Anecdotal,Historical and Critical Commentaries on Genetics: In the Beginning Was the Worm …

The replicative life span (RLS) of Saccharomyces cerevisiae has been established as a model for the genetic regulation of longevity despite the inherent difficulty of the RLS assay, which requires separation of mother and daughter cells by micromanipulation after every division. Here we present the mother enrichment program (MEP), an inducible genetic system in which mother cells maintain a normal RLS—a median of 36 generations in the diploid MEP strain—while the proliferative potential of daughter cells is eliminated. Thus, the viability of a population over time becomes a function of RLS, and it displays features of a survival curve such as changes in hazard rate with age. We show that viability of mother cells in liquid culture is regulated by SIR2 and FOB1, two opposing regulators of RLS in yeast. We demonstrate that viability curves of these short- and long-lived strains can be easily distinguished from wild type, using a colony formation assay. This provides a simplified screening method for identifying genetic or environmental factors that regulate RLS. Additionally, the MEP can provide a cohort of cells at any stage of their life span for the analysis of age-associated phenotypes. These capabilities effectively remove the hurdles presented by RLS analysis that have hindered S. cerevisiae aging studies since their inception 50 years ago.THE budding yeast Saccharomyces cerevisiae is a popular model system for studying fundamental processes of cellular aging (reviewed in Steinkraus et al. 2008). Analyses over the past 50 years have led to the idea that budding yeast can be used to study three types of cellular aging. Replicative aging describes the division potential of individual cells and relies on the asymmetric cell divisions of budding yeast that yield distinct mother and daughter cells. Replicative life span (RLS) is defined as the number of times an individual cell divides before it undergoes senescence (Mortimer and Johnston 1959). Chronological aging describes the capacity of cells in stationary phase (analogous to G₀ in higher eukaryotes) to maintain viability over time, which is assayed by their ability to reenter the cell cycle when nutrients are reintroduced (Longo et al. 1996). Finally, budding yeast have been used to study clonal senescence, which is analogous to the Hayflick limit imposed on mammalian tissue culture cells and characterized by a finite number of times a population of cells can divide. Although wild-type yeast populations do not senesce, this phenomenon has been observed in mutant strains such as those lacking telomerase components (Lundblad and Szostak 1989; Singer and Gottschling 1994).While genetic screens have been applied to examine clonal and chronological aging (Lundblad and Szostak 1989; Powers et al. 2006; Murakami et al. 2008), they have been limited in their application to studying replicative aging (Kaeberlein and Kennedy 2005; Kaeberlein et al. 2005b). This limitation arises from the arduous nature of isolating replicatively aged yeast cells. The current “gold standard” for isolating aged mother cells is by micromanipulation, where daughter cells are counted and removed after every division (Park et al. 2002). Although micromanipulation is currently the only method capable of accurately measuring RLS in yeast, it is severely constrained by the small number of cells that can be analyzed. Thus, genetic analysis of the regulation of RLS has been limited to a candidate gene approach (reviewed in Steinkraus et al. 2008).True genetic analysis of RLS will require large populations of aged cells. However, there are two confounding issues that make isolation of aged individuals difficult. First, single-cell pedigree analysis has shown that age-associated phenotypes, such as replicative life span potential, segregate asymmetrically between mother and daughter cells, rendering age-associated phenotypes nonheritable (Egilmez and Jazwinski 1989; Kennedy et al. 1994). Thus, daughter cells are generally “reset” to a young state with every generation. Second, when age is measured in terms of cell divisions, an unfractionated population is predominately young. The fraction of the population at an age of n cell divisions is ∼1/2ⁿ. Individual cells that reach the median RLS, which is ∼26 generations for haploid cells of the S288C strain background (Kaeberlein et al. 2005a), represent an insignificant fraction of the total population. In fact, it is unlikely that any cell reaches such an advanced age because nutrient depletion will limit the division potential of the population (Dickinson and Schweizer 1999).As an alternative to micromanipulation, methods were developed to isolate aged cells from liquid cultures (Smeal et al. 1996; Sinclair and Guarente 1997; Chen and Contreras 2007). However, due to the exponential growth of progeny cells, these populations are technically limited to 7–12 generations before nutrient depletion interferes with replicative aging. While sequential rounds of growth and purification are possible, the inability to continuously follow an undisturbed cohort of cells prevents the measurement of RLS by these methods. Instead, purification methods are primarily used for the examination of molecular changes associated with aging cells. Unfortunately, low yields and loss of viability due to purification methods diminish their utility for analyzing phenotypes that affect cells of advanced age. As an alternative to purification from natural populations, a strategy to genetically regulate the replicative capacity of daughter cells and avoid the limits imposed by exponential growth has been described (Jarolim et al. 2004). While this system effectively prevents division of daughter cells, it unintentionally decreases the median RLS of mother cells to four cell divisions, thus restricting its usefulness.Here we describe the development of a novel genetic selection against newborn daughter cells, the “mother enrichment program” (MEP), which restricts the replicative capacity of daughter cells while allowing mother cells to achieve a normal RLS. We demonstrate that upon induction of the selection, the viability of MEP strains growing in liquid culture is determined by the RLS of the initial population of mother cells. MEP cultures therefore allow the comparison of RLS between strains without the need for micromanipulation. Additionally, because MEP cultures are not subject to nutrient limitation, single-step affinity purification of aged cells can be achieved at any point during their life span. Together, these capabilities substantially resolve the technical hurdles that have made replicative aging studies in S. cerevisiae exceptionally challenging.     

