Genetic and environmental influences on human responses to odors

Olfaction, the sense of smell, has many important functions in humans. Human responses to odors show substantial individual variation. Olfactory receptor genes have been identified and other genes may also influence olfaction. However, the proportion of phenotypic variation in odor response due to genetic variation remains largely unknown. Little is also known about which genes modify specific responses to odors. This study aimed to elucidate genetic and environmental influences on human responses to odors. Individuals from Finnish families (n=146) and Australian (n=413), British (n=163), Danish (n=336), and Finnish (n=399) twins rated intensity and pleasantness of a set of 12 (families) or 6 (twins) odors and tried to identify the odors. In addition, the participants rated their own sense of smell and annoyance experienced with different environmental odors. The odor stimuli of a commercial smell test (The Brief Smell Identification Test; banana, chocolate, cinnamon, gasoline, lemon, onion, paint thinner, pineapple, rose, smoke, soap, and turpentine) were presented in the family study. Based on the results of the family study and a literature survey, a new set of odor stimuli (androstenone, chocolate, cinnamon, isovaleric acid, lemon, and turpentine) was designed for the twin studies. In the family sample, heritabilities of the traits were estimated and underlying genomic regions were searched using a genome-wide linkage scan. In the pooled twin sample, variation in the measured traits was decomposed into genetic and environmental components using quantitative genetic modeling. In addition, associations between nongenetic factors (e.g., sex, age, and smoking) and olfactory-related traits were explored. Suggestive evidence for a genetic linkage for pleasantness of cinnamon at a locus on chromosome 4q32.3 emerged from the family sample. High heritability for the pleasantness of cinnamon was found in the family but not the twin study. Heritability of perceived intensity of androstenone odor was determined to be ~30% in the twin sample. A strong genetic correlation between perceived intensity and pleasantness of androstenone, in the absence of any environmental correlation, indicated that only the genetic correlation explained the phenotypic correlation between the traits (r=-0.27) and that the traits were influenced by an overlapping set of genes. Self-rated olfactory function appeared to reflect the odor annoyance experienced rather than actual olfactory acuity or genetic involvement. Results from nongenetic analyses supported the speculated superiority of females' olfactory abilities, the age-related diminishing of olfactory acuity, and the influences of experience-dependent factors on odor responses. This was the first study to estimate heritabilities and perform linkage screens for individual odors. A genetic effect was detected for only a few responses to specific odors, suggesting the predominance of environmental effects in odor perceptions.

Variation in the hindgut microbial communities of the Florida manatee, Trichechus manatus latirostris over winter in Crystal River, Florida

The Florida manatee, Trichechus manatus latirostris, is a hindgut-fermenting herbivore. In winter, manatees migrate to warm water overwintering sites where they undergo dietary shifts and may suffer from cold-induced stress. Given these seasonally induced changes in diet, the present study aimed to examine variation in the hindgut bacterial communities of wild manatees overwintering at Crystal River, west Florida. Faeces were sampled from 36 manatees of known sex and body size in early winter when manatees were newly arrived and then in mid-winter and late winter when diet had probably changed and environmental stress may have increased. Concentrations of faecal cortisol metabolite, an indicator of a stress response, were measured by enzyme immunoassay. Using 454-pyrosequencing, 2027 bacterial operational taxonomic units were identified in manatee faeces following amplicon pyrosequencing of the 16S rRNA gene V3/V4 region. Classified sequences were assigned to eight previously described bacterial phyla; only 0.36% of sequences could not be classified to phylum level. Five core phyla were identified in all samples. The majority (96.8%) of sequences were classified as Firmicutes (77.3 ± 11.1% of total sequences) or Bacteroidetes (19.5 ± 10.6%). Alpha-diversity measures trended towards higher diversity of hindgut microbiota in manatees in mid-winter compared to early and late winter. Beta-diversity measures, analysed through permanova, also indicated significant differences in bacterial communities based on the season.

