DIRECT AND CORRELATED RESPONSES TO SELECTION ON AGE AT REPRODUCTION IN DROSOPHILA MELANOGASTER

Aging may be a consequence of mutation accumulation or of negative pleiotropic correlations between performance late and earlier in the lifespan. This study used artificial selection on flies derived from two different base stocks to produce “young” and “old” lines, propagated by breeding from young and old adults respectively. Virgin and mated adults of both sexes from the “old” lines lived longer than “young” line flies. “Young” and “old” mated females did not differ in fecundity or fertility early in the lifespan, but “old” line females had higher fecundity and fertility late in life. The results therefore suggested either that the response to selection had revealed the effect of mutation accumulation, or that pleiotropy involving characters other than early fecundity must have been involved. Development time from egg to adult was longer in the “old” lines. Competition of selected line larvae from one base stock against mutant marked larvae from the same base stock revealed that, at a wide range of larval densities, “old” line larvae showed lower survival rates than “young” line larvae. Thorax length and wet weight were significantly greater in the “old” line flies from one base stock. The results may imply that the selection regime in the “old” lines favored extended growth during development to produce a more durable adult soma, despite the cost in increased larval mortality and delayed reproduction, because the potential reproductive benefits later in life were increased. However, the differences between larvae from “old” and “young” lines could also be attributable to density differences, and this possibility needs systematic investigation.     

Kuhnian revolutions in neuroscience: the role of tool development

The terms “paradigm” and “paradigm shift” originated in “The Structure of Scientific Revolutions” by Thomas Kuhn. A paradigm can be defined as the generally accepted concepts and practices of a field, and a paradigm shift its replacement in a scientific revolution. A paradigm shift results from a crisis caused by anomalies in a paradigm that reduce its usefulness to a field. Claims of paradigm shifts and revolutions are made frequently in the neurosciences. In this article I will consider neuroscience paradigms, and the claim that new tools and techniques rather than crises have driven paradigm shifts. I will argue that tool development has played a minor role in neuroscience revolutions.     

Presence of Old Individuals in a Population Accelerates and Optimizes the Process of Selection: <Emphasis Type="Italic">in silico</Emphasis> Experiments

One of the important components of the concept of aging-phenoptosis (programmed aging) is the notion of aging as an accelerator of evolution having the rank of subconcept. For many reasons, the main being the problematic experimental testing of evolutionary hypotheses, verification of the above-mentioned subconcept can be based primarily on analysis of the internal inconsistency of heuristic models and their correspondence to undisputedly observed facts. To illustrate the acceleration mechanism, and most importantly to structure the evolutionary process in communities that include naturally weakened individuals, V. P. Skulachev offered in 2003 a conceptual model that he later called a “fable about hares”. Despite its simplicity, this model has undoubted internal logic. The natural trend in the development of conceptual models is their translation into the language of mathematics. The purpose of the present work was to create a variation of the known multi-agent model “predator–prey” that would allow us to “see” how the presence in the prey population of naturally weakened (old) members stimulates the selection of individuals with traits whose adaptive potential is not devaluated with age. The model (http://homebear.ru/PD) was developed on the Java platform, version 6, NetBeans development environment 8.2. Statistical analysis and preparation of illustrative materials were carried out using environment R, version 3.4.1. The results of numerical experiments set using our model correspond in principle to the provisions of the heuristic model of Skulachev and, consequently, confirm the absence in it of logical contradictions.     

Evolution of the term “cellular senescence” and its impact on the current cytogerontological research

