Evaluation of two methods for assessing gene-environment interactions using data from the Danish case-control study of facial clefts

BACKGROUND: Epidemiological investigations have begun to consider gene-environment (GE) interactions as potential risk factors for many diseases, including several different birth defects. However, traditional methodological approaches for the analysis of case-control data tend to have low power for detection of interaction effects. A log-linear approach that can impose the assumption that the genotype and exposure of interest occur independently in the population has been proposed as a potentially more powerful method for assessing GE interactions but has not been widely applied in the published literature. METHODS: The present analyses were undertaken to compare the results obtained when stratified analyses and a log-linear approach were used to assess potential GE interactions. The analyses were conducted using data from a population-based, case-control study conducted in Denmark and considered associations between nonsyndromic cleft lip with or without cleft palate (CL+/-P), infant genotype for variants of RAR-alpha, TGF-alpha, TGF-beta3, and MSX1, and maternal exposure to smoking, alcohol, and multivitamins. RESULTS: Neither the stratified nor the log-linear analyses provided evidence that that risk of CL+/-P is influenced by any of the GE interactions that were evaluated, despite the potential increase in power offered by the latter approach. Further, the analyses highlight concerns regarding the power to reject the assumption of independence of the genetic and environmental factor of interest in the controls and related concerns regarding the validity of results obtained using the log-linear approach when the underlying assumption is violated. CONCLUSIONS: The potential increase in power offered by the log-linear approach is offset by concerns regarding the validity of this approach when the independence assumption is violated.     

Relationships of microclimatic variables to colonization of rose debris by Botrytis cinerea and the biocontrol agent Clonostachys rosea

Biological control of Botrytis cinerea by Clonostachys rosea is an alternative to chemical control of rose Botrytis blight in greenhouses. Environmental conditions affect the colonization of senescing and dead tissues by both fungi. The contribution of microclimatic variables to debris colonization/sporulation by both fungi was estimated by path coefficient analysis. We monitored daily values of: maximum, average, and minimum temperatures (T _max, T _ave, and T _min), and relative humidity (RH_max, RH_ave, and RH_min); accumulated rainfall; vapour pressure deficit average; hours with RH?>?90% (RH₉₀); and average temperature during RH₉₀ (T _ave90). Association of variables accumulated between the first and seventh day before sampling explained colonization/sporulation variation: R ²=0.81–0.86 for B. cinerea and 0.91–0.96 for C. rosea. RH_max and RH₉₀ were the main factors that directly favoured colonization/sporulation of both fungi. Colonization/sporulation negatively correlated with RH_min, T _min, and T _ave for B. cinerea and T _min, T _ave, and T _ave90 for C. rosea. The antagonist can suppress B. cinerea colonization/sporulation on rose debris under a wide range of environmental conditions.     

Time-concentration-mortality response of potato tuber moth pupae to the biocontrol agent Cordyceps tenuipes

ABSTRACT

The potato tuber moth (PTM) Phthorimaea operculella is a critical potato pest. Larvae infest both foliage and tubers and mature larvae pupate in the soil or other safe places. Cordyceps tenuipes, an entomopathogenic fungus, infect lepidopteran pupae. To determine the effectiveness of this fungus as a biocontrol agent for PTM, we evaluated the time-concentration-mortality (TCM) response of PTM pupae to C. tenuipes using the following bioassays: (1) direct immersion in conidial suspensions, (2) incubation in sterilised or (3) unsterilised soilpremixed with conidia, and (4) incubation in unsterilised soil drenched with conidial suspensions to simulate field conditions. Fungal infection caused 100%, 83.3%, 73.3%, and 85.0% mortality of PTM pupae in assays 1–4, respectively. At 10⁸ conidia/mL or conidia/g concentration, assays 1 and 4 had short lethal times (LT₅₀) of 2.2 and 2.6 days compared with 3.7 and 4.8 days for assays 2 and 3, respectively. On day 7 after inoculation, assays 1 and 4 also had low lethal concentrations (LC₅₀) of 1.69 × 10³ conidia/mL and 1.10 × 10⁵ conidia/g compared with those of assays 2 and 3, which showed low virulence, with LC₅₀ of 3.50 × 10⁵ and 3.60 × 10⁶ conidia/mL, respectively. Our results demonstrate that C. tenuipes is a promising candidate for PTM biocontrol at the pupal stage. Drenching the soil surface with conidial suspensions may be the most effective method of field application.     