Ecological Genetics and the Restoration of Plant Communities: Mix or Match?

We present a conceptual framework for choosing native plant material to be used in restoration projects on the basis of ecological genetics. We evaluate both the likelihood of rapid establishment of plants and the probability of long-term persistence of restored or later successional communities. In addition, we consider the possible harmful effects of restoration projects on nearby ecosystems and their native resident populations. Two attributes of the site to be restored play an important role in determining which genetic source will be most appropriate: (1) degree of disturbance and (2) size of the disturbance. Local plants or plants from environments that “match” the habitat to be restored are best suited to restore sites where degree of disturbance has been low. Hybrids or “mixtures” of genotypes from different sources may provide the best strategy for restoring highly disturbed sites to which local plants are not adapted. Cultivars that have been modified by intentional or inadvertent selection have serious drawbacks. Nevertheless, cultivars may be appropriate when the goal is rapid recovery of small sites that are highly disturbed.     

Opportunism, photoperiodism, and puberty: Different mechanisms or variations on a theme?

There are many parallels between the neural regulation of seasonal breeding in birds and puberty in primates, but most studies of the regulation of puberty in vertebrates involve the use of rodents. The findings from rodent studies are often perceived as being typical of mammals and therefore pertinent to human reproductive biology and in many cases, rodent models have a great deal to offer in terms of an understanding of the regulation of puberty and reproductive biology. However, knowledge available from comparative work perhaps highlights mechanistic similarities that may not exist between rodent and primate systems. In this short review, we highlight some of the advantages of studying avian reproductive biology in this regard. We discuss disparities between rodent puberty and primate puberty, and similarities between primates and birds. Thus, understanding the mechanisms regulating avian puberty and seasonal breeding might in some cases provide greater insight into the mechanistic control of puberty in nonrodent mammals. We also describe in detail the neuroendocrine regulation of reproduction in birds and aim to provoke discussion of the possible roles of thyroid hormones and multiple forms of gonadotropin-releasing hormone in avian and mammalian reproduction.     

The Creativity of Natural Selection? Part I: Darwin,Darwinism, and the Mutationists

This is the first of a two-part essay on the history of debates concerning the creativity of natural selection, from Darwin through the evolutionary synthesis and up to the present. Here I focus on the mid-late nineteenth century to the early twentieth, with special emphasis on early Darwinism and its critics, the self-styled “mutationists.” The second part focuses on the evolutionary synthesis and some of its critics, especially the “neutralists” and “neo-mutationists.” Like Stephen Gould, I consider the creativity of natural selection to be a key component of what has traditionally counted as “Darwinism.” I argue that the creativity of natural selection is best understood in terms of (1) selection initiating evolutionary change, and (2) selection being responsible for the presence of the variation it acts upon, for example by directing the course of variation. I consider the respects in which both of these claims sound non-Darwinian, even though they have long been understood by supporters and critics alike to be virtually constitutive of Darwinism.     