The term “cellular/cell senescence” was first introduced by Leonard Hayflick to describe the “age-related” changes in normal eukaryotic cells during aging in vitro, i.e., over the exhaustion of their mitotic potential. In the “classic” variant, it was assumed that cells “grow old” with the help of some internal mechanism, which leads to accumulation of various macromolecular defects (DNA damage in the first place). Currently, as a rule, “cellular senescence” means accumulation/appearance of particular “biomarkers of aging” in cells (they are most often transformed cells that do not demonstrate any replicative senescence) under the influence of various external factors (oxidative stress, H₂O₂, mitomycin C, ethanol, ionizing radiation, doxorubicin, etc.) that cause DNA damage. This phenomenon has been called DDR (DNA Damage Response). Among the said biomarkers, there are senescence-associated beta-galactosidase activity, expression of p53 and p21 proteins as well as of proteins involved in the regulation of inflammation, such as IL-6 or IL-8, activation of oncogenes, etc. Thus, “aging/senescence” of cells does not occur simply by itself—it takes place because of the influence of DNA-damaging agents. This approach, in my opinion, despite being very important to define a strategy to fight cancer, distracts us, yet again, from the study of the real mechanisms of aging. It should be emphasized that the “stationary phase aging” model developed in my laboratory also allows registering the occurrence of certain biomarkers of aging in cultured cells, but in this case they arise due to the restriction of their proliferation by contact inhibition, i.e., due to a rather physiological impact, which does not cause any damage to cells by itself (the situation is similar to what we observe in a whole multicellular organism).     

Laboratory evolution of longevity in the bean weevil (Acanthoscelides obtectus)

In this study we examined the effects of long-term selection on early and late reproduction in the bean weevil. The pure lines and the hybrids between the lines within a selection regime were compared for longevity, early and late female fecundity, male mating ability, pre-adult developmental time and wet adult weight. Comparison of hybrid with pure lines provided some evidence for inbreeding despression in the lines from both selection regimes. We found that virgin and mated adults of both sexes from the “old” lines lived longer than “young” line beetles. Comparisons of the hybrid “young” with hybrid “old” lines revealed a trade-off between early and late fecundity of females. For noncompetitive mating ability of males there was no difference between the lines with different rates of senescence when the males were young. But, when the males were older, beetles from the lines selected for delayed senescence expressed superior mating ability. In addition, the “old” line beetles take longer to develop and are heavier than those from “young” line beetles. Although these data suggest that shorter pre-adult developmental time may imply more rapid senescence, there is the possibility of inadvertent selection for rapid development in the “young” lines and this complicates the interpretation of the observed trade-off between the pre-adult and adult performances.     

Transcriptome analysis reveals the difference between “healthy” and “common” aging and their connection with age‐related diseases

A key goal of aging research was to understand mechanisms underlying healthy aging and develop methods to promote the human healthspan. One approach is to identify gene regulations unique to healthy aging compared with aging in the general population (i.e., “common” aging). Here, we leveraged Genotype‐Tissue Expression (GTEx) project data to investigate “healthy” and “common” aging gene expression regulations at a tissue level in humans and their interconnection with diseases. Using GTEx donors' disease annotations, we defined a “healthy” aging cohort for each tissue. We then compared the age‐associated genes derived from this cohort with age‐associated genes from the “common” aging cohort which included all GTEx donors; we also compared the “healthy” and “common” aging gene expressions with various disease‐associated gene expressions to elucidate the relationships among “healthy,” “common” aging and disease. Our analyses showed that 1. GTEx “healthy” and “common” aging shared a large number of gene regulations; 2. Despite the substantial commonality, “healthy” and “common” aging genes also showed distinct function enrichment, and “common” aging genes had a higher enrichment for disease genes; 3. Disease‐associated gene regulations were overall different from aging gene regulations. However, for genes regulated by both, their regulation directions were largely consistent, implying some aging processes could increase the susceptibility to disease development; and 4. Possible protective mechanisms were associated with some “healthy” aging gene regulations. In summary, our work highlights several unique features of GTEx “healthy” aging program. This new knowledge could potentially be used to develop interventions to promote the human healthspan.     