Effects of experimental warming on fungal disease progress in oilseed rape

Global warming will influence the growth and development of both crops and pathogens. The aims of this study were to investigate potential effects of future warming on oilseed rape growth and the epidemiology of the three economically important pathogens Verticillium longisporum, Sclerotinia sclerotiorum, and Leptosphaeria maculans (anamorph: Phoma lingam). We utilized climate chambers and a soil warming facility, where treatments represented regional warming scenarios for Lower Saxony, Germany, by 2050 and 2100, and compared results of both approaches on a thermal time scale by calculating degree‐days (dd) from day of sowing, December 1st and March 1st until sampling, the latter correlating best with disease progress. Regression analysis showed that plant growth and growth stages in spring responded almost linearly to increasing thermal time until 1000–1500 dd. Colonization of plant tissue by V. longisporum showed an exponential increase when exceeding 1300–1500 dd and reaching plant growth stage BBCH 74/75 (pod development). V. longisporum colonization of plants may be advanced, potentially leading to higher inoculum densities after harvest and increased economic importance of this pathogen under future warming. Sclerotia germination of S. sclerotiorum reached its maximum at 600–900 dd. Advance of these critical degree‐days may lead to earlier apothecia production, potentially advancing the infection window, whereas the future importance of S. sclerotiorum may remain constant. Severity of phoma crown canker increased linearly with increasing thermal time, but showed also large variation in response to the warming scenarios, suggesting that factors such as canopy microclimate in fall or leaf shedding over winter may play a bigger role for L. maculans infection and disease severity than higher soil temperatures. Thermal time was a suitable tool to combine and integrate data on biological responses to soil and air temperature increases from climate chamber and field experiments.     

Effectiveness of honey bees in delivering the biocontrol agent Bacillus subtilis to blueberry flowers to suppress mummy berry disease

Honey bees are important pollinators of commercial blueberries in the southeastern United States, and blueberry producers often use supplemental bees to achieve adequate fruit set. However, honey bees also vector the plant pathogenic fungus Monilinia vaccinii-corymbosi which infects open blueberry flowers through the gynoecial pathway causing mummy berry disease. Here, we report the results of a 3-year field study to test the hypothesis that using bee hives equipped with dispensers containing the biocontrol product Serenade, a commercial formulation of the bacterium Bacillus subtilis which has shown activity against flower infection by M. vaccinii-corymbosi in laboratory experiments, can reduce mummy berry disease incidence when honey bees are used as pollinators in blueberries. Individual honey bees carried 5.1–6.4 × 10⁵ colony-forming units (CFU) of B. subtilis when exiting hive-mounted dispensers with Serenade. On caged rabbiteye blueberry bushes in the field, population densities of B. subtilis vectored by honey bees reached a carrying capacity of <10³ CFU per flower stigma within 2 days of exposure, and there was a highly significant non-linear relationship between B. subtilis populations per stigma and bee activity, expressed as number of legitimate flower visits per time interval per cage (R = 0.6928, P < 0.0001, n = 32). Honey bee density (1600 or 6400 individuals per 5.8-m³ cage) and Serenade treatment (presence or absence of the product in hive-mounted dispensers) significantly (P < 0.05) affected the incidence of fruit mummification on caged bushes, whereby increasing bee density increased disease incidence and application of Serenade reduced disease levels. Taken together, results of this study suggest that use of a hive-dispersed biocontrol product such as Serenade as a supplement during pollination can reduce the risk of mummy berry disease. This may be a prudent practice that optimizes the benefits to pollination of high bee densities while reducing the associated disease-vectoring risk.     