A physiological framework to explain genetic and environmental regulation of tillering in sorghum

Tillering determines the plant size of sorghum (Sorghum bicolor) and an understanding of its regulation is important to match genotypes to prevalent growing conditions in target production environments. The aim of this study was to determine the physiological and environmental regulation of variability in tillering among sorghum genotypes, and to develop a framework for this regulation. * Diverse sorghum genotypes were grown in three experiments with contrasting temperature, radiation and plant density to create variation in tillering. Data on phenology, tillering, and leaf and plant size were collected. A carbohydrate supply/demand (S/D) index that incorporated environmental and genotypic parameters was developed to represent the effects of assimilate availability on tillering. Genotypic differences in tillering not explained by this index were defined as propensity to tiller (PTT) and probably represented hormonal effects. * Genotypic variation in tillering was associated with differences in leaf width, stem diameter and PTT. The S/D index captured most of the environmental effects on tillering and PTT most of the genotypic effects. * A framework that captures genetic and environmental regulation of tillering through assimilate availability and PTT was developed, and provides a basis for the development of a model that connects genetic control of tillering to its phenotypic consequences.

Effects of environmental variation on ecological and evolutionary dynamics

Environmental variation is a fact of life for all the species on earth: for any population of any particular species, the local environmental conditions are liable to vary in both time and space. In today's world, anthropogenic activity is causing habitat loss and fragmentation for many species, which may profoundly alter the characteristics of environmental variation in remaining habitat. Previous research indicates that, as habitat is lost, the spatial configuration of remaining habitat will increasingly affect the dynamics by which populations are governed. Through the use of mathematical models, this thesis asks how environmental variation interacts with species properties to influence population dynamics, local adaptation, and dispersal evolution. More specifically, we couple continuous-time continuous-space stochastic population dynamic models to landscape models. We manipulate environmental variation via parameters such as mean patch size, patch density, and patch longevity. Among other findings, we show that a mixture of high and low quality habitat is commonly better for a population than uniformly mediocre habitat. This conclusion is justified by purely ecological arguments, yet the positive effects of landscape heterogeneity may be enhanced further by local adaptation, and by the evolution of short-ranged dispersal. The predicted evolutionary responses to environmental variation are complex, however, since they involve numerous conflicting factors. We discuss why the species that have high levels of local adaptation within their ranges may not be the same species that benefit from local adaptation during range expansion. We show how habitat loss can lead to either increased or decreased selection for dispersal depending on the type of habitat and the manner in which it is lost. To study the models, we develop a recent analytical method, Perturbation expansion, to enable the incorporation of environmental variation. Within this context, we use two methods to address evolutionary dynamics: Adaptive dynamics, which assumes mutations occur infrequently so that the ecological and evolutionary timescales can be separated, and via Genotype distributions, which assume mutations are more frequent. The two approaches generally lead to similar predictions yet, exceptionally, we show how the evolutionary response of dispersal behaviour to habitat turnover may qualitatively depend on the mutation rate.

Association between molecular variation in the phosphoglucose isomerase (Pgi) locus and migration propensity in the Glanville fritillary butterfly

