对九种天然产物清除自由基活性的理论评价

用量子化学方法计算了源自灯盏花、丹参、银杏和红花的九种天然产物--灯盏花乙素、焦袂康酸、3,5-二咖啡酰氧基奎宁酸、飞蓬酯B、丹酚酸B、丹参素、银杏双黄酮、银杏苦内酯B和羟基红花黄色素A的O-H键解离焓和电离势,并以此为理论指标评价了其清除自由基活性.结果发现,在非极性溶剂中3,5-二咖啡酰氧基奎宁酸、飞蓬酯B、丹酚酸B、丹参素等均具有较高的活性;而在极性溶剂中,相比其它八种化合物,灯盏花乙素显示出优良的清除自由基活性,提示这些化合物有望作为药物的有效成分治疗自由基引起的心、脑血管疾病.     

Clinical tolerability and pharmacokinetics of Erigerontis hydroxybenzene injection: Results of a randomized phase I study in healthy Chinese volunteers

Multiple phenolic compounds in the extract of Erigeron breviscapus synergistically contribute to the neurovascular protective effects. We conducted a phase I and pharmacokinetic study with the phenolic compound-enriched product extracted from Erigeron breviscapus, Erigerontis hydroxybenzenes injection (EHI), in healthy Chinese volunteers.A randomized, open-label, single-center, double-arm, dose-escalation study of EHI was conducted. The tolerability of intravenously EHI administrated in single- or multiple-dose (once daily for 7 days) was studied in 40 healthy Chinese volunteers and the pharmacokinetics of EHI was studied in additional 10 volunteers.The tolerated dose of intravenous infusion of EHI in healthy Chinese volunteers was 6 vials (equivalent to 90 mg bioactive phenolic compounds). The main limitations to dose escalation of EHI were transit changes in electrocardiogram and mild, transit increase in alanine aminotransferase. After intravenous administration of EHI, the average systemic clearance of multiple phenolic compounds of scutellarin, 1,3-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid, and 3,4-dicaffeoylquinic acid were 131, 29, 262, 112 L/h for male volunteers and 202, 28, 252, 117 L/h for female volunteers.The intervention of intravenous infusion of EHI in healthy Chinese volunteers was generally tolerated. The findings from this study provide data on the tolerability and pharmacokinetics of the extract from Erigeron breviscapus and support further trials.     

Screening of free radical scavengers from Erigeron breviscapus using on-line HPLC-ABTS/DPPH based assay and mass spectrometer detection

Erigeron breviscapus is a well-known traditional Chinese herbal medicine. In this study, on-line HPLC-ABTS/DPPH assay coupled with MS detection were applied to screen and identify the free radical scavengers in 70% methanol extracts of E. breviscapus. Using on-line HPLC-ABTS-MS and HPLC-DPPH-MS assay, 13 radical scavengers (including 4-O-caffeoylquinic acid (4-CQA) (1), 9-caffeoyl-2,7-anhydro-2-octulosonic acid (9-COA) (2), 3-caffeoyl-2,7-anhydro-3-deoxy-2-octulopyranosonic acid (3-CDOA) (3), erigeside I (4), quercetin-3-O-glucuronide (5), eriodictyol-7-O-glucuronide (6), scutellarin (7), 1,4-di-O-caffeoylquinic acid (1,4-di-CQA) (8), 3,5-di-CQA (9), 1-malonyl-3,5-di-CQA (10), erigoster B (11), 4,5-di-CQA (12) and 4,9-di-CDOA (13)) and 9 radical scavengers (including 1, 4, 7, 8, 9, 10, 11, 12 and 13) were discovered, respectively. Furthermore, the anti-oxidative activities of 4 compounds, including 7, 9, 11 and 12 were evaluated. Reverse anti-oxidative activity order of scutellarin and 3,5-di-CQA was observed in on-line HPLC-ABTS assay and on-line HPLC-DPPH assay. To validate their anti-oxidative activities, the off-line ABTS and DPPH assays were performed. Given sufficient reaction time, 3,5-di-CQA showed higher activity than scutellarin, which was consistent with the order obtained in on-line HPLC-ABTS assay. These results revealed that on-line HPLC-ABTS assay is a more sensitive method for screening and determining free radical scavengers, especially more suitable for those compounds with slower reaction kinetics.     

