Temperature and microclimate refugia use influence migratory timings of a threatened grassland bird

BACKGROUND

Seasonal changes in resource availability are known to influence the migratory behaviour of animals, including both timing and distance. While the influence of environmental cues on migratory behaviour has been widely studied at the population level, it has rarely been examined at the spatial scale at which individuals experience their environment. Here, we test the hypothesis that individuals exposed to similar large-scale environmental cues may vary in migratory behaviour in response to the different microclimate conditions they experience at fine scales.

METHODS

We combine high-spatial and temporal resolution microclimate and habitat information with GPS tracking data for a partially migratory threatened grassland bird. Data from 47 little bustards (Tetrax tetrax; 67 breeding events) tracked between 2009 and 2019 was used to (i) evaluate individual consistency in migratory behaviour (timing and distance) and (ii) assess whether the local environmental characteristics experienced by individuals - and in particular their use of microclimate refugia - influence distance and timing of migration, from and to the breeding sites.

RESULTS

Migratory distance was consistent for birds tracked over multiple years, while the timing of migration showed high variability among individuals. Departures from breeding areas spanned from May to August, with a few birds remaining in their breeding areas. Vegetation greenness (a proxy for food availability) was positively associated with the time birds spent in the breeding area. The best model also included a positive effect of microclimate refugia availability on breeding season length, although an interaction with temperature suggested that this effect did not occur at the highest relative temperatures. The return date to breeding grounds, although spanning from September to April, was not influenced by the environmental conditions or food availability.

CONCLUSIONS

Food availability, measured by a vegetation greenness proxy, was associated with later migration at the end of the breeding season. Availability of cooler microclimate refugia may also allow for later departures from the breeding sites in all but the hottest conditions. Management measures that increase microclimate refugia availability and provide foraging resources can thus potentially increase the length of the breeding season for this species.

MRXCAT2.0: Synthesis of realistic numerical phantoms by combining left-ventricular shape learning, biophysical simulations and tissue texture generation

BACKGROUND

Standardised performance assessment of image acquisition, reconstruction and processing methods is limited by the absence of images paired with ground truth reference values. To this end, we propose MRXCAT2.0 to generate synthetic data, covering healthy and pathological function, using a biophysical model. We exemplify the approach by generating cardiovascular magnetic resonance (CMR) images of healthy, infarcted, dilated and hypertrophic left-ventricular (LV) function.

METHOD

In MRXCAT2.0, the XCAT torso phantom is coupled with a statistical shape model, describing population (patho)physiological variability, and a biophysical model, providing known and detailed functional ground truth of LV morphology and function. CMR balanced steady-state free precession images are generated using MRXCAT2.0 while realistic image appearance is ensured by assigning texturized tissue properties to the phantom labels.

FINDING

Paired CMR image and ground truth data of LV function were generated with a range of LV masses (85-140 g), ejection fractions (34-51%) and peak radial and circumferential strains (0.45 to 0.95 and - 0.18 to - 0.13, respectively). These ranges cover healthy and pathological cases, including infarction, dilated and hypertrophic cardiomyopathy. The generation of the anatomy takes a few seconds and it improves on current state-of-the-art models where the pathological representation is not explicitly addressed. For the full simulation framework, the biophysical models require approximately two hours, while image generation requires a few minutes per slice.

CONCLUSION

MRXCAT2.0 offers synthesis of realistic images embedding population-based anatomical and functional variability and associated ground truth parameters to facilitate a standardized assessment of CMR acquisition, reconstruction and processing methods.