Habitat fragmentation produces patches of suitable habitat surrounded by unfavourable matrix habitat. A species may persist in such a fragmented landscape in an equilibrium between the extinctions and recolonizations of local populations, thus forming a metapopulation. Migration between local populations is necessary for the long-term persistence of a metapopulation. The Glanville fritillary butterfly (Melitaea cinxia) forms a metapopulation in the Åland islands in Finland. There is migration between the populations, the extent of which is affected by several environmental factors and variation in the phenotype of individual butterflies. Different allelic forms of the glycolytic enzyme phosphoglucose isomerase (Pgi) has been identified as a possible genetic factor influencing flight performance and migration rate in this species. The frequency of a certain Pgi allele, Pgi-f, follows the same pattern in relation to population age and connectivity as migration propensity. Furthermore, variation in flight metabolic performance, which is likely to affect migration propensity, has been linked to genetic variation in Pgi or a closely linked locus. The aim of this study was to investigate the association between Pgi genotype and the migration propensity in the Glanville fritillary both at the individual and population levels using a statistical modelling approach. A mark-release-recapture (MRR) study was conducted in a habitat patch network of M. cinxia in Åland to collect data on the movements of individual butterflies. Larval samples from the study area were also collected for population level examinations. Each butterfly and larva was genotyped at the Pgi locus. The MRR data was parameterised with two mathematical models of migration: the Virtual Migration Model (VM) and the spatially explicit diffusion model. VM model predicted and observed numbers of emigrants from populations with high and low frequencies of Pgi-f were compared. Posterior predictive data sets were simulated based on the parameters of the diffusion model. Lack-of-fit of observed values to the model predicted values of several descriptors of movements were detected, and the effect of Pgi genotype on the deviations was assessed by randomizations including the genotype information. This study revealed a possible difference in the effect of Pgi genotype on migration propensity between the two sexes in the Glanville fritillary. The females with and males without the Pgi-f allele moved more between habitat patches, which is probably related to differences in the function of flight in the two sexes. Females may use their high flight capacity to migrate between habitat patches to find suitable oviposition sites, whereas males may use it to acquire mates by keeping a territory and fighting off other intruding males, possibly causing them to emigrate. The results were consistent across different movement descriptors and at the individual and population levels. The effect of Pgi is likely to be dependent on the structure of the landscape and the prevailing environmental conditions.

Sensitivity of wetland methane emissions to model assumptions: application and model testing against site observations

Abstract. Methane emissions from natural wetlands and rice paddies constitute a large proportion of atmospheric methane, but the magnitude and year-to-year variation of these methane sources is still unpredictable. Here we describe and evaluate the integration of a methane biogeochemical model (CLM4Me; Riley et al., 2011) into the Community Land Model 4.0 (CLM4CN) in order to better explain spatial and temporal variations in methane emissions. We test new functions for soil pH and redox potential that impact microbial methane production in soils. We also constrain aerenchyma in plants in always-inundated areas in order to better represent wetland vegetation. Satellite inundated fraction is explicitly prescribed in the model because there are large differences between simulated fractional inundation and satellite observations. A rice paddy module is also incorporated into the model, where the fraction of land used for rice production is explicitly prescribed. The model is evaluated at the site level with vegetation cover and water table prescribed from measurements. Explicit site level evaluations of simulated methane emissions are quite different than evaluating the grid cell averaged emissions against available measurements. Using a baseline set of parameter values, our model-estimated average global wetland emissions for the period 1993–2004 were 256 Tg CH4 yr−1, and rice paddy emissions in the year 2000 were 42 Tg CH4 yr−1. Tropical wetlands contributed 201 Tg CH4 yr−1, or 78 % of the global wetland flux. Northern latitude (>50 N) systems contributed 12 Tg CH4 yr−1. We expect this latter number may be an underestimate due to the low high-latitude inundated area captured by satellites and unrealistically low high-latitude productivity and soil carbon predicted by CLM4. Sensitivity analysis showed a large range (150–346 Tg CH4 yr−1) in predicted global methane emissions. The large range was sensitive to: (1) the amount of methane transported through aerenchyma, (2) soil pH (± 100 Tg CH4 yr−1), and (3) redox inhibition (± 45 Tg CH4 yr−1).

Novel signal demodulation technique to estimate the amount of chirp in fiber Bragg gratings

A novel detection technique to estimate the amount of chirp in fiber Bragg gratings (FBGs) is proposed. This method is based on the fact that reflectivity at central wavelength of FBG reflection changes with strain/temperature gradient (linear chirp) applied to the same. Transfer matrix approach was used to vary different grating parameters (length, strength and apodization) to optimize variation of reflectivity with linear chirp. Analysis is done for different sets of `FBG length-refractive index strength' combinations for which reflectivity vary linearly with linear chirp over a decent measurement range. This article acts as a guideline to choose appropriate grating parameters in designing sensing apparatus based on change in reflectivity at central wavelength of FBG reflection.