Screening of free radical scavengers from Erigeron breviscapus using on-line HPLC-ABTS/DPPH based assay and mass spectrometer detection

Erigeron breviscapus is a well-known traditional Chinese herbal medicine. In this study, on-line HPLC-ABTS/DPPH assay coupled with MS detection were applied to screen and identify the free radical scavengers in 70% methanol extracts of E. breviscapus. Using on-line HPLC-ABTS-MS and HPLC-DPPH-MS assay, 13 radical scavengers (including 4-O-caffeoylquinic acid (4-CQA) (1), 9-caffeoyl-2,7-anhydro-2-octulosonic acid (9-COA) (2), 3-caffeoyl-2,7-anhydro-3-deoxy-2-octulopyranosonic acid (3-CDOA) (3), erigeside I (4), quercetin-3-O-glucuronide (5), eriodictyol-7-O-glucuronide (6), scutellarin (7), 1,4-di-O-caffeoylquinic acid (1,4-di-CQA) (8), 3,5-di-CQA (9), 1-malonyl-3,5-di-CQA (10), erigoster B (11), 4,5-di-CQA (12) and 4,9-di-CDOA (13)) and 9 radical scavengers (including 1, 4, 7, 8, 9, 10, 11, 12 and 13) were discovered, respectively. Furthermore, the anti-oxidative activities of 4 compounds, including 7, 9, 11 and 12 were evaluated. Reverse anti-oxidative activity order of scutellarin and 3,5-di-CQA was observed in on-line HPLC-ABTS assay and on-line HPLC-DPPH assay. To validate their anti-oxidative activities, the off-line ABTS and DPPH assays were performed. Given sufficient reaction time, 3,5-di-CQA showed higher activity than scutellarin, which was consistent with the order obtained in on-line HPLC-ABTS assay. These results revealed that on-line HPLC-ABTS assay is a more sensitive method for screening and determining free radical scavengers, especially more suitable for those compounds with slower reaction kinetics.     

Natural variation in germination responses of Arabidopsis to seasonal cues and their associated physiological mechanisms

Background and Aims

Despite the intense interest in phenological adaptation to environmental change, the fundamental character of natural variation in germination is almost entirely unknown. Specifically, it is not known whether different genotypes within a species are germination specialists to particular conditions, nor is it known what physiological mechanisms of germination regulation vary in natural populations and how they are associated with responses to particular environmental factors.

Methods

We used a set of recombinant inbred genotypes of Arabidopsis thaliana, in which linkage disequilibrium has been disrupted over seven generations, to test for genetic variation and covariation in germination responses to distinct environmental factors. We then examined physiological mechanisms associated with those responses, including seed-coat permeability and sensitivity to the phytohormones gibberellic acid (GA) and abscisic acid (ABA).

Key Results

Genetic variation for germination was environment-dependent, but no evidence for specialization of germination to different conditions was found. Hormonal sensitivities also exhibited significant genetic variation, but seed-coat properties did not. GA sensitivity was associated with germination responses to multiple environmental factors, but seed-coat permeability and ABA sensitivity were associated with specific germination responses, suggesting that an evolutionary change in GA sensitivity could affect germination in multiple environments, but that of ABA sensitivity may affect germination under more restricted conditions.

Conclusions

The physiological mechanisms of germination responses to specific environmental factors therefore can influence the ability to adapt to diverse seasonal environments encountered during colonization of new habitats or with future predicted climate change.     

Temperament and Character in the Child and Adolescent Twin Study in Sweden (CATSS): Comparison to the General Population,and Genetic Structure Analysis

Background

The Child and Adolescent Twin Study in Sweden (CATSS) is an on-going, large population-based longitudinal twin study. We aimed (1) to investigate the reliability of two different versions (125-items and 238-items) of Cloninger''s Temperament and Character Inventory (TCI) used in the CATSS and the validity of extracting the short version from the long version, (2) to compare these personality dimensions between twins and adolescents from the general population, and (3) to investigate the genetic structure of Cloninger''s model.