Trainmasters or Easyjet pilots? Historical production,labor organizing,and the Spanish engine drivers’ union

This article presents an analysis of the relationship between historical memory and the emergence and reproduction of a specific model of unionism. I argue that in order to understand the militant particularism of the Spanish engine drivers, we need to look at the historical representations that it is embedded in. Recourse to a generational framework makes possible the sustained presentation of the union as a case of successful workers’ organizing, in spite of evidence to the contrary. The historical ethnographic analysis of SEMAF, the Spanish engine drivers’ union, contributes to the analysis of historical memory within the contemporary anthropology of class. The article contributes to theoretical debates in the anthropology of class by reclaiming Michel Trouillot’s conceptualization of the historical process. Two aspects of Trouillot’s work are singled out: his dynamic understanding of the process of historical production and the corollary formulation of the overlapping capacities in which people participate in it (as agents, actors, and subjects) and his emphasis on the importance of expanding scholarly views of the field of historical production.     

The ‘root-brain’ hypothesis of Charles and Francis Darwin: Revival after more than 125 years

This year celebrates the 200^th aniversary of the birth of Charles Darwin, best known for his theory of evolution summarized in On the Origin of Species. Less well known is that, in the second half of his life, Darwin’s major scientific focus turned towards plants. He wrote several books on plants, the next-to-last of which, The Power of Movement of Plants, published together with his son Francis, opened plants to a new view. Here we amplify the final sentence of this book in which the Darwins proposed that: “It is hardly an exaggeration to say that the tip of the radicle thus endowed [with sensitivity] and having the power of directing the movements of the adjoining parts, acts like the brain of one of the lower animals; the brain being seated within the anterior end of the body, receiving impressions from the sense-organs, and directing the several movements.” This sentence conveys two important messages: first, that the root apex may be considered to be a ‘brain-like’ organ endowed with a sensitivity which controls its navigation through soil; second, that the root apex represents the anterior end of the plant body. In this article, we discuss both these statements.Key words: auxin, cognition, plant neurobiology, plant tropisms, roots, sensory biology, signaling     

Human longevity: Genetics or Lifestyle? It takes two to tango

Healthy aging and longevity in humans are modulated by a lucky combination of genetic and non-genetic factors. Family studies demonstrated that about 25 % of the variation in human longevity is due to genetic factors. The search for genetic and molecular basis of aging has led to the identification of genes correlated with the maintenance of the cell and of its basic metabolism as the main genetic factors affecting the individual variation of the aging phenotype. In addition, studies on calorie restriction and on the variability of genes associated with nutrient-sensing signaling, have shown that ipocaloric diet and/or a genetically efficient metabolism of nutrients, can modulate lifespan by promoting an efficient maintenance of the cell and of the organism. Recently, epigenetic studies have shown that epigenetic modifications, modulated by both genetic background and lifestyle, are very sensitive to the aging process and can either be a biomarker of the quality of aging or influence the rate and the quality of aging.On the whole, current studies are showing that interventions modulating the interaction between genetic background and environment is essential to determine the individual chance to attain longevity.     

Darwin and Mendel: who was the pioneer of genetics?

Although Mendel is now widely recognized as the founder of genetics, historical studies have shown that he did not in fact propose the modern concept of paired characters linked to genes, nor did he formulate the two "Mendelian laws" in the form now given. Furthermore, Mendel was accused of falsifying his data, and Mendelism has been met with scepticism because of its failure to provide scientific explanation for evolution, to furnish a basis for the process of genetic assimilation and to explain the inheritance of acquired characters, graft hybridization and many other facts. Darwin was the first to clearly describe almost all genetical phenomena of fundamental importance, and was the first to present a developmental theory of heredity--Pangenesis, which not only greatly influenced many subsequent theories of inheritance, particularly those of de Vries, Galton, Brooks and Weismann, but also tied all aspects of variation, heredity and development together, provided a mechanism for most of the observable facts, and is supported by increasing evidence. It has also been indicated that Darwin's influence on Mendel, primarily from The Origin, is evident. The word "gene" was derived from "pangen", itself a derivative of "Pangenesis" which Darwin had coined. It seems that Darwin should have been regarded as the pioneer, if not of transmissional genetics, of developmental genetics and molecular genetics.     

Vitamins, phytoplankton and bacteria: symbiosis or scavenging?