Dynamic properties of sand from dry to fully saturated states

By using bender and extender elements test, the velocities of the primary and shear waves, V(P) and V(s) respectively, were measured for a sandy material by gradually varying the degree of saturation, S(r), between the dry and fully saturated states. The effect on the results of varying the relative density and effective confining pressure was also studied. The measurements clearly reveal that for a certain optimum S(r), which is around 0.7-0.9% for the chosen sand, the value of the shear modulus G reaches a maximum value, whereas the corresponding Poisson's ratio nu attains a minimum value. The values of the shear modulus corresponding to S(r) approximate to 0% and S(r) = 100% tend towards the same value. For values of Skempton's B parameter greater than 0.99, the values of V(P) and nu rise very sharply to those of water. The predictions from Biot's theory with respect to the variation of V(P) with S(r) match well with the measured experimental data.

Numerical Investigation on Laminar Flow Due to Sudden Expansion Using Nanofluids

Laminar two-dimensional sudden expansion flow of different nanofluids is studied numerically. The governing equations are solved using stream function-vorticity method. The effect of volume fraction of the nanoparticles and type of nanoparticles on flow behaviour is examined and found significant impact. The flow response to Reynolds number in the presence of nanoparticles is examined. The presence of nanoparticles decreases the flow bifurcation Reynolds number. The size and the reattachment length of the bottom wall recirculation increase with increasing volume fraction and particle density. The effect of volume fraction and density of nanoparticles on friction factor is reported. The bottom wall recirculation strongly respond to the variation in volume faction and type of particles. However, weak response is observed for top wall recirculation.

A Stochastic Chemical Dynamic Approach to Correlate Autoimmunity and Optimal Vitamin-D Range

Motivated by several recent experimental observations that vitamin-D could interact with antigen presenting cells (APCs) and T-lymphocyte cells (T-cells) to promote and to regulate different stages of immune response, we developed a coarse grained but general kinetic model in an attempt to capture the role of vitamin-D in immunomodulatory responses. Our kinetic model, developed using the ideas of chemical network theory, leads to a system of nine coupled equations that we solve both by direct and by stochastic (Gillespie) methods. Both the analyses consistently provide detail information on the dependence of immune response to the variation of critical rate parameters. We find that although vitamin-D plays a negligible role in the initial immune response, it exerts a profound influence in the long term, especially in helping the system to achieve a new, stable steady state. The study explores the role of vitamin-D in preserving an observed bistability in the phase diagram (spanned by system parameters) of immune regulation, thus allowing the response to tolerate a wide range of pathogenic stimulation which could help in resisting autoimmune diseases. We also study how vitamin-D affects the time dependent population of dendritic cells that connect between innate and adaptive immune responses. Variations in dose dependent response of anti-inflammatory and pro-inflammatory T-cell populations to vitamin-D correlate well with recent experimental results. Our kinetic model allows for an estimation of the range of optimum level of vitamin-D required for smooth functioning of the immune system and for control of both hyper-regulation and inflammation. Most importantly, the present study reveals that an overdose or toxic level of vitamin-D or any steroid analogue could give rise to too large a tolerant response, leading to an inefficacy in adaptive immune function.

Second-to-Fourth Digit Ratio Has a Non-Monotonic Impact on Altruism

Gene-culture co-evolution emphasizes the joint role of culture and genes for the emergence of altruistic and cooperative behaviors and behavioral genetics provides estimates of their relative importance. However, these approaches cannot assess which biological traits determine altruism or how. We analyze the association between altruism in adults and the exposure to prenatal sex hormones, using the second-to-fourth digit ratio. We find an inverted U-shaped relation for left and right hands, which is very consistent for men and less systematic for women. Subjects with both high and low digit ratios give less than individuals with intermediate digit ratios. We repeat the exercise with the same subjects seven months later and find a similar association, even though subjects' behavior differs the second time they play the game. We then construct proxies of the median digit ratio in the population (using more than 1000 different subjects), show that subjects' altruism decreases with the distance of their ratio to these proxies. These results provide direct evidence that prenatal events contribute to the variation of altruistic behavior and that the exposure to fetal hormones is one of the relevant biological factors. In addition, the findings suggest that there might be an optimal level of exposure to these hormones from social perspective.

