Phenological response of sea turtles to environmental variation across a species' northern range

Variations in environmental parameters (e.g. temperature) that form part of global climate change have been associated with shifts in the timing of seasonal events for a broad range of organisms. Most studies evaluating such phenological shifts of individual taxa have focused on a limited number of locations, making it difficult to assess how such shifts vary regionally across a species range. Here, by using 1445 records of the date of first nesting for loggerhead sea turtles (Caretta caretta) at different breeding sites, on different continents and in different years across a broad latitudinal range (25–39° ′N), we demonstrate that the gradient of the relationship between temperature and the date of first breeding is steeper at higher latitudes, i.e. the phenological responses to temperature appear strongest at the poleward range limit. These findings support the hypothesis that biological changes in response to climate change will be most acute at the poleward range limits and are in accordance with the predictions of MacArthur''s hypothesis that poleward range limit for species range is environmentally limited. Our findings imply that the poleward populations of loggerheads are more sensitive to climate variations and thus they might display the impacts of climate change sooner and more prominently.     

Relating geographical variation in pollination types to environmental and spatial factors using novel statistical methods

The relative frequencies of functional traits of plant species show notable spatial variation, which is often related to environmental factors. Pollination type (insect-, wind- or self-pollination) is a critical trait for plant reproduction and provision of ecosystem services. Here, we mapped the distribution of pollination types across Germany by combining databases on plant distribution and plant pollination types. Applying a new method, we modelled the composition of pollination types using a set of 12 environmental variables as predictors within a Bayesian framework which allows for the analysis of compositional data in the presence of spatial autocorrelation. A clear biogeographical pattern in the distribution of pollination types was revealed which was adequately captured by our model. The most striking relationship was a relative increase in insect-pollination and a corresponding decrease of selfing with increasing altitude. Further important factors were wind speed, geology and land use. We present a powerful tool to analyse the distribution patterns of plant functional types such as pollination types and their relationship with environmental parameters in a spatially explicit framework.     

EDDY: a novel statistical gene set test method to detect differential genetic dependencies

Identifying differential features between conditions is a popular approach to understanding molecular features and their mechanisms underlying a biological process of particular interest. Although many tests for identifying differential expression of gene or gene sets have been proposed, there was limited success in developing methods for differential interactions of genes between conditions because of its computational complexity. We present a method for Evaluation of Dependency DifferentialitY (EDDY), which is a statistical test for differential dependencies of a set of genes between two conditions. Unlike previous methods focused on differential expression of individual genes or correlation changes of individual gene–gene interactions, EDDY compares two conditions by evaluating the probability distributions of dependency networks from genes. The method has been evaluated and compared with other methods through simulation studies, and application to glioblastoma multiforme data resulted in informative cancer and glioblastoma multiforme subtype-related findings. The comparison with Gene Set Enrichment Analysis, a differential expression-based method, revealed that EDDY identifies the gene sets that are complementary to those identified by Gene Set Enrichment Analysis. EDDY also showed much lower false positives than Gene Set Co-expression Analysis, a method based on correlation changes of individual gene–gene interactions, thus providing more informative results. The Java implementation of the algorithm is freely available to noncommercial users. Download from: http://biocomputing.tgen.org/software/EDDY.     

Genetic and environmental factors causing variation in drug response

Large pharmacokinetic variations, ranging in magnitude from 4- to 40-fold, often exist among the members of a given population. These variations create differences in risk of cancer by accelerating metabolic activation of certain environmental carcinogens in some subjects, while retarding such rates in other subjects. To identify specific genetic and environmental causes of large interindividual variations in these rates, several methods have been developed to probe hepatic cytochrome P-450 isozymes responsible for xenobiotic activation. In patients, dynamic interactions occur between genetic and environmental factors causing large interindividual variations in xenobiotic metabolism. Even the same patient can change dosage requirements with time and condition. Appropriate marker drugs can sensitively indicate pharmacokinetic capacity at any given time in a patient or normal volunteer. With respect to genetic factors, twin and family studies are the traditional methods used to test pharmacogenetic hypotheses. Representative examples are cited to illustrate how twin and family studies serve this purpose. Monogenic control of large interindividual variations in the activity of approx. 12 P-450 isozymes has been described. Individual metabolic pathways need to be investigated for drugs biotransformed by multiple pathways. Since many hepatic P-450 isozymes are extremely sensitive to perturbation by numerous environmental alterations, the critical role of selection criteria is stressed to assure that all subjects of twin and family studies are under as uniform environmental conditions as possible. Otherwise, the operation of genetic factors may be concealed or misinterpreted in studies that do not use gene cloning or protein sequence.     

