Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in Africa

A history of Pleistocene population expansion has been inferred from the frequency spectrum of polymorphism in the mitochondrial DNA (mtDNA) of many human populations. Similar patterns are not typically observed for autosomal and X-linked loci. One explanation for this discrepancy is a recent population bottleneck, with different rates of recovery for haploid and autosomal loci as a result of their different effective population sizes. This hypothesis predicts that mitochondrial and Y chromosomal DNA will show a similar skew in the frequency spectrum in populations that have experienced a recent increase in effective population size. We test this hypothesis by resequencing 6.6 kb of noncoding Y chromosomal DNA and 780 basepairs of the mtDNA cytochrome c oxidase subunit III (COIII) gene in 172 males from 5 African populations. Four tests of population expansion are employed for each locus in each population: Fu's Fs statistic, the R(2) statistic, coalescent simulations, and the mismatch distribution. Consistent with previous results, patterns of mtDNA polymorphism better fit a model of constant population size for food-gathering populations and a model of population expansion for food-producing populations. In contrast, none of the tests reveal evidence of Y chromosome growth for either food-gatherers or food-producers. The distinct mtDNA and Y chromosome polymorphism patterns most likely reflect sex-biased demographic processes in the recent history of African populations. We hypothesize that males experienced smaller effective population sizes and/or lower rates of migration during the Bantu expansion, which occurred over the last 5,000 years.     

The Precautionary Principle,Science and Human Health Protection

As technology advances rapidly, so do applications with potential adverse implications on human health. The possible threats include risks that can be substantial, far-reaching and irreversible, and currently available methods of investigation, designed to deal with direct exposure-disease associations, are not always suitable. Growing interest is being paid to health effects that may be the consequence of distal, “upstream” determinants. Considering the complex chain of events that links such determinants with health can be extremely difficult, and exposes severe limitations in science. Thus, there is often a mismatch between what is known and what would be required to inform rational, evidence-based decision making, which is increasingly called for. It has become apparent how production and use of scientific evidence in decision making must be accompanied by precaution, especially in those circumstances, more and more common in recent times, where there is an uncertain possibility that serious health consequences might take place. Several cautionary approaches have been proposed, but the Precautionary Principle (PP) has been the object of especially intense debate in recent years. Developed in the field of environmental health, the PP has been clarified, and has been applied or called for in several instances in public health. Although a unique definition is not available, the principle has been characterised, and criteria for its application have been proposed. However, many questions remain open on general as well as specific issues. In this paper, we address some of the questions that are relevant for the PP to support rational decision making in environment and health and more in general to strengthen its contribution towards human health protection.     

Uracil, contained in DNA, can direct the correction of mispaired nucleotides in human cells

The mismatch correction has been studied in human cells and presented in this paper. In the study the experimental model with half-containing hetroduplex (-1 residue in the polylinker region of lac gene) M13 DNA has been used. M 13 DNA was isolated from human cells 24 hours after transfection and transformed into ung+ and ung- cells of Escherichia coli. The percentage of lac- colonies (formed due to frameshift mutation in the lac gene) was analyzed. The increased percent of lac- mutations after human transfection indicated that DNA-uracil can polarize mismatch correction in human cells.     

Continuity or discontinuity of the life-style in central Italy during the Roman Imperial Age-Early Middle Ages transition: diet, health, and behavior