Method

Reliability and correlation analyses were conducted for both TCI versions, 2,714 CATSS-twins were compared to 631 adolescents from the general population, and the genetic structure was investigated through univariate genetic analyses, using a model-fitting approach with structural equation-modeling techniques based on same-sex twin pairs from the CATSS (423 monozygotic and 408 dizygotic pairs).

Results

The TCI scores from the short and long versions showed comparable reliability coefficients and were strongly correlated. Twins scored about half a standard deviation higher in the character scales. Three of the four temperament dimensions (Novelty Seeking, Harm Avoidance, and Persistence) had strong genetic and non-shared environmental effects, while Reward Dependence and the three character dimensions had moderate genetic effects, and both shared and non-shared environmental effects.

Conclusions

Twins showed higher scores in character dimensions compared to adolescents from the general population. At least among adolescents there is a shared environmental influence for all of the character dimensions, but only for one of the temperament dimensions (i.e., Reward Dependence). This specific finding regarding the existence of shared environmental factors behind the character dimensions in adolescence, together with earlier findings showing a small shared environmental effects on character among young adults and no shared environmental effects on character among adults, suggest that there is a shift in type of environmental influence from adolescence to adulthood regarding character.     

Stability and bioavailability of antioxidants in garland (Chrysanthemum coronarium L.)

The stability and bioavailability of the major antioxidants in garland (Chrysanthemum coronarium L.), chlorogenic acid, 3,5-dicaffeoylquinic acid and 4-succinyl-3,5-dicaffeoylquinic acid, were investigated together with caffeic acid. These compounds were stable in artificial digestive juice, but more than 90% of them disappeared from plasma within 30 min after intravenous injection into rats. When they were orally administered, only caffeic acid could be detected.     

Plant hormone interaction and phenolic metabolism in the regulation of russet spotting in iceberg lettuce

Russet spotting (RS) is a physiological disorder induced in iceberg lettuce (Lactuca sativa L.) by exposure to parts per million levels of ethylene at 5 ± 2°C. Ethylene induced phenylalanine ammonia-lyase and ionically bound peroxidase activities that correlated with development of RS symptoms. The ethylene-treated tissue had significantly higher lignin content than air control tissue with lignification localized in walls of RS-affected cells. Ethylene also caused the accumulation of the flavonoids (+)catechin and (−)epicatechin and the chlorogenic acid derivatives 3-caffeoyl-quinic acid, 3,5-dicaffeoylquinic acid, and 4,5-dicaffeoylquinic acid. These soluble phenolic compounds were readily oxidized to brown substances by polyphenol oxidase isolated from RS tissue. Ethylene substantially increased ionically bound indole-3-acetic acid (IAA) oxidase activity, while IAA application greatly reduced ethylene-induced phenylalanine ammonia-lyase, peroxidase, and IAA oxidase activities, soluble phenolic content, and RS development.     

Temporal changes in population genetic diversity and structure in red and white clover grown in three contrasting environments in northern Europe

Backgound and Aims

Extending the cultivation of forage legume species into regions where they are close to the margin of their natural distribution requires knowledge of population responses to environmental stresses. This study was conducted at three north European sites (Iceland, Sweden and the UK) using AFLP markers to analyse changes in genetic structure over time in two population types of red and white clover (Trifolium pratense and T. repens, respectively): (1) standard commercial varieties; (2) wide genetic base (WGB) composite populations constructed from many commercial varieties plus unselected material obtained from germplasm collections.

Methods

At each site populations were grown in field plots, then randomly sampled after 3–5 years to obtain survivor populations. AFLP markers were used to calculate genetic differentiation within and between original and survivor populations.