THE EVOLUTION OF PHENOTYPIC CORRELATIONS AND “DEVELOPMENTAL MEMORY”

Development introduces structured correlations among traits that may constrain or bias the distribution of phenotypes produced. Moreover, when suitable heritable variation exists, natural selection may alter such constraints and correlations, affecting the phenotypic variation available to subsequent selection. However, exactly how the distribution of phenotypes produced by complex developmental systems can be shaped by past selective environments is poorly understood. Here we investigate the evolution of a network of recurrent nonlinear ontogenetic interactions, such as a gene regulation network, in various selective scenarios. We find that evolved networks of this type can exhibit several phenomena that are familiar in cognitive learning systems. These include formation of a distributed associative memory that can “store” and “recall” multiple phenotypes that have been selected in the past, recreate complete adult phenotypic patterns accurately from partial or corrupted embryonic phenotypes, and “generalize” (by exploiting evolved developmental modules) to produce new combinations of phenotypic features. We show that these surprising behaviors follow from an equivalence between the action of natural selection on phenotypic correlations and associative learning, well‐understood in the context of neural networks. This helps to explain how development facilitates the evolution of high‐fitness phenotypes and how this ability changes over evolutionary time.     

Ecological theatre and the evolutionary game: how environmental and demographic factors determine payoffs in evolutionary games

In the standard approach to evolutionary games and replicator dynamics, differences in fitness can be interpreted as an excess from the mean Malthusian growth rate in the population. In the underlying reasoning, related to an analysis of “costs” and “benefits”, there is a silent assumption that fitness can be described in some type of units. However, in most cases these units of measure are not explicitly specified. Then the question arises: are these theories testable? How can we measure “benefit” or “cost”? A natural language, useful for describing and justifying comparisons of strategic “cost” versus “benefits”, is the terminology of demography, because the basic events that shape the outcome of natural selection are births and deaths. In this paper, we present the consequences of an explicit analysis of births and deaths in an evolutionary game theoretic framework. We will investigate different types of mortality pressures, their combinations and the possibility of trade-offs between mortality and fertility. We will show that within this new approach it is possible to model how strictly ecological factors such as density dependence and additive background fitness, which seem neutral in classical theory, can affect the outcomes of the game. We consider the example of the Hawk–Dove game, and show that when reformulated in terms of our new approach new details and new biological predictions are produced.     

Microbiota and mitobiota. Putting an equal sign between mitochondria and bacteria

The recent revival of old theories and setting them on modern scientific rails to a large extent are also relevant to mitochondrial science. Given the widespread belief that mitochondria are symbionts of ancient bacterial origin, the processes inherent to mitochondrial physiology can be revised based on their comparative analysis with possible involvement of bacteria. Such comparison combined with discussion of the role of microbiota in pathogenesis allows discussion of the role of “mitobiota” (we introduce this term) as the combination of different phenotypic manifestations of mitochondria in the organism reflecting pathological changes in the mitochondrial genome. When putting an equal sign between mitochondria and bacteria, we find similarity between the mitochondrial and bacterial theories of cancer. The presence of the term “bacterial infection” suggests “mitochondrial infection”, and mitochondrial (oxidative) theory of aging can in some way be transformed into a “bacterial theory of aging”. The possible existence of such processes and the data confirming their presence are discussed in this review. If such a comparison has the right to exist, the homeostasis of “mitobiota” is of not lesser physiological importance than homeostasis of microbiota, which has been so intensively discussed recently.     

Differentiation trees,a junk DNA molecular clock,and the evolution of neoteny in salamanders

Obligate neotenic salamanders die if forced to metamorphose. We suggest that this can be explained by assuming: 1) their “excess” DNA is “junk” DNA; 2) the “adult” specifying portion of the DNA becomes junk DNA and is available for repeated duplication. This suggests a “new” junk DNA molecular clock. We obtain remarkable agreement in “predicting” the amount of DNA per nucleus in present day non-obligate neotene salamanders from this molecular clock. These observatons are consistent with the idea that the development of these animals is describable in terms of differentiation trees whose branches (gene cascades) corresponding to adult somatic tissues accumulate deleterious mutations over evolutionary time. We show that the amount of DNA per nucleus increases linearly with the phylogenetic age of salamander families. The lack of constraints by natural selection, on unused adult branches, may account for the large amount of so-called “junk DNA” in obligate neotenic salamanders. The effects of this excess DNA, via increased cell size, suggest a positive feedback, ecophysiological explanation for such junk DNA: adaptation to cool water environments is enhanced by the lower metabolism associated with more DNA, larger cells and slower developmental time.     