Dento-alveolar pathologies and alterations (dental wear, caries, abscesses, ante mortem tooth loss (AMTL), calculus, hypoplastic defects, and chipping) and skeletal markers of health (cribra orbitalia and periostitis) were analyzed in two skeletal samples from the necropolises of Quadrella (I-IV c. AD) and Vicenne-Campochiaro (VII c. AD) in the Molise region of central Italy. The aim was to determine if the Roman Imperial Age-Early Middle Ages transition characterized by political, socioeconomic, and cultural transformations affected the biology of these populations, particularly their alimentation and health status. The frequencies of caries and AMTL, similar in the two samples, suggest a high consumption of carbohydrates. The higher levels of heavy wear, calculus, and interproximal chipping in the Vicenne population indicate a greater use of fibrous foods (both meat and others), in line with the dietary model of Germanic peoples. Health conditions do not appear to have been good in either period, as shown by the high frequencies of linear hypoplasia and the presence of cribra orbitalia and periostitis. The diet of the individuals buried with horses of the Vicenne population did not differ from that of the rest of the population, whereas there were evident differences in the use of the teeth for nonmasticatory activities among these individuals. Therefore, from the point of view of alimentation and health status, the profound socioeconomic and cultural transformations during the Late Antiquity-Early Middle Ages transition do not seem to have been translated into a true discontinuity of the two Molisan populations.     

Spring temperature, clutch initiation date and duck nest success: a test of the mismatch hypothesis

1. Increases in average global temperature during the twentieth century have prompted calls for research on the effect of temperature variation on avian population dynamics. Particular attention has been paid to the hypothesis that increased temperatures may affect a species' ability to shift their breeding efforts to match the phenology of their prey, and thus result in reduced reproductive success (the 'mismatch hypothesis'). 2. We used data from a long-term study of breeding ducks to investigate how duck nest success varied with clutch initiation date, and to test whether spring temperature affected this relationship in a manner consistent with the mismatch hypothesis. We modelled five possible functional forms of how nest success might vary with clutch initiation date and spring temperature, and used an information-theoretic approach to determine which model best described the nesting outcomes of five dabbling duck species nesting in Saskatchewan, Canada. 3. Probability of nest success for the five species did not vary strongly with clutch initiation date, and we found evidence consistent with the mismatch hypothesis for one species, northern pintail Anas acuta, although weight of evidence was weak. 4. Overall nest success of all five species was positively associated with spring temperature. These results suggest that increasing spring temperature alone (within the range observed in this study) may not affect nest success in a manner that would result in lower populations of breeding ducks.     

Analysis of interactions between mismatch repair initiation factors and the replication processivity factor PCNA

In eukaryotes, the DNA replication factor PCNA is loaded onto primer-template junctions to act as a processivity factor for DNA polymerases. Genetic and biochemical studies suggest that PCNA also functions in early steps in mismatch repair (MMR) to facilitate the repair of misincorporation errors generated during DNA replication. These studies have shown that PCNA interacts directly with several MMR components, including MSH3, MSH6, MLH1, and EXO1. At present, little is known about how these interactions contribute to the mismatch repair mechanism. The interaction between MLH1 and PCNA is of particular interest because MLH1-PMS1 is thought to act as a matchmaker to signal mismatch recognition to downstream repair events; in addition, PCNA has been hypothesized to act in strand discrimination steps in MMR. Here, we utilized both genetic and surface plasmon resonance techniques to characterize the MLH1-PMS1-PCNA interaction. These analyses enabled us to determine the stability of the complex (K(D) = 300 nM) and to identify residues (572-579) in MLH1 and PCNA (126,128) that appear important to maintain this stability. We favor a model in which PCNA acts as a scaffold for consecutive protein-protein interactions that allow for the coordination of MMR steps.     

The Combined Effect of Hydrophobic Mismatch and Bilayer Local Bending on the Regulation of Mechanosensitive Ion Channels

The hydrophobic mismatch between the lipid bilayer and integral membrane proteins has well-defined effect on mechanosensitive (MS) ion channels. Also, membrane local bending is suggested to modulate MS channel activity. Although a number of studies have already shown the significance of each individual factor, the combined effect of these physical factors on MS channel activity have not been investigated. Here using finite element simulation, we study the combined effect of hydrophobic mismatch and local bending on the archetypal mechanosensitive channel MscL. First we show how the local curvature direction impacts on MS channel modulation. In the case of MscL, we show inward (cytoplasmic) bending can more effectively gate the channel compared to outward bending. Then we indicate that in response to a specific local curvature, MscL inserted in a bilayer with the same hydrophobic length is more expanded in the constriction pore region compared to when there is a protein-lipid hydrophobic mismatch. Interestingly in the presence of a negative mismatch (thicker lipids), MscL constriction pore is more expanded than in the presence of positive mismatch (thinner lipids) in response to an identical membrane curvature. These results were confirmed by a parametric energetic calculation provided for MscL gating. These findings have several biophysical consequences for understanding the function of MS channels in response to two major physical stimuli in mechanobiology, namely hydrophobic mismatch and local membrane curvature.     