Thermodynamic calculations and statistical correlations for oligo-probes design

Optimization of probe design for array-based experiments requires improved predictability of oligonucleotide hybridization behavior. Currently, designing oligonucleotides capable of interacting efficiently and specifically with the relevant target is not a routine procedure. Multiple examples demonstrate that oligonucleotides targeting different regions of the same RNA differ in their hybridization ability. The present work shows how thermodynamic evaluations of oligo-target duplex or oligo self-structure stabilities can facilitate probe design. Statistical analysis of large sets of hybridization data reveals that thermodynamic evaluation of oligonucleotide properties can be used to avoid poor RNA binders. Thermodynamic criteria for the selection of 20 and 21mers, which, with high probability, interact efficiently and specifically with their targets, are suggested. The design of longer oligonucleotides can also be facilitated by the same calculations of ΔG°_T values for oligo-target duplex or oligo self-structure stabilities and similar selection schemes.     

Demographic response to environmental variation in breeding,stopover and non-breeding areas in a migratory passerine

Demographic rates of migratory species passing through several areas during their annual cycle may be affected by environmental conditions at each of these areas. Recent studies provide evidence that their impact is not necessarily immediate, but can be delayed. We studied survival, reproductive success and arrival date at the breeding grounds of red-backed shrikes Lanius collurio, a trans-Saharan migrant, in relation to weather and vegetation on the breeding grounds, the stopover sites during migration and in the wintering areas. These environmental factors are used as proxy of the shrike’s food supply. We analysed detailed demographic data of some 4,600 individuals from 25 years with multistate capture–recapture and mixed models. Survival probabilities of juveniles and breeders of both sexes varied in parallel across time, suggesting that all cohorts were sensitive to similar causes of mortality. Reproductive performance increased with temperature and decreased with rainfall on the breeding area. Moreover, it increased with vegetation cover in the Sahelian stopover area used on autumn migration suggesting a carry-over effect. Arrival date was negatively affected by spring temperatures in the breeding area. Hence, demographic rates were affected by environmental factors on the breeding grounds, but also outside and elsewhere. This suggests that the shrike’s population dynamics are driven by environmental factors operating at various scales of space and time. However, only a small amount of the temporal variation in demographic rates is explained by the environmental factors considered, suggesting that additional factors, such as those operating during migration, might be important.     

Intraocular lens power calculations using a Scheimpflug camera to measure corneal power

We measured corneal power using an Oculus Pentacam^® to assess its accuracy for calculating intraocular lens (IOL) power after myopic refractive surgery. A series of corneal power measurements were performed on 22 patients (43 eyes) who had undergone myopic refractive surgery. In 37 of the 43 eyes, phacoemulsification and IOL implantation subsequently were performed. Conventional keratometry and three corneal measurements (mean true net power, central true net power, and 4.5 mm equivalent K reading) obtained using a Pentacam were analyzed and compared to values derived from the clinical history method. Prediction errors of three Pentacam corneal power measurements inserted in third generation IOL formulas also were compared. Analysis of the variance showed that only two Pentacam corneal measurements, mean true net power and central true net power, were not significantly different from those of the clinical history method. Mean true net power was correlated more closely with the clinical history method corneal power than other corneal power values. The one-sample t-test showed that of three Pentacam corneal measurements combined with third-generation formulas, only the mean true net power inserted in the SRK/T implant power calculation formula was not significantly different from zero. The percentages of eyes within ± 0.50 D and ± 1.00 D of the refractive prediction error of this method were 67.6% and 86.5%, respectively. Mean true net power inserted in the SRK/T formula can be used to calculate directly IOL power after myopic refractive surgery.     

New approaches to direct gradient analysis using environmental scalars and statistical curve-fitting procedures

The conceptual framework of direct gradient analysis (DGA) is discussed in relation to the functional, factorial approach to vegetation. Both approaches use abstract simplified environment gradients with which to correlate vegetation response. Environmental scalars based on physical process models of environment and/or known biological growth processes can be incorporated to make analyses less location specific. An example of an environmental scalar (radiation index) for converting aspect and slope measurements to the more biologically relevant radiation input at a site is given. The problem of the shape of species response curves to environmental gradients is examined using a sample of 1 286 plots from eucalypt forest in southern New South Wales. An important conclusion is that skewed or bimodal response curves may be due to unsatisfactory distribution of observations and/or unrecognized environmental factors. The use of Generalized Linear Modelling (GLM) as a method for providing a statistical basis for DGA is presented. Analyses using GLM, and presence/absence data are presented for a range of eucalypt species (Eucalyptus rossii, E. dalrympleana, E. fastigata etc.). Successful prediction of species distributions (realized niches) can be achieved with mean annual temperature, mean annual rainfall, radiation index and geology. Quadratic terms are required in many cases, indicating bell-shaped response curves. The major variability associated with species niches is shown to be related to a limited number (4) of environmental factors. DGA with biologically relevant scalars and appropriate statistical methods is suitable for studying many problems of species' realized niches and plant community composition.     