Does Aging Have a Purpose?

Ideas of proponents and opponents of programmed aging concerning the expediency of this phenomenon for the evolution of living organisms are briefly considered. We think that evolution has no “gerontological” purpose, because the obligate restriction of cell proliferation during the development of multicellular organisms is a factor that “automatically” triggers aging due to the accumulation of various macromolecular lesions in cells as a result of the suppression, or even complete cessation of emergence of new, intact cells. This leads to the “dilution” of stochastic damage (the most important of which is DNA damage) at the level of the entire cellular population. Some additional arguments in favor of the inexpediency of aging for both species and individuals are also listed.     

Body size evolution in an old insect order: No evidence for Cope's Rule in spite of fitness benefits of large size

We integrate field data and phylogenetic comparative analyses to investigate causes of body size evolution and stasis in an old insect order: odonates (“dragonflies and damselflies”). Fossil evidence for “Cope's Rule” in odonates is weak or nonexistent since the last major extinction event 65 million years ago, yet selection studies show consistent positive selection for increased body size among adults. In particular, we find that large males in natural populations of the banded demoiselle (Calopteryx splendens) over several generations have consistent fitness benefits both in terms of survival and mating success. Additionally, there was no evidence for stabilizing or conflicting selection between fitness components within the adult life‐stage. This lack of stabilizing selection during the adult life‐stage was independently supported by a literature survey on different male and female fitness components from several odonate species. We did detect several significant body size shifts among extant taxa using comparative methods and a large new molecular phylogeny for odonates. We suggest that the lack of Cope's rule in odonates results from conflicting selection between fitness advantages of large adult size and costs of long larval development. We also discuss competing explanations for body size stasis in this insect group.     

SOLVING THE PARADOX OF STASIS: SQUASHED STABILIZING SELECTION AND THE LIMITS OF DETECTION

Despite the potential for rapid evolution, stasis is commonly observed over geological timescales—the so‐called “paradox of stasis.” This paradox would be resolved if stabilizing selection were common, but stabilizing selection is infrequently detected in natural populations. We hypothesize a simple solution to this apparent disconnect: stabilizing selection is hard to detect empirically once populations have adapted to a fitness peak. To test this hypothesis, we developed an individual‐based model of a population evolving under an invariant stabilizing fitness function. Stabilizing selection on the population was infrequently detected in an “empirical” sampling protocol, because (1) trait variation was low relative to the fitness peak breadth; (2) nonselective deaths masked selection; (3) populations wandered around the fitness peak; and (4) sample sizes were typically too small. Moreover, the addition of negative frequency‐dependent selection further hindered detection by flattening or even dimpling the fitness peak, a phenomenon we term “squashed stabilizing selection.” Our model demonstrates that stabilizing selection provides a plausible resolution to the paradox of stasis despite its infrequent detection in nature. The key reason is that selection “erases its traces”: once populations have adapted to a fitness peak, they are no longer expected to exhibit detectable stabilizing selection.     

Recognition memory for vibrotactile rhythms: An fMRI study in blind and sighted individuals

Calcarine sulcal cortex possibly contributes to semantic recognition memory in early blind (EB). We assessed a recognition memory role using vibrotactile rhythms and a retrieval success paradigm involving learned “old” and “new” rhythms in EB and sighted. EB showed no activation differences in occipital cortex indicating retrieval success but replicated findings of somatosensory processing. Both groups showed retrieval success in primary somatosensory, precuneus, and orbitofrontal cortex. The S1 activity might indicate generic sensory memory processes.     