Use of green fluorescent protein-based reporters to monitor balanced production of antifungal compounds in the biocontrol agent Pseudomonas fluorescens CHA0

AIMS: To develop reporter constructs based on stable and unstable variants of the green fluorescent protein (GFP) for monitoring balanced production of antifungal compounds that are crucial for the capacity of the root-colonizing Pseudomonas fluorescens strain CHA0 to control plant diseases caused by soil-borne pathogenic fungi. METHODS AND RESULTS: Pseudomonas fluorescens CHA0 produces the three antifungal metabolites 2,4-diacetylphloroglucinol (DAPG), pyoluteorin (PLT) and pyrrolnitrin (PRN). The gfp[mut3] and gfp[AAV] reporter genes were fused to the promoter regions of the DAPG, PLT and PRN biosynthetic genes. The reporter fusions were then used to follow the kinetics of expression of the three antifungal metabolites in a microplate assay. DAPG and PLT were found to display an inverse relationship in which each metabolite activates its own biosynthesis while repressing the synthesis of the other metabolite. PRN appears not to be involved in this balance. However, the microbial and plant phenolic metabolite salicylate was found to interfere with the expression of both DAPG and PLT. CONCLUSIONS: The results obtained provide evidence that P. fluorescens CHA0 may keep the antifungal compounds DAPG and PLT at a fine-tuned balance that can be affected by certain microbial and plant phenolics. SIGNIFICANCE AND IMPACT OF THE STUDY: To our knowledge, the present study is the first to use stable and unstable GFP variants to study antibiotic gene expression in a biocontrol pseudomonad. The developed reporter fusions will be a highly valuable tool to study in situ expression of this bacterial biocontrol trait on plant roots, i.e. at the site of pathogen suppression.     

The effects of hatching asynchrony on growth and mortality patterns in Eurasian Hoopoe Upupa epops nestlings

Growth is a fundamental life history trait in all organisms and is closely related to individual fitness. In altricial birds, growth of many traits is restricted to the short period between hatching and fledging and strongly depends on the amount of food that parents deliver and the extent of hatching asynchrony. However, empirical studies of energy allocation to growth of different body size traits as a function of hatching asynchrony are scarce. We studied growth and mortality of Eurasian Hoopoe Upupa epops, a species with a long breeding season and high brood size variance, whose nestlings show pronounced hatching asynchrony, in order to test how hatching asynchrony affects different growth traits in the context of territory quality, season and brood size. The growth of five body traits (body mass, and lengths of tarsus, third primary, bill and longest crest feather) was investigated to understand how it was affected by brood size, hatching date and order, and territory quality. In total, 241 nestlings from 39 nests were measured every 4 days in 2014 in south‐western Switzerland. Brood size, hatching date and hatching order had the strongest influence on growth trajectories, although tarsus growth was only marginally affected by these variables. Nestlings that hatched earlier than their siblings were heavier and had longer third primaries, bills and crest feathers compared with later‐hatched siblings. In territories of high quality, hatching order differences disappeared for body mass growth, but persisted for lengths of third primary, bill and crest feathers. Brood size was inversely associated with third primary, bill and crest feather lengths, but positively associated with body mass. Nestling mortality was higher in later‐hatched nestlings and in broods that were raised in territories of lower quality. Our study shows that in nestlings, energy was allocated differentially between body traits and this allocation interacted with hatching order and territory quality. Rapid mass gain by nestlings was prioritized in order to increase competitive ability. Our results provide support for the brood reduction hypothesis as an explanation of hatching asynchrony in Hoopoes.     

Effects of the biocontrol agent Bacillus amyloliquefaciens SN16‐1 on the rhizosphere bacterial community and growth of tomato