A surface energy model and application to mechanical behavior analysis of single crystals at sub-micron scale

Size effects of mechanical behaviors of materials are referred to the variation of the mechanical behavior due to the sample sizes changing from macroscale to micro-/nanoscales. At the micro-/nanoscale, since sample has a relatively high specific surface area (SSA) (ratio of surface area to volume), the surface although it is often neglected at the macroscale, becomes prominent in governing the energy effect, although it is often neglected at the macroscale, becomes prominent in governing the mechanical behavior. In the present research, a continuum model considering the surface energy effect is developed through introducing the surface energy to total potential energy. Simultaneously, a corresponding finite element method is developed. The model is used to analyze the axial equilibrium strain problem for a Cu nanowire at the external loading-free state. As another application of the model, from dimensional analysis, the size effects of uniform compression tests on the microscale cylinder specimens for Ni and Au single crystals are analyzed and compared with experiments in literatures. (C) 2009 Elsevier B.V. All rights reserved.

Spontaneous and stimulated light emission due to radiative recombination in forward biased lead telluride P-N junctions

Since the discovery in 1962 of laser action in semiconductor diodes made from GaAs, the study of spontaneous and stimulated light emission from semiconductors has become an exciting new field of semiconductor physics and quantum electronics combined. Included in the limited number of direct-gap semiconductor materials suitable for laser action are the members of the lead salt family, i.e . PbS, PbSe and PbTe. The material used for the experiments described herein is PbTe . The semiconductor PbTe is a narrow band- gap material (E_g = 0.19 electron volt at a temperature of 4.2°K). Therefore, the radiative recombination of electron-hole pairs between the conduction and valence bands produces photons whose wavelength is in the infrared (λ ≈ 6.5 microns in air).

The p-n junction diode is a convenient device in which the spontaneous and stimulated emission of light can be achieved via current flow in the forward-bias direction. Consequently, the experimental devices consist of a group of PbTe p-n junction diodes made from p –type single crystal bulk material. The p - n junctions were formed by an n-type vapor- phase diffusion perpendicular to the (100) plane, with a junction depth of approximately 75 microns. Opposite ends of the diode structure were cleaved to give parallel reflectors, thereby forming the Fabry-Perot cavity needed for a laser oscillator. Since the emission of light originates from the recombination of injected current carriers, the nature of the radiation depends on the injection mechanism.

The total intensity of the light emitted from the PbTe diodes was observed over a current range of three to four orders of magnitude. At the low current levels, the light intensity data were correlated with data obtained on the electrical characteristics of the diodes. In the low current region (region A), the light intensity, current-voltage and capacitance-voltage data are consistent with the model for photon-assisted tunneling. As the current is increased, the light intensity data indicate the occurrence of a change in the current injection mechanism from photon-assisted tunneling (region A) to thermionic emission (region B). With the further increase of the injection level, the photon-field due to light emission in the diode builds up to the point where stimulated emission (oscillation) occurs. The threshold current at which oscillation begins marks the beginning of a region (region C) where the total light intensity increases very rapidly with the increase in current. This rapid increase in intensity is accompanied by an increase in the number of narrow-band oscillating modes. As the photon density in the cavity continues to increase with the injection level, the intensity gradually enters a region of linear dependence on current (region D), i.e. a region of constant (differential) quantum efficiency.

Data obtained from measurements of the stimulated-mode light-intensity profile and the far-field diffraction pattern (both in the direction perpendicular to the junction-plane) indicate that the active region of high gain (i.e. the region where a population inversion exists) extends to approximately a diffusion length on both sides of the junction. The data also indicate that the confinement of the oscillating modes within the diode cavity is due to a variation in the real part of the dielectric constant, caused by the gain in the medium. A value of τ ≈ 10^-9 second for the minority- carrier recombination lifetime (at a diode temperature of 20.4°K) is obtained from the above measurements. This value for τ is consistent with other data obtained independently for PbTe crystals.