New data on programmed aging — slow phenoptosis

This review summarizes the latest data on biochemistry and physiology of living organisms. These data suggest that aging, i.e. coordinated age-dependent weakening of many vital functions leading to gradual increase in the probability of dying, is not common to all organisms. Some species have been described whose probability of death does not depend on age or even decreases with age, this being accompanied by constant or increasing fertility. In the case of the naked mole rat (a non-aging mammal), a mechanism has been identified that protects this animal from cancer and the most common age-related diseases. The high molecular weight polysaccharide hyaluronan, a linear polymer composed of multiple repeated disaccharide of glucuronic acid and glucosamine, plays the key role in this mechanism. Hyaluronan is accumulated in the intercellular spaces in the organs and tissues of the naked mole rat. This polysaccharide provides early contact inhibition of cell division (anti-cancer effect). In addition, hyaluronan prevents the development of certain types of apoptosis, in particular, those induced by reactive oxygen species (ROS) (geroprotective effect preventing ROS-induced decrease in cellularity in the organs and tissues of aging organisms). Extraordinary longevity of the naked mole rat (over 30 years, which is long for a rodent the size of a mouse) is connected to its eusocial lifestyle, when only the “queen” and its few “husbands” breed, while the huge army of non-breeding “subordinates” provide the “royal family” with protection from predators, food, and construction and maintenance of an underground labyrinth size of a football field. This way of life removes the pressure of natural selection from the “family” and makes aging — the program that is counterproductive for the individual but increases “evolvability” of its offspring — unnecessary. The example of the naked mole rat demonstrates the optional character of the aging program for the organism. Many facts indicating that aging can be regulated by an organism provide another argument in favor of optionality of aging. Cases have been described when aging as a program useful for the evolution of offspring but counterproductive for the parental individual slows under conditions that threaten the very existence of the individual. These conditions include food restriction (the threat of death from starvation), heavy muscular work, decrease or increase in the environmental temperature, small amounts of poisons (including ROS; here we speak about the paradoxical geroprotective effect of the low doses of prooxidants that inhibit apoptosis). On the other hand, aging can be inhibited (and maybe even cancelled) artificially. This can be done by turning off the genes encoding the proteins participating in the aging program, such as FAT10, p66shc, and some others. In addition, the gene of the antioxidant enzyme catalase can be addressed into mitochondria, where it will split mitochondrial hydrogen peroxide, the level of which increases with age. However, today the simplest way to slow down the aging program is the use of mitochondria-targeted low molecular weight antioxidant compounds of plastoquinonyl decyltriphenylphosphonium-type (SkQ1), which prolong the life of animals, plants, and fungi and inhibit the development of many age-related diseases and symptoms.     

A membrane hypothesis of aging

Experimental data show that cell membranes become more rigid during aging. If this involves a decrease of resting potassium permeability, the intracellular potassium concentration will increase. Such an increase is beneficial for the maintenance of cell excitability, however, it represents a drawback for the nuclear functions, since the intracellular ionic strength may reach values even above 400 mEq kg^?1 cell water, where the chromatin becomes more condensed and the activity of DNA-dependent RNA-polymerase as well as other enzymes probably decreases. This “membrane hypothesis” of aging may explain the decreased protein synthetic activity of old cells, especially of postmitotic ones.X-ray microanalysis has revealed that potassium concentrations significantly increase in the nucleus and cytoplasm of brain and liver cells of old rats. The chromatin of old nerve cells is more condensed than that of the young ones, the rates of nucleolar and nucleoplasmic RNA-synthesis are significantly lower in the old brain cells, and also the number of perichromatin granules decreases with age.A decrease of intracellular potassium content, in brain cells of old rats can be brought about by phytohemagglutinin-P and centrophenoxine. This is accompanied by a sort of rejuvenation: the chromatin becomes decondensed, the rates of nucleolar and nucleoplasmic RNA-synthesis increase together with the number of perichromatin granules, the medium life-span and the learning capacity of the animals increase. These experimental results support the “membrane hypothesis” of aging.     