The variability of phenolic constituents and antioxidant properties among wild populations of Ziziphora clinopodioides Lam

In this study, phenolic derivatives and antioxidant activities of fourteen Ziziphora clinopodioides populations, as well as LC-MS/MS analysis of three specific flavonoids were evaluated. Generally, high contents of phenolic derivatives were found in shoot extracts compared to roots. LC-MS/MS, a powerful analytical technique, was employed for the identification and quantify the individual flavonoids in Z. clinopodioides populations' extracts, in a quantity order of quercetin > rutin > apigenin. Scavenging activity by DPPH and FRAP was performed, and accordingly, in the shoot, the highest values for the DDPH were 4.61 ± 0.4 and 7.59 ± 0.26 µg ml- 1 in populations 1 and 13, respectively, and for the FRAP were 328.61 ± 5.54 and 292.84 ± 2.85 mg g DW- 1, in populations 6 and 1 respectively. Multivariate analysis results of the principal component analysis indicated the amount of polyphenols to be useful indicators in differentiating the geographical localities which explain 92.7% of the total variance. According to the results of hierarchical cluster analysis, the studied populations could be separated into two groups in that the contents of phenolic derivatives and antioxidant activities of different plant parts. Both shoot and root samples were well discriminated with the orthogonal partial least squares discriminant analysis (R2X: 0.861; Q2: 0.47) model. The validity of the model was confirmed by using receiver operating characteristic curve analysis and permutation tests. Such data make an important addition to our current knowledge of Ziziphora chemistry and are decisive in the identification of germplasms with a homogeneous phytochemical profile, high chemical content and bioactivity. The present results could also be helpful for the potential application of Z. clinopodioides in different kinds of industries as natural antioxidants.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01283-y.

A tiered approach to population-based in vitro testing for cardiotoxicity: Balancing estimates of potency and variability

Population-wide in vitro studies for characterization of cardiotoxicity hazard, risk, and population variability show that human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) are a powerful and high-throughput testing platform for drugs and environmental chemicals alike. However, studies in multiple donor-derived hiPSC-CMs, across large libraries of chemicals tested in concentration-response are technically complex, and study design optimization is needed to determine sufficient and fit-for-purpose population size considerations. Therefore, we tested a hypothesis that a computational down-sampling analysis based on the data from hiPSC-CM screening of 136 diverse compounds in a population of 43 non-diseased donors, including multiple replicates of the "standard" donor hiPSC-CMs, will inform optimal study designs depending on the decision context (hazard, risk and/or inter-individual variability in cardiotoxicity). Through 50 independent random subsamples of 5, 10, or 20 donors, we estimated accuracy and precision for quantifying potency, inter-individual variability, and QT prolongation risk; the results were compared to the full 43-donor cohort. We found that for potency and clinical risk of QT prolongation, a cohort of 5 randomly-selected unique donors provides accurate and precise estimates. Larger cohort sizes afforded marginal improvements, and 5 replicates of a single donor performed worse. For estimating inter-individual variability, cohorts of at least 20 donors are needed, with smaller populations on average showing bias towards underestimation in population variance. Collectively, this study shows that a variable-size hiPSC-CM-based population-wide in vitro model can be used in a number of decision scenarios for identifying cardiotoxic hazards of drugs and environmental chemicals in the population context.

Interpopulational differences in the frequency and distribution of delta types

The classification of the main pattern types, arch, loop and whorls, is based on the number and location of deltas or triradii, which are areas defined by the confluence of three ridge systems carrying different directions on the fingerprint. Despite being areas that give place to an important morphological variability, their study has only been approached from the quantitative point of view, in relation to the number with which they appear per finger, hand, or individual (intensity pattern), and their sexual and population differences; while the qualitative aspects have not been evaluated so far. The following paper aims to study and analyze the qualitative variability, both intra and interpopulation, of the frequency of occurrence of the different types of deltas or triradii, in four fingerprint samples from males of different population origin: 100 individuals from China, 100 individuals from Colombia, 100 individuals from Nigeria and 100 individuals from Romania, which has meant the analysis of 4000 fingerprints. For this purpose, the classification of 24 types used by the Scientific Police and Criminalist Departments of the Guardia Civil of Spain has been employed. The results obtained showed the non-equiprobability of the frequency distribution of the different delta types in the four populations. In all cases, sunk open total deltas (Hat), sunk open total with point (Hat(p)) and tripod long (Tl) were the most frequent types, while the sunk closed total with point (Hct(p)) had the lowest frequency. Furthermore, for the first time, interpopulation differences in the frequency distribution of different types of deltas have become noticeable. The data provided in this paper are a pioneer in the field of dactyloscopy and can be used as a reference by the departments of criminalistics of the different countries for the estimation of the scientific value of the evidence in dactyloscopy.