Key Results

No consistent changes in average genetic diversity were observed between original and survivor populations. In both species the original varieties were always genetically distinct from each other. Significant genetic shift was observed in the white clover ‘Ramona’ grown in Sweden. The WGB original populations were more genetically similar. However, genetic differentiation occurred between original and survivor WGB germplasm in both species, particularly in Sweden. Regression of climatic data with genetic differentiation showed that low autumn temperature was the best predictor. Within the set of cold sites the highest level of genetic shift in populations was observed in Sweden.

Conclusions

The results suggest that changes in population structure can occur within a short time span in forage legumes, resulting in the rapid formation of distinct survivor populations in environmentally challenging sites.     

The genetic liability to disability retirement: a 30-year follow-up study of 24,000 Finnish twins

Background

No previous studies on the effect of genetic factors on the liability to disability retirement have been carried out. The main aim of this study was to investigate the contribution of genetic factors on disability retirement due to the most common medical causes, including depressive disorders.

Methods

The study sample consisted of 24 043 participants (49.7% women) consisting of 11 186 complete same-sex twin pairs including 3519 monozygotic (MZ) and 7667dizygotic (DZ) pairs. Information on retirement events during 1.1.1975–31.12.2004, including disability pensions (DPs) with diagnoses, was obtained from the Finnish nationwide official pension registers. Correlations in liability for MZ and DZ twins and discrete time correlated frailty model were used to investigate the genetic liability to age at disability retirement.

Results

The 30 year cumulative incidence of disability retirement was 20%. Under the best fitting genetic models, the heritability estimate for DPs due to any medical cause was 0.36 (95% CI 0.32–0.40), due to musculoskeletal disorders 0.37 (0.30–0.43), cardiovascular diseases 0.48 (0.39–0.57), mental disorders 0.42 (0.35–0.49) and all other reasons 0.24 (0.17–0.31). The effect of genetic factors decreased with increasing age of retirement. For DP due to depressive disorders, 28% of the variance was explained by environmental factors shared by family members (95% CI 21–36) and 58% of the variance by the age interval specific environmental factors (95% CI 44–71).

Conclusions

A moderate genetic contribution to the variation of disability retirement due to any medical cause was found. The genetic effects appeared to be stronger at younger ages of disability retirement suggesting the increasing influence of environmental factors not shared with family members with increasing age. Familial aggregation in DPs due to depressive disorders was best explained by the common environmental factors and genetic factors were not needed to account for the pattern of familial aggregation.     

Preparative isolation and purification of dicaffeoylquinic acids from the Ainsliaea fragrans champ by high-speed counter-current chromatography

Two dicaffeoylquinic acids, namely 3,5-dicaffeoylquinic acid and 4,5-dicaffeoylquinic acid, have been successfully separated by high-speed counter-current chromatography (HSCCC) from an extract of Ainsliaea fragrans Champ, followed by an initial clean-up step using AB-8 resin. A two-phase solvent system composed of chloroform:methanol:water (8:8:4) was selected for the isolation with the aqueous-rich phase as the stationary phase and the organic-rich phase as the mobile phase. The developed HSCCC method yielded 34 mg of 3,5-dicaffeoylquinic acid and 17 mg of 4,5-dicaffeoylquinic acid from 150 mg of the crude sample in a one-step separation with purities of 98 and 95%, respectively, as determined by HPLC. The structures of the two compounds were identified from ESI/MS, (1)H- and (13)C-NMR spectroscopic data.     

Global distribution of outbreaks of water-associated infectious diseases

Background

Water plays an important role in the transmission of many infectious diseases, which pose a great burden on global public health. However, the global distribution of these water-associated infectious diseases and underlying factors remain largely unexplored.

Methods and Findings

Based on the Global Infectious Disease and Epidemiology Network (GIDEON), a global database including water-associated pathogens and diseases was developed. In this study, reported outbreak events associated with corresponding water-associated infectious diseases from 1991 to 2008 were extracted from the database. The location of each reported outbreak event was identified and geocoded into a GIS database. Also collected in the GIS database included geo-referenced socio-environmental information including population density (2000), annual accumulated temperature, surface water area, and average annual precipitation. Poisson models with Bayesian inference were developed to explore the association between these socio-environmental factors and distribution of the reported outbreak events. Based on model predictions a global relative risk map was generated. A total of 1,428 reported outbreak events were retrieved from the database. The analysis suggested that outbreaks of water-associated diseases are significantly correlated with socio-environmental factors. Population density is a significant risk factor for all categories of reported outbreaks of water-associated diseases; water-related diseases (e.g., vector-borne diseases) are associated with accumulated temperature; water-washed diseases (e.g., conjunctivitis) are inversely related to surface water area; both water-borne and water-related diseases are inversely related to average annual rainfall. Based on the model predictions, “hotspots” of risks for all categories of water-associated diseases were explored.