Fusarium oxysporum is a common soil‐borne pathogen that causes serious economic losses in tomato crops worldwide. The purpose of this study was to evaluate the influence of the bio‐control agents Bacillus amyloliquefaciens SN16‐1 and Pseudomonas fluorescens SN15‐2 and the pathogen Fusarium oxysporum f.sp. lycopersici (FOL) inoculation on tomato rhizosphere bacterial communities and growth, as measured by terminal restriction fragment length polymorphism (T‐RFLP). Treatment with SN16‐1 and SN15‐2 had a transient influence on indigenous bacterial communities, withSN16‐1 showing great potential for controlling FOL. The corresponding genera of terminal restriction fragments (T‐RFs) that were significantly altered after 10 days were obtained using Ribosomal Database Project (RDP) database comparison. Genera that produce antibiotics and promote plant growth were activated by SN16‐1 and FOL treatments, indicating that SN16‐1 responds quickly to FOL invasion. Moreover, the bioremediation activity characteristic of certain genera and the levels of enzymes that degrade pathogen cell walls were decreased while bacterial nutrient cycling and plant growth promotion were enhanced with FOL treatment. In conclusion, we found that SN16‐1 possesses the capacity to control tomato wilt, acts synergistically with soil microbes and does not have a persistent effect on the rhizosphere bacterial communities of tomato.     

Infectious disease in animal metapopulations: the importance of environmental transmission

Motivated by an array of infectious diseases that threaten wildlife populations, a simple metapopulation model (subpopulations connected by animal movement) is developed, which allows for both movement-based and environmental transmission. The model demonstrates that for a range of plausible parameterizations of environmental transmission, increased movement rate of animals between discrete habitats can lead to a decrease in the overall proportion of sites that are occupied. This can limit the ability of the rescue effect to ensure locally extinct populations become recolonized and can drive metapopulations down in size so that extinction by mechanisms other than disease may become more likely. It further highlights that, in the context of environmental transmission, the environmental persistence time of pathogens and the probability of acquiring infection by environmental transmission can affect host metapopulations both qualitatively and quantitatively. Additional spillover sources of infection from alternate reservoir hosts are also included in the model and a synthesis of all three types of transmission, acting alone or in combination, is performed revealing that movement-based transmission is the only necessary condition for a decline in the proportion of occupied sites with increasing movement rate, but that the presence of other types of transmission can reverse this qualitative result. By including the previously neglected role of environmental transmission, this work contributes to the general discussion of when dispersal by wild animals is beneficial or detrimental to populations experiencing infectious disease.     

A laboratory study of the effects of shelter availability and invasive crayfish on the growth of native stream fish

1. The alteration of stream habitats by urbanisation reduces the availability of shelter. Reduced shelter availability may increase both predation risks and metabolic costs, negatively affecting the growth performance of stream fish. Although urbanised streams often allow the establishment of invasive species, the additive or interactive effects of shelter availability and invasive species are rarely explored. The invasive red swamp crayfish (Procambarus clarkii) is a strong shelter competitor and predator in streams. 2. We conducted a stream‐channel experiment to investigate how shelter availability and this invasive crayfish species affect the growth performance (measured as the loss in body mass under starved conditions) of two native benthic species, Japanese crucian carp (Carassius auratus complex) and an endangered cobitid fish (Lefua echigonia). 3. We found that both the absence of shelter and the presence of crayfish increased body mass loss in the crucian carp. However, the growth performance of the crucian carp was improved by the presence of shelter except in the presence of crayfish, in which case the shelter available did not ameliorate the negative effect of the crayfish on growth performance (i.e. an interactive effect). This result suggests that crayfish may affect the growth performance of the crucian carp through chemical cues as well as through shelter occupancy. 4. In contrast, shelter availability is the primary factor affecting the body mass loss of the cobitid fish. However, the growth performance of these fish was unaffected by the presence of crayfish. The change in the growth performance of the cobitid fish in response to the absence of shelter was greater than that of the crucian carp. This finding suggests that the cobitid fish may be more vulnerable than the crucian carp to a reduction in shelter availability. 5. Our study demonstrates that reduced shelter availability and/or crayfish invasion can have significant, indirect negative effects on the growth performance of native fish, but whether those effects are interactive might vary depending on the species. Our findings have clear implications for stream restoration and habitat assessment.     