Data on the threshold current for stimulated emission (for a diode temperature of 20. 4°K) as a function of the reciprocal cavity length were obtained. These data yield a value of J’_th = (400 ± 80) amp/cm² for the threshold current in the limit of an infinitely long diode-cavity. A value of α = (30 ± 15) cm^-1 is obtained for the total (bulk) cavity loss constant, in general agreement with independent measurements of free- carrier absorption in PbTe. In addition, the data provide a value of n_s ≈ 10% for the internal spontaneous quantum efficiency. The above value for n_s yields values of t_b ≈ τ ≈ 10^-9 second and t_s ≈ 10^-8 second for the nonradiative and the spontaneous (radiative) lifetimes, respectively.

The external quantum efficiency (n_d) for stimulated emission from diode J-2 (at 20.4° K) was calculated by using the total light intensity vs. diode current data, plus accepted values for the material parameters of the mercury- doped germanium detector used for the measurements. The resulting value is n_d ≈ 10%-20% for emission from both ends of the cavity. The corresponding radiative power output (at λ = 6.5 micron) is 120-240 milliwatts for a diode current of 6 amps.

A Comparison of the SNP Variation in the Calcification PMCA Gene of Lottia gigantea between a Santa Barbara Population and a More Acidic Monterey Bay Population

As the atmospheric levels of CO2 rise from human activity, the carbonic acid levels of the ocean increase, causing ocean acidification. This increase in acidity breaks down the calcified bodies that many marine organisms depend upon. Upwelling regions such as Monterey Bay in California have pH levels that are not expected to reach the open ocean for a few decades. This study reviews one of the common intertidal animals of the California coast, the Owl Limpet Lottia gigantea, and its genetic variation of the plasma membrane Ca2+ ATPase (PMCA) in relation to the acidity of its environment. The PMCA protein functions in the calcification process of many organisms. Specifically in limpets, this gene functions to form its protective shell. Single-nucleotide polymorphisms (SNPs) were found among five sections of the gene to determine variation between the acidic environment population in Monterey, California and the non-acidic environment population in Santa Barbara, California. While some variation was determined, the Monterey Bay and Santa Barbara Lottia gigantea populations are not significantly distinct at the PMCA gene. Sections B, C, and D were found to be linked. Only one location in Section B was found to have an amino acid change within an exon. Section A has the strongest connection to the sampling location. Monterey individuals were seen to be more genetically recognizable, while Santa Barbara individuals showed slightly more variation. Understanding the trends of ocean acidification, upwelling region activities, and population genetics will assist in determining how the ocean environment will behave in the future.

Genetic variation between outer-coastal and fjord populations of Pacific herring (Clupea pallasii) in the eastern Gulf of Alaska

Pacific herring (Clupea pallasii) from the Gulf of Alaska were screened for temporal and spatial genetic variation with 15 microsatellite loci. Thirteen collections were examined in this study: 11 from Southeast Alaska and 2 from Prince William Sound, Alaska. Although FST values were low, a neighbor-joining tree based on genetic distance, homogeneity, and FST values revealed that collectively, the Berners Bay and Lynn Canal (interior) collections were genetically distinct from Sitka Sound and Prince of Wales Island (outer-coastal) collections. Temporal genetic variation within regions (among three years of Berners Bay spawners and between the two Sitka Sound spawners) was zero, whereas 0.05% was attributable to genetic variation between Berners Bay and Sitka Sound. This divergence may be attributable to environmental differences between interior archipelago waters and outer-coast habitats, such as differences in temperature and salinity. Early spring collections of nonspawning Lynn Canal herring were nearly genetically identical to collections of spawning herring in Berners Bay two months later—an indication that Berners Bay spawners over-winter in Lynn Canal. Southeast Alaskan herring (collectively) were significantly different from those in Prince William Sound. This study illustrates that adequate sample size is needed to detect variation in pelagic fish species with a large effective population size, and microsatellite markers may be useful in detecting low-level genetic divergence in Pacific herring in the Gulf of Alaska.