Interactions between exotic and native lady beetle species stabilize community abundance

A 23-year time-series of abundance for 13 lady beetle species (Coccinellidae) was used to investigate community stability. The community exhibited persistence in ten habitats, no overall trend in abundance, and low temporal variability quantified as Population variability (PV) = 0.33 on a scale from 0 to 1 that declined to 0.16 in the past 8 years. This high level of stability occurred as exotic lady beetles disrupted populations of the native species. For hypothetical communities of pairs of species (with randomly generated annual abundances in the range for lady beetles), PV increased linearly with the correlation coefficients between individual time series, illustrating a "portfolio effect". PV for the real community and the negative correlation between the abundance of exotics and natives fit this relationship precisely. A gradual decline of natives matched by an equal gradual rise in the abundance of exotics contributed to the negative correlation that stabilized the community. The abundance of the dominant species, an exotic, was negatively correlated with other exotics and most natives, and its stability increased over time, helping to stabilize the community. The community was most stable in habitats where beetle abundance was high (crops, particularly perennial crops) and, unexpectedly, was least stable in habitats with high diversity and stability of vegetation cover (forests). These data are consistent with the hypothesis that competition between exotic and native species, with release from competition for natives in some years, stabilized the abundance of this community. Stability may not last if populations of native species continue declining.

Profiling of RNAi sensitivity after foliar dsRNA exposure in different European populations of Colorado potato beetle reveals a robust response with minor variability

In recent years, substantial effort was spent on the exploration and implementation of RNAi technology using double-stranded RNA (dsRNA) for pest management purposes. However, only few studies investigated the geographical variation in RNAi sensitivity present in field-collected populations of the targeted insect pest. In this baseline study, 2nd instar larvae of 14 different European populations of Colorado potato beetle (CPB), Leptinotarsa decemlineata, collected from nine different countries were exposed to a foliarly applied diagnostic dose of dsactin (dsact) to test for possible variations in RNAi response. Only minor variability in RNAi sensitivity was observed between populations. However, the time necessary to trigger a dsRNA-mediated phenotypic response varied significantly among populations, indicated by significant differences in mortality figures obtained five days after treatment. An inbred German laboratory reference strain D01 and a Spanish field strain E02 showed almost 100% mortality after foliar exposure to 30 ng dsactin (equal to 0.96 g/ha), whereas another Spanish strain E01 was least responsive and showed only 30% mortality. Calculated LD₅₀-values for foliarly applied dsact against strains D01 (most sensitive) and E01 (least sensitive) were 9.22 and 68.7 ng/leaf disc, respectively. The variability was not based on target gene sequence divergence or knock-down efficiency. Variability in expression of the core RNAi machinery genes dicer (dcr2a) and argonaute (ago2a) was observed but did not correlate with sensitivity. Interestingly, RT-qPCR data collected for all strains revealed a strong correlation between the expression level of dcr2a and ago2a (r 0.93) as well as ago2a and stauC (r 0.94), a recently described dsRNA binding protein in Coleopterans. Overall, this study demonstrates that sensitivity of CPB to sprayable RNAi slightly varies between strains but also shows that foliar RNAi as a control method works against all tested CPB populations collected across a broad geographic range in Europe. Thus, underpinning the potential of RNAi-based CPB control as a promising component in integrated pest management (IPM) and resistance management programs.

Influence of population variability in ligament material properties on the mechanical behavior of ankle: a computational investigation

Biomechanical behavior of ankle ligaments varies among individuals, with the underlying mechanism at multiple scales remaining unquantified. The present probabilistic study investigated how population variability in ligament material properties would influence the joint mechanics. A previously developed finite element ankle model with parametric ligament properties was used. Taking the typical external rotation as example loading scenario, joint stability of the investigated population was consistently shared by specific ligaments within a narrow tolerance range, i.e. 62.8 ± 8.2 Nm under 36.1 ± 5.7° foot rotation. In parallel, the inherent material variability significantly alters the consequent injury patterns. Three most vulnerable ligaments and the consequent rupture sequences were identified, with the structural weak spot and the following progressive stability loss dominated by the relative stiffness among ligaments. This study demonstrated the feasibility of biofidelic models in investigating individual difference at the material level, and emphasized the importance of probabilistic description of individual difference when identifying the injury mechanism of a broad spectrum.