Human mismatch repair, drug-induced DNA damage, and secondary cancer

DNA mismatch repair (MMR) is an important replication error avoidance mechanism that prevents mutation. The association of defective MMR with familial and sporadic gastrointestinal and endometrial cancer has been acknowledged for some years. More recently, it has become apparent that MMR defects are common in acute myeloid leukaemia/myelodysplastic syndrome (AML/MDS) that follows successful chemotherapy for a primary malignancy. Therapy-related haematological malignancies are often associated with treatment with alkylating agents. Their frequency is increasing and they now account for at least 10% of all AML cases. There is also evidence for an association between MMR deficient AML/MDS and immunosuppressive treatment with thiopurine drugs. Here we review how MMR interacts with alkylating agent and thiopurine-induced DNA damage and suggest possible ways in which MMR defects may arise in therapy-related AML/MDS.     

Late pleistocene population dynamics: An alternative view

An attempt is made to argue for a more dynamic view of huntergatherer population behavior in place of the largely static one that has been widely accepted. Following a review of how the concept of carrying capacity has been used in both huntergatherer and ecological studies, attention is drawn to the role of stochastic factors in producing fluctuations over time among populations that are small in size. Some of the implications of this alternative view are briefly discussed.Research supported in part by NIH Grant GM 20467-03.This is a revised version of a paper presented at the symposium, Systems and Their Environments, at the Annual Meeting of the American Anthropological Association, 1973, New Orleans.     

Environmental metabolomics: a SWOT analysis (strengths, weaknesses, opportunities, and threats)

Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively explored. This review will use a SWOT analysis model to discuss some of the strengths, weaknesses, opportunities, and threats that are apparent to an investigator venturing into this relatively new field. SWOT has been used extensively in business settings to uncover new outlooks and identify problems that would impede progress. The field of environmental metabolomics provides great opportunities for discovery, and this is recognized by a high level of interest in potential applications. However, understanding the biological consequence of environmental exposures can be confounded by inter- and intra-individual differences. Metabolomic profiles can yield a plethora of data, the interpretation of which is complex and still being evaluated and researched. The development of the field will depend on the availability of technologies for data handling and that permit ready access metabolomic databases. Understanding the relevance of metabolomic endpoints to organism health vs adaptation vs variation is an important step in understanding what constitutes a substantive environmental threat. Metabolomic applications in reproductive research are discussed. Overall, the development of a comprehensive mechanistic-based interpretation of metabolomic changes offers the possibility of providing information that will significantly contribute to the protection of human health and the environment.     

The associations between chronotype,a healthy diet and obesity

Unhealthy diet has been associated with obesity. Evening type has been associated with unhealthier food and nutrient intake that could predict a higher risk of obesity among them as compared to morning type. However, thus far no study has examined the interrelationships between chronotype, a healthy diet and obesity. We examined whether a healthy diet mediates the association between chronotype and obesity and whether chronotype modifies the association between a healthy and obesity. The National FINRISK 2007 Study included 4421 subjects aged 25–74 years. Diet was assessed using a validated food frequency questionnaire. Baltic Sea diet score (BSDS), including nine dietary components, was used as a measure of adherence to a healthy Nordic diet. Weight, height, body fat percentage and waist circumference were measured, and body mass index values were calculated. Chronotype was assessed using a shortened version of Horne and Östberg’s morningness–eveningness questionnaire (MEQ). The sum score calculated from MEQ was either used as a continuous variable or divided into tertiles of which the lowest tertile demonstrated evening preference and the highest tertile demonstrated morning preference. A series of regression analyses were conducted to determine whether the BSDS mediates the association between chronotype and obesity. Likelihood ratio test was used to determine whether chronotype modifies the association between the BSDS and the obesity measures. After testing the interaction, chronotype-stratified analysis for the association between the BSDS and obesity measures was determined by linear regression. Generally, the evening types had lower adherence to the BSDS and were more often smokers (men), physically inactive and had lower perceived health than the other chronotypes (p < 0.05). The poorer health behavior of this group, however, was not manifested in their obesity measures, and no evidence that the BSDS would mediate the association between chronotype and obesity was found (p > 0.05). No evidence that chronotype would modify the association between the BSDS and obesity was found either (p > 0.05).     