Using life‐history information to assess potential effects of shrimp trawling on small fishes

The current study presents information on size distributions, size at recruitment to the fishery, size at maturity and patterns of reproduction for several small benthic fishes caught as by‐catch in the southern Gulf of California (Mexico) shrimp trawl fishery: sand perch Diplectrum spp., lumptail searobin Prionotus stephanophrys, bigscale goatfish Pseudupeneus grandisquamis and silver stardrum Stellifer illecebrosus. Pseudupeneus grandisquamis, P. stephanophrys and S. illecebrosus populations were all sexually dimorphic in size. Total‐length (L_T)‐based analyses did not provide reliable information on survival and growth. The majority of sampled P. grandisquamis and S. illecebrosus were caught before reproductive maturity, whereas the majority of Diplectrum spp. and almost all P. stephanophrys were mature when caught. L_T at 50% gear retention (L_Tc, mm) v. 50% maturity (L_Tm, mm): Diplectrum spp. 124·53 v. 131·43; P. grandisquamis 90·98 v. 135·20; S. illecebrosus 82·55 v. 137·30. L_Tc for P. stephanophrys was 104·73, but L_Tm could not be modelled for this species as almost all captured individuals were mature. Diplectrum spp., P. grandisquamis and S. illecebrosus were indeterminate spawners, whereas P. stephanophrys appeared to be a determinate spawner. Sex ratios were equal for each of the gonochoristic species. In general, the gonado‐somatic index (I_G) increased with increasing L_T for all except P. stephanophrys, where I_G decreased with increasing L_T for both males and females. Mature individuals of all taxa were found throughout the sampling period (September to March), and I_G increased with sample day for all except females of P. grandisquamis. The current data suggest the potential for fishery effects on sampled populations of P. grandisquamis and S. illecebrosus.     

Opposing effects of allogrooming on disease transmission in ant societies

To prevent epidemics, insect societies have evolved collective disease defences that are highly effective at curing exposed individuals and limiting disease transmission to healthy group members. Grooming is an important sanitary behaviour—either performed towards oneself (self-grooming) or towards others (allogrooming)—to remove infectious agents from the body surface of exposed individuals, but at the risk of disease contraction by the groomer. We use garden ants (Lasius neglectus) and the fungal pathogen Metarhizium as a model system to study how pathogen presence affects self-grooming and allogrooming between exposed and healthy individuals. We develop an epidemiological SIS model to explore how experimentally observed grooming patterns affect disease spread within the colony, thereby providing a direct link between the expression and direction of sanitary behaviours, and their effects on colony-level epidemiology. We find that fungus-exposed ants increase self-grooming, while simultaneously decreasing allogrooming. This behavioural modulation seems universally adaptive and is predicted to contain disease spread in a great variety of host–pathogen systems. In contrast, allogrooming directed towards pathogen-exposed individuals might both increase and decrease disease risk. Our model reveals that the effect of allogrooming depends on the balance between pathogen infectiousness and efficiency of social host defences, which are likely to vary across host–pathogen systems.     

Use of a novel two-stage cultivation method to determine the effects of environmental factors on the growth and sporulation of several biocontrol fungi

To supply essential information for improving mass production and biocontrol efficacy, two-stage cultivation on agar plates was used to evaluate the environmental conditions affecting mycelial growth and sporulation of seven biocontrol fungi. Maximum growth and sporulation occurred on acid media for Paecilomyces (Pa.) lilacinus IPC-P, Pochonia (Po.) chlamydosporia HSY-12-14, and Lecanicillium lecanii CA-1-G, and on alkaline media for Metarhizium anisopliae isolates. All fungi preferred a certain water potential and temperature for sporulation. Light greatly inhibited the growth of P. lilacinus IPC-P, M. anisopliae SQZ-1-21, and L. lecanii CA-1-G but enhanced the sporulation of P. lilacinus M-14, P. chlamydosporia HSY-12-14, and L. lecanii CA-1-G.     