Population structure and genotypic variation of Crataegus pontica inferred by molecular markers

Information about the natural patterns of genetic variability and their evolutionary bases are of fundamental practical importance for sustainable forest management and conservation. In the present study, the genetic diversity of 164 individuals from fourteen natural populations of Crataegus pontica K.Koch was assessed for the first time using three genome-based molecular techniques; inter-retrotransposon amplified polymorphism (IRAP); inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) polymorphism. IRAP, ISSR and SCoT analyses yielded 126, 254 and 199 scorable amplified bands, respectively, of which 90.48, 93.37 and 83.78% were polymorphic. ISSR revealed efficiency over IRAP and SCoT due to high effective multiplex ratio, marker index and resolving power. The dendrograms based on the markers used and combined data divided individuals into three major clusters. The correlation between the coefficient matrices for the IRAP, ISSR and SCoT data was significant. A higher level of genetic variation was observed within populations than among populations based on the markers used. The lower divergence levels depicted among the studied populations could be seen as evidence of gene flow. The promotion of gene exchange will be very beneficial to conserve and utilize the enormous genetic variability.

Reprint of PopGen: A virtual human population generator

The risk assessment of environmental chemicals and drugs is moving towards a paradigm shift in approach which seeks the full replacement animal testing with high throughput, mechanistic, in vitro systems. This new vision will be reliant on the measurement in vitro, of concentration-dependent responses where prolonged excessive perturbations of specific biochemical pathways are likely to lead to adverse health effects in an intact organism. Such an approach requires a framework, into which disparate data generated using in vitro, in silico and in chemico systems, can be integrated and utilised for quantitative in vitro-to-in vivo extrapolation (QIVIVE), ultimately to the human population level. Physiologically based pharmacokinetic (PBPK) models are ideally suited for this and are obligatory in order to translate in vitro concentration-response relationships to an exposure or dose, route and duration regime in people. In this report we describe PopGen a virtual human population generator which is a user friendly, open access web-based application for the prediction of realistic anatomical, physiological and phase 1 metabolic variation in a wide range of healthy human populations. We demonstrate how PopGen can be used for QIVIVE by providing input to a PBPK model, at an appropriate level of detail, to reconstruct exposure from human biomonitoring data. We discuss how the process of exposure reconstruction from blood biomarkers, in general, is analogous to exposure or dose reconstruction from concentration-response measurements made in proposed in vitro cell based systems which are assumed to be surrogates for target organs.

Uncertainty quantification of fast sodium current steady-state inactivation for multi-scale models of cardiac electrophysiology

Perhaps the most mature area of multi-scale systems biology is the modelling of the heart. Current models are grounded in over fifty years of research in the development of biophysically detailed models of the electrophysiology (EP) of cardiac cells, but one aspect which is inadequately addressed is the incorporation of uncertainty and physiological variability. Uncertainty quantification (UQ) is the identification and characterisation of the uncertainty in model parameters derived from experimental data, and the computation of the resultant uncertainty in model outputs. It is a necessary tool for establishing the credibility of computational models, and will likely be expected of EP models for future safety-critical clinical applications. The focus of this paper is formal UQ of one major sub-component of cardiac EP models, the steady-state inactivation of the fast sodium current, INa. To better capture average behaviour and quantify variability across cells, we have applied for the first time an 'individual-based' statistical methodology to assess voltage clamp data. Advantages of this approach over a more traditional 'population-averaged' approach are highlighted. The method was used to characterise variability amongst cells isolated from canine epi and endocardium, and this variability was then 'propagated forward' through a canine model to determine the resultant uncertainty in model predictions at different scales, such as of upstroke velocity and spiral wave dynamics. Statistically significant differences between epi and endocardial cells (greater half-inactivation and less steep slope of steady state inactivation curve for endo) was observed, and the forward propagation revealed a lack of robustness of the model to underlying variability, but also surprising robustness to variability at the tissue scale. Overall, the methodology can be used to: (i) better analyse voltage clamp data; (ii) characterise underlying population variability; (iii) investigate consequences of variability; and (iv) improve the ability to validate a model. To our knowledge this article is the first to quantify population variability in membrane dynamics in this manner, and the first to perform formal UQ for a component of a cardiac model. The approach is likely to find much wider applicability across systems biology as current application domains reach greater levels of maturity.

