaccharins, brassinolides, and JA, can exert major effects on plant growth and development. However, in many cases, the mechanisms by which these compounds are involved in the endogenous regulation of morphogenesis remain to be established. Nevertheless, the use of mutant or transgenic plants with altered levels or perception of these hormones is leading to phenomenal increases in our understanding of the roles they play in the life cycle of plants. It is likely that in the future, novel modulators of plant growth and development will be identified; some will perhaps be related to the peptide encoded by ENOD40 (Van de Sande et al., 1996), which modifies the action of auxin.