Gene–Environment Interactions at Nucleotide Resolution

Interactions among genes and the environment are a common source of phenotypic variation. To characterize the interplay between genetics and the environment at single nucleotide resolution, we quantified the genetic and environmental interactions of four quantitative trait nucleotides (QTN) that govern yeast sporulation efficiency. We first constructed a panel of strains that together carry all 32 possible combinations of the 4 QTN genotypes in 2 distinct genetic backgrounds. We then measured the sporulation efficiencies of these 32 strains across 8 controlled environments. This dataset shows that variation in sporulation efficiency is shaped largely by genetic and environmental interactions. We find clear examples of QTN:environment, QTN: background, and environment:background interactions. However, we find no QTN:QTN interactions that occur consistently across the entire dataset. Instead, interactions between QTN only occur under specific combinations of environment and genetic background. Thus, what might appear to be a QTN:QTN interaction in one background and environment becomes a more complex QTN:QTN:environment:background interaction when we consider the entire dataset as a whole. As a result, the phenotypic impact of a set of QTN alleles cannot be predicted from genotype alone. Our results instead demonstrate that the effects of QTN and their interactions are inextricably linked both to genetic background and to environmental variation.     

Plant–Environment Interactions in the Low Arctic Torngat Mountains of Labrador

Ecosystems - The eastern Canadian Subarctic and Arctic are experiencing significant environmental change with widespread implications for the people, plants, and animals living there. In this...     

Transgene × Environment Interactions in Genetically Modified Wheat

Background

The introduction of transgenes into plants may cause unintended phenotypic effects which could have an impact on the plant itself and the environment. Little is published in the scientific literature about the interrelation of environmental factors and possible unintended effects in genetically modified (GM) plants.

Methods and Findings

We studied transgenic bread wheat Triticum aestivum lines expressing the wheat Pm3b gene against the fungus powdery mildew Blumeria graminis f.sp. tritici. Four independent offspring pairs, each consisting of a GM line and its corresponding non-GM control line, were grown under different soil nutrient conditions and with and without fungicide treatment in the glasshouse. Furthermore, we performed a field experiment with a similar design to validate our glasshouse results.The transgene increased the resistance to powdery mildew in all environments. However, GM plants reacted sensitive to fungicide spraying in the glasshouse. Without fungicide treatment, in the glasshouse GM lines had increased vegetative biomass and seed number and a twofold yield compared with control lines. In the field these results were reversed. Fertilization generally increased GM/control differences in the glasshouse but not in the field. Two of four GM lines showed up to 56% yield reduction and a 40-fold increase of infection with ergot disease Claviceps purpurea compared with their control lines in the field experiment; one GM line was very similar to its control.

Conclusions

Our results demonstrate that, depending on the insertion event, a particular transgene can have large effects on the entire phenotype of a plant and that these effects can sometimes be reversed when plants are moved from the glasshouse to the field. However, it remains unclear which mechanisms underlie these effects and how they may affect concepts in molecular plant breeding and plant evolutionary ecology.     

Biodynamic Interfaces Are Essential for Human–Environment Interactions

The environment impacts human health in profound ways, yet few theories define the form of the relationship between human physiology and the environment. It is conjectured that such complex systems cannot interact directly, but rather their interaction requires the formation of an intermediary “interface.” This position contrasts with current epidemiological constructs of causation, which implicitly assume that two complex systems transfer information directly while remaining separate entities. Further, it is contended that dynamic, process-based interfaces incorporate components from all the interacting systems but exhibit operational independence. This property has many consequences, the foremost being that characteristics of the interface cannot be fully resolved by only studying the systems involved in the interaction. The interface itself must be the subject of inquiry. Without refocusing the attention on biodynamic interfaces, how the environment impacts health cannot be discerned. Also see the video abstract here https://youtu.be/XeyjeZeyo4o .     

Glucose and Intermediary Metabolism and Astrocyte–Neuron Interactions Following Neonatal Hypoxia–Ischemia in Rat