Oxidative stress as a mediator of life history trade-offs: mechanisms, measurements and interpretation

The concept of trade-offs is central to our understanding of life-history evolution. The underlying mechanisms, however, have been little studied. Oxidative stress results from a mismatch between the production of damaging reactive oxygen species (ROS) and the organism's capacity to mitigate their damaging effects. Managing oxidative stress is likely to be a major determinant of life histories, as virtually all activities generate ROS. There is a recent burgeoning of interest in how oxidative stress is related to different components of animal performance. The emphasis to date has been on immediate or short-term effects, but there is an increasing realization that oxidative stress will influence life histories over longer time scales. The concept of oxidative stress is currently used somewhat loosely by many ecologists, and the erroneous assumption often made that dietary antioxidants are necessarily the major line of defence against ROS-induced damage. We summarize current knowledge on how oxidative stress occurs and the different methods for measuring it, and highlight where ecologists can be too simplistic in their approach. We critically review the potential role of oxidative stress in mediating life-history trade-offs, and present a framework for formulating appropriate hypotheses and guiding experimental design. We indicate throughout potentially fruitful areas for further research.     

B cell development leads off with a base hit: dU:dG mismatches in class switching and hypermutation

The mechanisms underlying somatic hypermutation (SHM) and class switch recombination (CSR) have been the subject of much debate. Recent studies from the Neuberger and Honjo labs have lent insight into these distinct processes, and we discuss a new, comprehensive model for how AID, uracil DNA glycosylase (UNG) and the mismatch repair system function in both SHM and CSR.     

NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA

NMR studies provide insights into structural features of internal loops. These insights can be combined with thermodynamic studies to generate models for predicting structure and energetics. The tandem mismatch internal loop, 5'GUGG3'(3'CUAC5'), has been studied by NMR. The NMR structure reveals an internal loop with no hydrogen bonding between the loop bases and with the G in the AG mismatch flipped out of the helix. The sequence of this internal loop is highly conserved in rRNA. The loop is located in the large ribosomal subunit and is part of a conserved 58-nt fragment that is the binding domain of ribosomal protein L11. Structural comparisons between variants of this internal loop in crystal structures of the 58-nt domain complexed with L11 protein and of the large ribosomal subunit (LSU) suggest that this thermodynamically destabilizing internal loop is partially preorganized for tertiary interactions and for binding L11. A model for predicting the base pairing and free energy of 2 x 2 nucleotide internal loops with a purine-purine mismatch next to a pyrimidine-pyrimidine mismatch is proposed on the basis of the present NMR structure and previously reported thermodynamics.     

Understanding Land Use, Livelihoods, and Health Transitions among Tibetan Nomads: A Case from Gangga Township, Dingri County, Tibetan Autonomous Region of China

Tibetan nomads in the Tibetan Autonomous Region of China have experienced profound transitions in recent decades with important implications for land use, livelihoods, and health development. The change from being traditional nomads to agropastoralists engaged in permanent agriculture, a sedentary village life (known as “sedentarization”), has been associated with a remarkable change in diet and lifestyle, decline in spatial mobility, increase in food production, and emerging infectious and noncommunicable diseases. The overarching response of the government has been to emphasize infrastructure and technological solutions. The local adaptation strategies of Tibetan nomads through maintaining balanced mobile herding, reindeer husbandry, as well as off-farm labor and trade could address both the cause of environmental degradation and improve the well-being of local people. Drawing on transdisciplinary, preliminary field work in Gangga Township of Dingri County in the foothills of Mt. Everest, we identify pertinent linkages between land use and health, and spatial and temporal mismatch of livelihoods and health care services, in the transition to sedentary village life. We suggest emerging imperatives in Ecohealth to help restore Tibetan livelihoods in transition to a sedentary lifestyle.     