Edge effects on dung beetle assemblages in an Andean mosaic of forest and coffee plantations

In landscapes dominated by agriculture, conspicuous edges often occur between landscape elements. However, there is disagreement about the existence and intensity of edge effects, and information about species‐specific responses remains scarce. Studying such edge effects can help elucidate functional landscape connectivity and contribute to agricultural management. We, therefore, assessed whether sun‐grown coffee represents a barrier to dung beetles in an Andean agricultural landscape. We also evaluated whether the response to edge effects differs among species. We found that diversity and abundance tend to decrease from forest to sun‐grown coffee and that there are sharp increases in species turnover at the forest–coffee edge. We detected several different species‐specific responses to the forest–coffee edge, suggesting differences in the mobility of the species (or spillover) and in the degree of penetration that takes place from forest patches to sun‐grown coffee plantations. This study demonstrates that the sun‐grown coffee matrix constitutes a barrier to forest species and suggests that the forest–coffee ecotone is more complex than expected. Our results support the notion that the conservation value of native forest patches in agricultural scenarios depends on the functional connectivity of forest units in the landscape to maximize the opportunities species have to disperse through the agricultural matrix.     

Comparison of procedures to assess non-linear and time-varying effects in multivariable models for survival data

The focus of many medical applications is to model the impact of several factors on time to an event. A standard approach for such analyses is the Cox proportional hazards model. It assumes that the factors act linearly on the log hazard function (linearity assumption) and that their effects are constant over time (proportional hazards (PH) assumption). Variable selection is often required to specify a more parsimonious model aiming to include only variables with an influence on the outcome. As follow-up increases the effect of a variable often gets weaker, which means that it varies in time. However, spurious time-varying effects may also be introduced by mismodelling other parts of the multivariable model, such as omission of an important covariate or an incorrect functional form of a continuous covariate. These issues interact. To check whether the effect of a variable varies in time several tests for non-PH have been proposed. However, they are not sufficient to derive a model, as appropriate modelling of the shape of time-varying effects is required. In three examples we will compare five recently published strategies to assess whether and how the effects of covariates from a multivariable model vary in time. For practical use we will give some recommendations.     

Use of microelectrodes to investigate the effects of 2-chlorophenol on microbial activities in biofilms

In order to assess the applicability of using microelectrodes as a tool for inhibition tests, temporal and spatial inhibitory effects of 2-chlorophenol (2-CP) on O(2) respiration and nitrification activities in municipal wastewater biofilms were investigated using microelectrodes for O(2) and NH(4)(+). The time-course microelectrode measurements demonstrated that 2-CP inhibited O(2) respiration and nitrification activities within 6-18 min. The microbial activities were inhibited only in the upper 400 microm of the biofilms by 2-CP, and the bacteria present in the deeper parts of the biofilms were still active, probably due to limited penetration of 2-CP. These results could reasonably explain the difference in inhibitory ratios of the O(2) respiration and nitrification activities in the biofilms. O(2) respiration activity was incompletely inhibited, which was attributed to the presence of O(2) respiration activities in the deeper parts of the biofilm. In contrast, nitrification activity was significantly inhibited because ammonia-oxidizing bacteria were present in the upper parts of the biofilm. These results indicate that the microelectrodes with a very quick response time and a high spatial resolution are useful tools to study temporal and spatial inhibitory effects of inhibitors on in situ microbial activities in biofilms.     

Dynamic secretion changes in the salt glands of the mangrove tree species Avicennia officinalis in response to a changing saline environment

The specialized salt glands on the epidermis of halophytic plants secrete excess salts from tissues by a mechanism that is poorly understood. We examined the salt glands as putative salt and water bi‐regulatory units that can respond swiftly to altering environmental cues. The tropical mangrove tree species (Avicennia officinalis) is able to grow under fluctuating salinities (0.7–50.0 dS m^?1) at intertidal zones, and its salt glands offer an excellent platform to investigate their dynamic responses under rapidly changing salinities. Utilizing a novel epidermal peel system, secretion profiles of hundreds of individual salt glands examined revealed that these glands could secrete when exposed to varying salinities. Notably, rhythmic fluctuations observed in secretion rates were reversibly inhibited by water channel (aquaporin) blocker, and two aquaporin genes (PIP and TIP) preferentially expressed in the salt gland cells were rapidly induced in response to increasing salt concentration. We propose that aquaporins are involved and contribute to the re‐absorption of water during salt removal in Avicennia officinalis salt glands. This constitutes an adaptive feature that contributes to salt balance of trees growing in saline environments where freshwater availability is limited.