Sensitivity to hepatotoxicity due to epigallocatechin gallate is affected by genetic background in diversity outbred mice

Consumer use of herbal and dietary supplements has recently grown in the United States and, with increased use, reports of rare adverse reactions have emerged. One such supplement is green tea extract, containing the polyphenol epigallocatechin gallate (EGCG), which has been shown to be hepatotoxic at high doses in animal models. The Drug-Induced Liver Injury Network has identified multiple patients who have experienced liver injury ascribed to green tea extract consumption and the relationship to dose has not been straightforward, indicating that differences in sensitivity may contribute to the adverse response in susceptible people. The Diversity Outbred (DO), a genetically heterogeneous mouse population, provides a potential platform for study of interindividual toxicity responses to green tea extract. Within the DO population, an equal exposure to EGCG (50 mg/kg; daily for three days) was found to be tolerated in the majority of mice; however, a small fraction of the animals (16%; 43/272) exhibited severe hepatotoxicity (10-86.8% liver necrosis) that is analogous to the clinical cases. The data indicate that the DO mice may provide a platform for informing risk of rare, adverse reactions that may occur in consumer populations upon ingestion of concentrated herbal products.

PopGen: A virtual human population generator

The risk assessment of environmental chemicals and drugs is moving towards a paradigm shift in approach which seeks the full replacement animal testing with high throughput, mechanistic, in vitro systems. This new vision will be reliant on the measurement in vitro, of concentration-dependent responses where prolonged excessive perturbations of specific biochemical pathways are likely to lead to adverse health effects in an intact organism. Such an approach requires a framework, into which disparate data generated using in vitro, in silico and in chemico systems, can be integrated and utilised for quantitative in vitro-to-in vivo extrapolation (QIVIVE), ultimately to the human population level. Physiologically based pharmacokinetic (PBPK) models are ideally suited for this and are obligatory in order to translate in vitro concentration-response relationships to an exposure or dose, route and duration regime in people. In this report we describe PopGen, a virtual human population generator which is a user friendly, open access web-based application for the prediction of realistic anatomical, physiological and phase 1 metabolic variation in a wide range of healthy human populations. We demonstrate how PopGen can be used for QIVIVE by providing input to a PBPK model, at an appropriate level of detail, to reconstruct exposure from human biomonitoring data. We discuss how the process of exposure reconstruction from blood biomarkers, in general, is analogous to exposure or dose reconstruction from concentration-response measurements made in proposed in vitro cell based systems which are assumed to be surrogates for target organs.

Predicting extinctions: interspecific competition, predation and population variability in experimental Daphnia populations

We examine how interspecific competition and two types of size-selective predation affect population density, variability and persistence in laboratory cultures of two species of Daphnia, D. magna and D. longispina. When both species were analysed together, and for D. longispina alone, there were weak negative relationships between mean population density and population variability. Interspecific competition resulted in lower population densities and higher population variability. Extinct populations had lower densities and were also more variable than persisting ones. There was still an effect of population variability on extinction probability after the effect of density on population variability had been accounted for. Hence, the effects of population density and variability on population persistence were partly independent of each other. The effects of size-selective predation on population persistence were more species-specific and not directly related to density or variability. Since the effects of species interactions on persistence were large, we suggest that it is likely that population vulnerability analyses not incorporating effects of interspecific interactions are often misleading.