Developing a statistical support system for environmental hazard evaluation

Estimating the hazard or risk to both human health and the environment has been based almost exclusively on single species toxicity tests low in environmental realism and without validation of their accuracy in more complex systems. While this may be quite appropriate for humans in a large variety of circumstances, there is no substantive body of direct experimental evidence indicating that precise predictions of harm from hazardous materials can be extrapolated from single species laboratory tests (or even multispecies laboratory tests) to the more complex highly variable natural systems. Now added to the hazardous chemical assessment problem is the accidental or deliberate release of genetically engineered microorganisms into the environment that have the additional capability of multiplying and expanding their numbers and also transferring genetic information to other organisms. This paper focuses entirely on hazard evaluation for organisms other than humans, namely predicting the potential risk or probability of harm to natural systems based on laboratory toxicity testing using single species. Not only will the basic risk assessment strategy itself be examined but also the question of determining the statistical reliability of various extrapolations from one level of biological organization to another. ‘For every complex problem, there is a simple, direct solution ... and it is invariably wrong!’ H. L. Mencken     

Use of random amplified polymorphic DNA analysis to detect genetic variation inPyrus species

Pyrus communis L. is the most important pear species for European production. Very few cultivars satisfy standards for fruit quality and clonal fidelity; thus, accurate verification of cultivar identity for checking propagation material and patent protection is important. We evaluated the randomly amplified polymorphic DNA (RAPD) technique for its ability to identify genetic differences among standard pear (Pyrus communis L.) cultivars, William, Passa Crassana, and Conference, and three gamma-ray induced variants. To identify genotype-specific markers, we used thirty 10-mer and two 11-mer sequences, annealing temperatures from 36–45°C, 2Taq polymerases (AmpliTaq and Stoffel fragment, both from former Perkin Elmer Cetus), and 2–4 replicate amplifications. Of the 32 primers (30 from Operon Technologies, Alameda, CA, USA), very few distinguished William from Passa Crassana, and only 1 could clearly differentiate all 3 cultivars. Two primers that did not reveal polymorphisms when used singly, generated polymorphic patterns that distinguished standard from gamma-ray-treated material when used in combination. We show that RAPD analyses can discriminate pear genotypes and suggest this technique as a reliable and inexpensive method for marker-facilitated screening of propagation material and for patent protection.     

Genetic and environmental variation in the LH response of ovariectomized sheep to LH-RH.

The influence of breed and season on the sensitivity of the pituitary gland of sheep to LH-RH was assessed. Ovariectomized ewes of 3 breeds (Finnish Landrace, Scottish Blackface and Tasmanian Merino) with differing normal breeding seasons and with differing ovulation rates were injected (i.v.) with 3 doses of LH-RH (1.56, 6.25 or 25.0 micrograms) at 3 different times of the year covering the anoestrous and the breeding seasons of intact ewes; 9 ewes of each breed (3 per sub-class) were examined on the first and third occasions, 6 (2 per sub-class) on the second. The response was measured in terms of the concentration of LH in peripheral plasma 20, 40, 60 and 80 min after injection. Time of year, but not the breed of sheep, affected the magnitude of the response; the data indicated that the duration of LH secretion was greater during the breeding season than during anoestrus. It was concluded that changes in the spontaneous activity of the hypothalamus/hypophysis could contribute to seasonal changes in LH secretion independently of the modifying effects of gonadal steroids. Such variation in unmodulated activity apparently does not contribute to the differences in ovulation rate among the 3 breeds.     