LABORATORY EVOLUTION OF LIFE-HISTORY TRAITS IN THE BEAN WEEVIL (ACANTHOSCELIDES OBTECTUS): THE EFFECTS OF SELECTION ON DEVELOPMENTAL TIME IN POPULATIONS WITH DIFFERENT PREVIOUS HISTORY

In this study we examined the direct and correlated responses for fast and slow preadult development time in three laboratory populations of the bean weevil (Acanthoscelides obtectus). The first population (“base,” B) has experienced laboratory conditions for more than 10 years; the second (“young,” Y) and the third (“old,” O) populations were selected for early and late reproduction, respectively, before the onset of the present experiments. All three populations are successfully selected for both fast and slow preadult development. The realized heritabilities are very similar in all populations, suggesting a similar level of the additive genetic variance for preadult development. We studied the correlated responses on the following life-history traits: egg-to-adult viability, wet body weight, early fecundity, late fecundity, total realized female fecundity, and adult longevity. All life-history traits examined here, except for the egg-to-adult viability, are affected by selection for preadult development in at least in one of the studied populations. In all three populations, beetles selected for slow preadult development are heavier and live longer than those from the fast-selected lines. The findings with respect to adult longevity are unexpected, because the control Y and O populations, selected for short- and long-lived beetles, respectively, do not show significant differences in preadult development. Thus, our results indicate that some kind of asymmetrical correlated responses occur for preadult development and adult longevity each time that direct selection has been imposed on one or the other of these two traits. In contrast to studies with Drosophila, it appears that for insect species that are aphagous as adults, selection for preadult development entails selection for alleles that also change the adult longevity, but that age-specific selection (applied in the Y and O populations) mostly affects the alleles that have no significant influence on the preadult development. Implications of these findings on the developmental and evolutionary theories of aging are also discussed.     

Growth and senescence of antibody-forming cells

Studies were performed on the capacity of mice for hemagglutinating antibody production throughout their life-span. An in vivo culture method was used for assessment of primary and secondary antibody-forming potentials of spleen cells of mice ranging in age from 1 to 130 weeks. There was a marked growth of potential for antibody formation during neonatal and juvenile life followed by a gradual decline in potential with advancing age. It was possible to show that the changes in potential were principally due to changes in the number of competent progenitor cells and not to changes in their performance. Death of very old animals was correlated with decline in number of immunologically competent progenitor cells. The decay in number of progenitor cells during aging of mice was random. Loss of progenitor cells was not entirely attributable to either generative failure of the pool of progenitor cells or the capacity of the milieu of the animal to support such cells. Thus, spleen cells from aged animals displayed increasing capacity for primary antibody formation during a 3-week period of culture in young, irradiated mice; identical cultures in old, irradiated recipients failed in respect to growth of primary antibody-forming potential. Progressive imparirment of the milieu of aging animals was suggested by the fact that spleen cells from very old animals were “toxic” when infused into lightly irradiated recipients which were themselves of advanced age but far short of the senescent phase of their life-span. These results lead to the argument that senescence may be, to a major degree, the result of progressive loss of progenitor, or “stem,” cells which are normally utilized to replace terminally differentiated, dying cells.     

Trends in biotechnology: Sustainable technology development: From high tech to Eco Tech

Biotechnology as a multidisciplinary and transdisciplinary field of science and engineering is regarded to be a key technology for the future, able to essentially contribute to sustainable development. In the first part of this paper, a critical analysis of the status quo in biotechnologies is given in the area of pharmaceutical, agricultural, environmental, and industrial biotechnology as well as food biotechnology. Here the general potential becomes clear, but also a series of disadvantages which are partly the result of the existing paradigm in science and technology and partly in direct connection to bioprocessing itself. Nevertheless, these biotechnologies will contribute to sustainable development, but mainly in a shallow sense of survival and livelihood. In the second part of this paper, another new dimension in bioprocessing is elucidated, which is in agreement with the new ecological, holistic world view. Here the so-called “eco-principles” are derived from a systems analysis of the ecosphere and represent the intelligence of nature as the result of evolution. The eco-principles will serve as guidelines for the general eco-restructuring of technology, being a drastic change within the next 2–5 decades. For the applying of eco-principles, a quantitative measure for sustainability in technology was developed (“sustainable process index”), which will enable us to design the new technology paradigm called “Eco Tech”. Ecological security and social equity, together with economic efficiency will define sustainable technology development in a deeper sense. Following this route, a completely new dimension of biotechnology will be reached, where the technosphere is fully embedded into the natural cycles of the ecosphere on a local basis.