The conclusion that over 25% of global primary production dependson direct algal/bacterial symbiosis involving vitamin B₁₂ [Croftet al., (2005) Algae acquire vitamin B₁₂ through a symbioticrelationship with bacteria. Nature, 438, 90–93] is patentlyfalse, for it is based on a misconception of the probable levelof the vitamin B₁₂ requirement in marine pelagic algae. A reviewof the various published attempts at measuring this requirementsuggests that it is likely to be so low that oceanic and coastalconcentrations of the vitamin would usually be sufficient tosustain the populations that occur without the assistance ofdirect algal/bacterial symbiosis. The levels measured are discussedin relation to method (batch or continuous culture) and protocolsused. Requirement values considered by the author to be acceptablerange from 0.1 to 0.3 pM for the vitamin growth saturation constant(K_S) and from 30 to 100 µL algal biomass pmol^–1vitamin for the yield.     

Are second-generation Filipinos ‘becoming’ Asian American or Latino? Historical colonialism,culture and panethnicity

Abstract

This article examines how second-generation Filipinos understand their panethnic identity, given their historical connection with both Asians and Latinos, two of the largest panethnic groups in the USA. While previous studies show panethnicity to be a function of shared political interests or class status, I argue that the cultural residuals of historical colonialism in the Philippines, by both Spain and the USA, shape how Filipinos negotiate panethnic boundaries with Asians and Latinos, albeit in different ways. Filipinos cite the cultural remnants of US colonialism as a reason to racially demarcate themselves from Asians, and they allude to the legacies of Spanish colonialism to blur boundaries with Latinos. While the colonial history of Filipinos is unique, these findings have implications for better understanding racialization in an increasingly multiethnic society – namely, how historical legacies in sending societies interact with new racial contexts to influence panethnic identity development.     

Childhood obesity and sleep: relatives, partners, or both?-a critical perspective on the evidence

In modern life, children are unlikely to obtain sufficient or regular sleep and waking schedules. Inadequate sleep affects the regulation of homeostatic and hormonal systems underlying somatic growth, maturation, and bioenergetics. Therefore, assessments of the obesogenic lifestyle, including as dietary and physical activity, need to be coupled with accurate evaluation of sleep quality and quantity, and coexistence of sleep apnea. Inclusion of sleep as an integral component of research studies on childhood obesity should be done as part of the study planning process. Although parents and health professionals have quantified normal patterns of activities in children, sleep has been almost completely overlooked. As sleep duration in children appears to have declined, reciprocal obesity rates have increased. Also, increases in pediatric obesity rates have markedly increased the risk of obstructive sleep apnea syndrome (OSAS) in children. Obesity and OSAS share common pathways underlying end-organ morbidity, potentially leading to reciprocal amplificatory effects. The relative paucity of data on the topics covered in the perspective below should serve as a major incentive toward future research on these critically important concepts.     

Idebenone and neuroprotection: antioxidant,pro-oxidant,or electron carrier?

Journal of Bioenergetics and Biomembranes - Ubiquinone, commonly called coenzyme Q10 (CoQ), is a lipophilic electron carrier and endogenous antioxidant found in all cellular membranes. In the...     

Clomiphene and hypospadias on a detailed level: Signal or chance?

BACKGROUND: Clomiphene, a drug used to induce ovulation, is chemically related to diethylstilbestrol (DES). DES is associated with vaginal cancer and infertility among daughters and with hypospadias among second-generation male offspring. Because clomiphene has a long half-life and metabolites have been found in feces up to 6 weeks after administration, fetal exposure is possible if the mother took this drug prior to becoming pregnant. METHODS: Case-control analyses were performed to investigate the association between clomiphene exposure and hypospadias. Cases were all male subjects registered in the European Concerted Action on Congenital Anomalies and Twins (EUROCAT) Northern Netherlands registry for congenital anomalies with nonsyndromal hypospadias. Controls were all male children born without hypospadias, including those with chromosomal and monogenic defects. Logistic regression analyses were performed to calculate odds ratios (ORs) and 95% confidence intervals (CIs). RESULTS: Of 392 cases, 7 (1.8%) were exposed to clomiphene compared with 64 of 4538 controls (1.4%). For penoscrotal hypospadias, we found that the OR was significantly increased (6.08; 95% CI, 1.40-26.33); for the mild and moderate forms of hypospadias, the ORs were not increased. CONCLUSIONS: Because penoscrotal hypospadias is rare, the effect is diluted when all forms of hypospadias are studied as a group. Therefore, our study stresses the importance of studying birth defects on as detailed a level as possible. Other studies should be conducted to confirm our findings.