Selection of nontarget arthropod taxa for field research on transgenic insecticidal crops: using empirical data and statistical power

One of the possible adverse effects of transgenic insecticidal crops is the unintended decline in the abundance of nontarget arthropods. Field trials designed to evaluate potential nontarget effects can be more complex than expected because decisions to conduct field trials and the selection of taxa to include are not always guided by the results of laboratory tests. Also, recent studies emphasize the potential for indirect effects (adverse impacts to nontarget arthropods without feeding directly on plant tissues), which are difficult to predict because of interactions among nontarget arthropods, target pests, and transgenic crops. As a consequence, field studies may attempt to monitor expansive lists of arthropod taxa, making the design of such broad studies more difficult and reducing the likelihood of detecting any negative effects that might be present. To improve the taxonomic focus and statistical rigor of future studies, existing field data and corresponding power analysis may provide useful guidance. Analysis of control data from several nontarget field trials using repeated-measures designs suggests that while detection of small effects may require considerable increases in replication, there are taxa from different ecological roles that are sampled effectively using standard methods. The use of statistical power to guide selection of taxa for nontarget trials reflects scientists' inability to predict the complex interactions among arthropod taxa, particularly when laboratory trials fail to provide guidance on which groups are more likely to be affected. However, scientists still may exercise judgment, including taxa that are not included in or supported by power analyses.     

Physiological and morphological response to water deficit in seedlings of five provenances of Pinus canariensis: potential to detect variation in drought-tolerance

To assess the potential of short-term screenings for drought resistance at the seedling stage to detect ecotypic variation and predict field performance, we studied the responses to water deficit of seedlings of Pinus canariensis from five geographic origins under controlled conditions and compared these responses with the performance of provenances in a multi-site field trial. Leaf water potential, the osmotic component, leaf chlorophyll fluorescence and growth and biomass partitioning were measured as seedlings were subjected for 11 days to two levels of osmotic potential generated by polyethylene glycol (PEG 6000), −1 MPa (slowly imposed water deficit; S) and −1.5 MPa (fast imposed water deficit; F), and a control treatment (no PEG added to the nutrient solution; C). Leaf water potential declined to final mean values of −1.2, −2.7 and −4.7 MPa in the C, S and F treatments, respectively. The ratio of variable to maximum chlorophyll fluorescence declined to final mean values of 0.77, 0.66 and 0.40 in the C, S and F treatments, respectively, with no differences amongst provenances. All provenances showed an active osmotic adjustment (OA) in response to water deficit which varied depending on the drying rate. A slow imposition of water deficit favoured solute accumulation. Pooling all treatments, the index of OA ranged from 0.28 to 0.40, but rose considerably when only C and S treatments were considered (0.56 to 0.70). There was a positive and significant correlation between the overall index of OA (all treatments pooled) and the drought period in the site of origin, suggesting ecotypic variation in OA as a result of drought duration. Seedlings allocated more dry matter to roots than shoots when subjected to moderate and slowly imposed water deficit; only one provenance showed no increase in the root to shoot ratio at the end of the treatment period compared with control seedlings. Responses to controlled water deficits were only qualitatively related to performance (survival and growth) of provenances in several field sites, indicating the involvement of complex mechanisms to cope with drought under natural conditions. However, the provenance with the highest overall index of OA outgrew and outsurvived the other provenances in the most arid site, and the only provenance not modifying the root to shoot ratio in response to water deficit survived the least in all field sites. Acclimation of root to shoot ratio and net solute accumulation to water deficit could hence favour drought-tolerance beyond the seedling stage and be used as preliminary predictors of field performance.     

Proteome analysis of Borrelia burgdorferi response to environmental change

We examined global changes in protein expression in the B31 strain of Borrelia burgdorferi, in response to two environmental cues (pH and temperature) chosen for their reported similarity to those encountered at different stages of the organism's life cycle. Multidimensional nano-liquid chromatographic separations coupled with tandem mass spectrometry were used to examine the array of proteins (i.e., the proteome) of B. burgdorferi for different pH and temperature culture conditions. Changes in pH and temperature elicited in vitro adaptations of this spirochete known to cause Lyme disease and led to alterations in protein expression that are associated with increased microbial pathogenesis. We identified 1,031 proteins that represent 59% of the annotated genome of B. burgdorferi and elucidated a core proteome of 414 proteins that were present in all environmental conditions investigated. Observed changes in protein abundances indicated varied replicon usage, as well as proteome functional distributions between the in vitro cell culture conditions. Surprisingly, the pH and temperature conditions that mimicked B. burgdorferi residing in the gut of a fed tick showed a marked reduction in protein diversity. Additionally, the results provide us with leading candidates for exploring how B. burgdorferi adapts to and is able to survive in a wide variety of environmental conditions and lay a foundation for planned in situ studies of B. burgdorferi isolated from the tick midgut and infected animals.