Craniometric variation,genetic theory,and modern human origins

Recent controversies surrounding models of modern human origins have focused on among-group variation, particularly the reconstruction of phylogenetic trees from mitochondrial DNA (mtDNA) and, the dating of population divergence. Problems in tree estimation have been seen as weakening the case for a replacement model and favoring a multiregional evolution model. There has been less discussion of patterns of within-group variation, although the mtDNA evidence has consistently shown the greatest diversity within African populations. Problems of interpretation abound given the numerous factors that can influence within-group variation, including the possibility of earlier divergence, differences in population size, patterns of population expansion, and variation in migration rates. We present a model of within-group phenotypic variation and apply it to a large set of craniometric data representing major Old World geographic regions (57 measurements for 1,159 cases in four regions: Europe, Sub-Saharan Africa, Australasia, and the Far East). The model predicts a linear relationship between variation within populations (the average within-group variance) and variation between populations (the genetic distance of populations to pooled phenotypic means). On a global level this relationship should hold if the long-term effective population sizes of each region are correctly specified. Other potential effects on withingroup variation are accounted for by the model. Comparison of observed and expected variances under the assumption of equal effective sizes for four regions indicates significantly greater within-group variation in Africa and significantly less within-group variation in Europe. These results suggest that the long-term effective population size was greatest in Africa. Closer examination of the model suggests that the long-term African effective size was roughly three times that of any other geographic region. Using these estimates of relative population size, we present a method for analyzing ancient population structure, which provides estimates of ancient migration. This method allows us to reconstruct migration history between geographic regions after adjustment for the effect of genetic drift on interpopulational distances. Our results show a clear isolation of Africa from other regions. We then present a method that allows direct estimation of the ancient migration matrix, thus providing us with information on the actual extent of interregional migration. These methods also provide estimates of time frames necessary to reach genetic equilibrium. The ultimate goal is extracting as much information from present-day patterns of human variation relevannt to issues of human origins. Our results are in agreement with mismatch distribution analysis of mtDNA, and they support a “weak Garden o Eden” model. In this model, modern-day variation can be explained by divergence from an initial source (perhaps Africa) into a number o small isolated populations, followed by later population expansion throughout our species. The major populationn expansions of Homo sapiens during and after the late Pleistocene have had the effect of “freezing” ancient patterns of population structure. While this is not the only possible scenario, we do note the close agreement with ecent analyses of mtDNA mismatch distibutions. © 1994 Wiley-Liss, Inc.     

Mismatches and bubbles in DNA

Single mismatches in the DNA double helix form nucleation sites for bubbles. Although the overall melting temperature of the duplex is affected to different degrees depending on the probe length, the statistical weights of the bubble states around the defect are always strongly affected. Here we show experimentally that a single mismatch has indeed a dramatic effect on the distribution of intermediate (bubble) states in the melting transition of DNA oligomers. For probe lengths in the range 20-40 bases, the mismatch transforms a transition with many intermediates into a nearly two-state transition. One surprising consequence is the existence of a regime where the sensitivity of a mismatch detection assay based on monitoring intermediate states would increase with probe length. Our results provide experimental constraints on how mismatches should be implemented in models of DNA melting, such as the widely used thermodynamic nearest neighbor model, to which we compare our data.     

Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins

Biological membranes are complex and highly cooperative structures. To relate biomembrane structure to their biological function it is often necessary to consider simpler systems. Lipid bilayers composed of one or two lipid species, and with embedded proteins, provide a model system for biological membranes. Here we present a mesoscopic model for lipid bilayers with embedded proteins, which we have studied with the help of the dissipative particle dynamics simulation technique. Because hydrophobic matching is believed to be one of the main physical mechanisms regulating lipid-protein interactions in membranes, we considered proteins of different hydrophobic length (as well as different sizes). We studied the cooperative behavior of the lipid-protein system at mesoscopic time- and lengthscales. In particular, we correlated in a systematic way the protein-induced bilayer perturbation, and the lipid-induced protein tilt, with the hydrophobic mismatch (positive and negative) between the protein hydrophobic length and the pure lipid bilayer hydrophobic thickness. The protein-induced bilayer perturbation was quantified in terms of a coherence length, xi(P), of the lipid bilayer hydrophobic thickness profile around the protein. The dependence on temperature of xi(P), and the protein tilt-angle, were studied above the main-transition temperature of the pure system, i.e., in the fluid phase. We found that xi(P) depends on mismatch, i.e., the higher the mismatch is, the longer xi(P) becomes, at least for positive values of mismatch; a dependence on the protein size appears as well. In the case of large model proteins experiencing extreme mismatch conditions, in the region next to the so-called lipid annulus, there appears an undershooting (or overshooting) region where the bilayer hydrophobic thickness is locally lower (or higher) than in the unperturbed bilayer, depending on whether the protein hydrophobic length is longer (or shorter) than the pure lipid bilayer hydrophobic thickness. Proteins may tilt when embedded in a too-thin bilayer. Our simulation data suggest that, when the embedded protein has a small size, the main mechanism to compensate for a large hydrophobic mismatch is the tilt, whereas large proteins react to negative mismatch by causing an increase of the hydrophobic thickness of the nearby bilayer. Furthermore, for the case of small, peptidelike proteins, we found the same type of functional dependence of the protein tilt-angle on mismatch, as was recently detected by fluorescence spectroscopy measurements.     

Human Health, Well-Being, and Global Ecological Scenarios

This article categorizes four kinds of adverse effects to human health caused by ecosystem change: direct, mediated, modulated, and systems failure. The effects are categorized on their scale, complexity, and lag-time. Some but not all of these can be classified as resulting from reduced ecosystem services. The articles also explores the impacts that different socioeconomic–ecologic scenarios are likely to have on human health and how changes to human health may, in turn, influence the unfolding of four different plausible future scenarios. We provide examples to show that our categorization is a useful taxonomy for understanding the complex relationships between ecosystems and human well-being and for predicting how future ecosystem changes may affect human health.Disclaimer: The views expressed in this article are those of the authors and do not necessarily reflect the position of the World Health Organization. This article has been subjected to EPA review and approved for publication but does not necessarily reflect EPA policy.     

Nutritional psychiatry research: an emerging discipline and its intersection with global urbanization,environmental challenges and the evolutionary mismatch

In 21st-century public health, rapid urbanization and mental health disorders are a growing global concern. The relationship between diet, brain function and the risk of mental disorders has been the subject of intense research in recent years. In this review, we examine some of the potential socioeconomic and environmental challenges detracting from the traditional dietary patterns that might otherwise support positive mental health. In the context of urban expansion, climate change, cultural and technological changes and the global industrialization and ultraprocessing of food, findings related to nutrition and mental health are connected to some of the most pressing issues of our time. The research is also of relevance to matters of biophysiological anthropology. We explore some aspects of a potential evolutionary mismatch between our ancestral past (Paleolithic, Neolithic) and the contemporary nutritional environment. Changes related to dietary acid load, advanced glycation end products and microbiota (via dietary choices and cooking practices) may be of relevance to depression, anxiety and other mental disorders. In particular, the results of emerging studies demonstrate the importance of prenatal and early childhood dietary practices within the developmental origins of health and disease concept. There is still much work to be done before these population studies and their mirrored advances in bench research can provide translation to clinical medicine and public health policy. However, the clear message is that in the midst of a looming global epidemic, we ignore nutrition at our peril.