Neonatal hypoxia–ischemia (HI) and the delayed injury cascade that follows involve excitotoxicity, oxidative stress and mitochondrial failure. The susceptibility to excitotoxicity of the neonatal brain may be related to the capacity of astrocytes for glutamate uptake. Furthermore, the neonatal brain is vulnerable to oxidative stress, and the pentose phosphate pathway (PPP) may be of particular importance for limiting this kind of injury. Also, in the neonatal brain, neurons depend upon de novo synthesis of neurotransmitters via pyruvate carboxylase in astrocytes to increase neurotransmitter pools during normal brain development. Several recent publications describing intermediary brain metabolism following neonatal HI have yielded interesting results: (1) Following HI there is a prolonged depression of mitochondrial metabolism in agreement with emerging evidence of mitochondria as vulnerable targets in the delayed injury cascade. (2) Astrocytes, like neurons, are metabolically impaired following HI, and the degree of astrocytic malfunction may be an indicator of the outcome following hypoxic and hypoxic-ischemic brain injury. (3) Glutamate transfer from neurons to astrocytes is not increased following neonatal HI, which may imply that astrocytes fail to upregulate glutamate uptake in response to the massive glutamate release during HI, thus contributing to excitotoxicity. (4) In the neonatal brain, the activity of the PPP is reduced following HI, which may add to the susceptibility of the neonatal brain to oxidative stress. The present review aims to discuss the metabolic temporal alterations observed in the neonatal brain following HI.     

Ectoparasite Infestations of Hedgehogs (Erinaceus europaeus) are Associated with Small-Scale Landscape Structures in an Urban–Suburban Environment

Animals that exploit heterogeneous and patchy environments encounter different local habitat conditions that influence their interaction with the environment, such as the acquisition of parasites. How and at which scales interaction processes between parasites, hosts, and the environment are realized remains largely unknown. We examined the infestation patterns of 56 hedgehogs (Erinaceus europaeus) with fleas and ticks at a small spatial scale within a 12 km² area along a suburban–urban gradient in southwestern Germany. The structure and type of habitats surrounding hedgehog capture locations were estimated from digital land cover data within radii of 20, 50, and 100 m. These were assumed to match the ranging area and underlying heterogeneous landscape matrix in which host–parasite interactions take place. Landscape-based models suggested that flea burdens significantly decreased with the diversity and heterogeneity of land cover, as well as with the areal coverage of roads within radii of 50 and 100 m. Overall tick infestation levels were mostly explained by the number of arable patches and the areal coverage of roads within radii of 50 and 100 m, as well as date of capture. Examination of the semivariance in model residuals revealed no evident spatial structure in any of the models with flea or tick infestation patterns as response variables. Our results, which are based on a sampling scheme within a relatively small spatio-temporal window, suggest that heterogeneous landscape matrices affect parasitization rates of animals in urban environments, with clear differences at the individual level.     

Changes in and Patterns of Smoking Exposure in an Elderly Urban Population in Beijing: 2001–2010

Objective

The study aims to explore the patterns and changes of active and passive smoking in the elderly population.

Methods

Two cross-sectional surveys with representative samples of urban populations, aged between 60 and 95 years old, were conducted in 2001 and 2010 in Beijing. A current smoker was defined as a person who smoked a tobacco product at the time of the survey, and a passive smoker was defined as a person who had been exposed to smoke exhaled by a smoker for more than 15 minutes per day more than once per week.

Results

A total of 2,277 participants in 2001 and 2,102 participants in 2010 completed the survey. The current smoking prevalence changed slightly in males (24.7 vs. 21.2%, P = 0.081), while the prevalence in females decreased significantly from 8.8% (95% CI: 7.3–10.3%) in 2001 to 4.1% (95% CI: 3.0–5.2%) in 2010 (P<0.001). The prevalence of passive smoking was 30.5% (95% CI: 28.6–32.4%) in 2001 and 30.0% (95% CI: 28.1–32.0%) in 2010. The main source of secondhand smoke switched from a spouse in 2001 to offspring in 2010. This trend was observed in both sexes. Passive smoking in males from a smoking spouse decreased from 5.7% to 2.4% (P<0.001), while that from smoking offspring increased from 7.3 to 14.5% (P<0.001). Passive smoking in females from a spouse decreased from 30.6 to 17.6%, while that from offspring increased from 5.3 to 15.4% (P<0.001).

Conclusion

Offspring became the main source of secondhand smoke for the elderly. Our findings demonstrated the importance of implementing smoking prevention programs, to educate older adults who live with a smoking spouse and/or offspring.     

Dipole–Dipole Interactions in Microtubules

Dimers in microtubules possess a dipole moment with components along three axes. The interaction energy among all dipole components in a microtubule was calculated for an un-deformed and an elliptically deformed microtubule in a dry condition. The interaction energy was found to increase with deformation. The total interaction energy among all dipoles is positive, which implies that the un-deformed cylindrical shape of a microtubule represents a condition of minimum energy. This suggests that the cylindrical shape of microtubules is a consequence of dipole–dipole interactions. There may be other causes as well but these are not discussed in this paper. From these results, the contributions of the dipole–dipole interaction energy to the microtubule longitudinal and transverse flexural rigidities were calculated. It is shown that the longitudinal contribution to the elastic modulus is approximately 50–60% of the total measured value while the calculated transverse contribution is smaller than the longitudinal contribution by a factor of approximately 3. The ratio of the measured axial to the measured transverse flexural rigidity is approximately 125, in agreement with recent observations. However, these values are uncertain for reasons discussed in the text.     

Spatial Dependency of Vegetation–Environment Linkages in an Anthropogenically Influenced Wetland Ecosystem

Management and restoration of vegetation patterns in ecosystems depends on an understanding of allogenic environmental factors that organize species assemblages and autogenic processes linked to assemblages. However, our ability to make strong inferences about vegetation–environment linkages in field studies is often limited due to correlations among environmental variables, spatial autocorrelation, and scale dependency of observations. This is particularly true in large, heterogeneous ecosystems such as the Everglades. Here, an extensive canal-and-levee system has modified historical fire regimes and hydropatterns while contributing large inputs of surface-water phosphorus (P), nitrogen (N) and cations such as sodium (Na). Some of these anthropogenic influences have been implicated as factors leading to the shift of sawgrass (Cladium jamaicense Crantz) and slough communities to an assemblage of weedy species such as cattail (Typha domingensis Pers.). To untangle the independent effect of multiple variables, we used a spatially explicit, multivariate approach to identify linkages among spatial patterns, environmental factors, and vegetation composition along a 10-km gradient of anthropogenic influence in the Everglades, an area immediately downstream from canal inflow structures. Clusters of plots were stratified among three zones (Impacted, Transition, and Reference), a design that allowed us to contrast vegetation–environment linkages and spatial patterns at multiple scales and degrees of ecosystem alteration. Along the 10-km gradient, partial Mantel tests showed that nutrients (phosphorus, nitrogen, and potassium) and hydropattern (frequency of dryness) were independently linked to patterns in fine-scale vegetation composition, but phosphorus was the only environmental variable linked to patterns of coarse-scale composition. Regardless of scale, the effect of distance from canal inflows accounted for variation in vegetation that could not be explained by other variables. A significant residual effect of spatial proximity among sampling locations also was detected and was highly suggestive of dispersal or other spatial determinants of vegetation pattern. However, this pure spatial effect was significantly stronger in the Transition and Impacted zones than in the Reference zone—fine-scale environmental variables explained all of the spatial structure in vegetation in the Reference zone. A further examination of spatial patterns in vegetation by using Mantel correlograms revealed significant heterogeneity at fine, local scales in the Reference zone, but this pattern progressively degraded toward homogeneity among closely neighboring locations in the Impacted zone. However, the fine-scale vegetation pattern in the Reference zone was hierarchically nested at a broader scale and yielded a similar coarse pattern across the landscape, whereas the coarse pattern in the Transition and Impacted zones was relatively heterogeneous and fragmented. Collectively, these results indicate that allogenic spatial and environmental factors related to the canal system have disrupted the coupling between pattern and process by altering fine-scale vegetation–environment linkages and spatial patterns characteristic of the natural Everglades ecosystem.     

Trichoderma–Plant–Pathogen Interactions: Advances in Genetics of Biological Control

Trichoderma spp. are widely used in agriculture as biofungicides. Induction of plant defense and mycoparasitism (killing of one fungus by another) are considered to be the most important mechanisms of Trichoderma-mediated biological control. Understanding these mechanisms at the molecular level would help in developing strains with superior biocontrol properties. In this article, we review our current understanding of the genetics of interactions of Trichoderma with plants and plant pathogens.     

Neuron–Astrocyte Interactions,Pyruvate Carboxylation and the Pentose Phosphate Pathway in the Neonatal Rat Brain

Glucose and acetate metabolism and the synthesis of amino acid neurotransmitters, anaplerosis, glutamate-glutamine cycling and the pentose phosphate pathway (PPP) have been extensively investigated in the adult, but not the neonatal rat brain. To do this, 7 day postnatal (P7) rats were injected with [1-¹³C]glucose and [1,2-¹³C]acetate and sacrificed 5, 10, 15, 30 and 45 min later. Adult rats were injected and sacrificed after 15 min. To analyse pyruvate carboxylation and PPP activity during development, P7 rats received [1,2-¹³C]glucose and were sacrificed 30 min later. Brain extracts were analysed using ¹H- and ¹³C-NMR spectroscopy. Numerous differences in metabolism were found between the neonatal and adult brain. The neonatal brain contained lower levels of glutamate, aspartate and N-acetylaspartate but similar levels of GABA and glutamine per mg tissue. Metabolism of [1-¹³C]glucose at the acetyl CoA stage was reduced much more than that of [1,2-¹³C]acetate. The transfer of glutamate from neurons to astrocytes was much lower while transfer of glutamine from astrocytes to glutamatergic neurons was relatively higher. However, transport of glutamine from astrocytes to GABAergic neurons was lower. Using [1,2-¹³C]glucose it could be shown that despite much lower pyruvate carboxylation, relatively more pyruvate from glycolysis was directed towards anaplerosis than pyruvate dehydrogenation in astrocytes. Moreover, the ratio of PPP/glucose-metabolism was higher. These findings indicate that only the part of the glutamate-glutamine cycle that transfers glutamine from astrocytes to neurons is operating in the neonatal brain and that compared to adults, relatively more glucose is prioritised to PPP and pyruvate carboxylation. Our results may have implications for the capacity to protect the neonatal brain against excitotoxicity and oxidative stress.     

Environment–host–parasite interactions in mass-reared insects

The mass production of insects is rapidly expanding globally, supporting multiple industrial needs. However, parasite infections in insect mass-production systems can lower productivity and can lead to devastating losses. High rearing densities and artificial environmental conditions in mass-rearing facilities affect the insect hosts as well as their parasites. Environmental conditions such as temperature, gases, light, vibration, and ionizing radiation can affect productivity in insect mass-production facilities by altering insect development and susceptibility to parasites. This review explores the recent literature on environment–host–parasite interactions with a specific focus on mass-reared insect species. Understanding these complex interactions offers opportunities to optimise environmental conditions for the prevention of infectious diseases in mass-reared insects.     

Tick–Host–Borrelia Population Interactions: Long-Term Records in Eastern Europe

During 10 spring and summer seasons (1992–2001), the dynamics of the epizootic process in natural foci were studied in taiga forests of the Pre-Ural region, Russia. In these foci, Borrelia garinii, Borrelia afzelii and tick-borne encephalitis (TBE) virus circulate transmitted by their main vector tick, Ixodes persulcatus. Main parameters of the epizootic process were calculated for each season. In three seasons (1993, 1996, and 1999) all parameters characterizing the abundance of unfed nymphs and adult ticks, as well as the prevalence of Borrelia and TBE virus in them, increased sharply and simultaneously. These seasons were preceded by years of population peaks in forest rodents (1992, 1995, and 1998), especially Clethrionomys glareolus voles, the dominant species in the local mammalian fauna. Apparently, the possibility of horizontal transmission of the agents of tick-borne infections sharply increases in such years and this results in the intensification of their dissemination. This revised version was published online in July 2006 with corrections to the Cover Date.     

Use of Bait to Increase Archery Deer Harvest in an Urban–Suburban Landscape

Abstract: Hunting is the primary tool for managing white-tailed deer (Odocoileus virginianus) populations. Effectiveness of hunting in suburban areas may be reduced due to limited hunter access to small properties, firearms-discharge laws, and public safety concerns. In Connecticut, USA, hunting over bait on private land was recently legalized to increase harvest opportunities. Our objective was to assess bow-hunter willingness to use bait and effects of bait type, hunter disturbance, time spent hunting, and property size on deer-harvest potential in a suburban landscape. We mailed a prebaiting survey in February 2002 and a postbaiting survey in February 2004 to the same group of hunters. Hunters using bait were more successful and harvested more deer than hunters using no bait. Hunters using bait on small properties observed similar numbers of deer within shooting range as hunters using bait on larger properties. Hunters using bait met their venison needs, whereas hunters using no bait did not meet their needs. Resource managers should implement strategies that increase hunter success when developing urban deer-management programs for communities.     

RNA Splicing: A New Paradigm in Host–Pathogen Interactions

RNA splicing brings diversity to the eukaryotic proteome. Different spliced variants of a gene may differ in their structure, function, localization, and stability influencing protein stoichiometry and physiological outcomes. Alternate spliced variants of different genes are known to associate with various chronic pathologies including cancer. Emerging evidence suggests precise regulation of splicing as fundamental to normal well-being. In this context, infection-induced alternative splicing has emerged as a new pivot of host function, which pathogenic microbes can alter—directly or indirectly—to tweak the host immune responses against the pathogen. The implications of these findings are vast, and although not explored much in the case of pathogenic infections, we present here examples from splicing mediated regulation of immune responses across a variety of conditions and explore how this fascinating finding brings a new paradigm to host–pathogen interactions.