Conclusions

At the global scale, water-associated infectious diseases are significantly correlated with socio-environmental factors, impacting all regions which are affected disproportionately by different categories of water-associated infectious diseases.     

A local dormancy cline is related to the seed maturation environment,population genetic composition and climate

Background and Aims

Seed dormancy varies within species in response to climate, both in the long term (through ecotypes or clines) and in the short term (through the influence of the seed maturation environment). Disentangling both processes is crucial to understand plant adaptation to environmental changes. In this study, the local patterns of seed dormancy were investigated in a narrow endemic species, Centaurium somedanum, in order to determine the influence of the seed maturation environment, population genetic composition and climate.

Methods

Laboratory germination experiments were performed to measure dormancy in (1) seeds collected from different wild populations along a local altitudinal gradient and (2) seeds of a subsequent generation produced in a common garden. The genetic composition of the original populations was characterized using intersimple sequence repeat (ISSR) PCR and principal co-ordinate analysis (PCoA), and its correlation with the dormancy patterns of both generations was analysed. The effect of the local climate on dormancy was also modelled.

Key Results

An altitudinal dormancy cline was found in the wild populations, which was maintained by the plants grown in the common garden. However, seeds from the common garden responded better to stratification, and their release from dormancy was more intense. The patterns of dormancy variation were correlated with genetic composition, whereas lower temperature and summer precipitation at the population sites predicted higher dormancy in the seeds of both generations.

Conclusions

The dormancy cline in C. somedanum is related to a local climatic gradient and also corresponds to genetic differentiation among populations. This cline is further affected by the weather conditions during seed maturation, which influence the receptiveness to dormancy-breaking factors. These results show that dormancy is influenced by both long-and short-term climatic variation. Such processes at such a reduced spatial scale highlight the potential of plants to adapt to fast environmental changes.     

Active Trachoma among Children in Mali: Clustering and Environmental Risk Factors

Background

Active trachoma is not uniformly distributed in endemic areas, and local environmental factors influencing its prevalence are not yet adequately understood. Determining whether clustering is a consistent phenomenon may help predict likely modes of transmission and help to determine the appropriate level at which to target control interventions. The aims of this study were, therefore, to disentangle the relative importance of clustering at different levels and to assess the respective role of individual, socio-demographic, and environmental factors on active trachoma prevalence among children in Mali.

Methodology/Principal Findings

We used anonymous data collected during the Mali national trachoma survey (1996–1997) at different levels of the traditional social structure (14,627 children under 10 years of age, 6,251 caretakers, 2,269 households, 203 villages). Besides field-collected data, environmental variables were retrieved later from various databases at the village level. Bayesian hierarchical logistic models were fit to these prevalence and exposure data. Clustering revealed significant results at four hierarchical levels. The higher proportion of the variation in the occurrence of active trachoma was attributable to the village level (36.7%), followed by household (25.3%), and child (24.7%) levels. Beyond some well-established individual risk factors (age between 3 and 5, dirty face, and flies on the face), we showed that caretaker-level (wiping after body washing), household-level (common ownership of radio, and motorbike), and village-level (presence of a women''s association, average monthly maximal temperature and sunshine fraction, average annual mean temperature, presence of rainy days) features were associated with reduced active trachoma prevalence.

Conclusions/Significance

This study clearly indicates the importance of directing control efforts both at children with active trachoma as well as those with close contact, and at communities. The results support facial cleanliness and environmental improvements (the SAFE strategy) as population-health initiatives to combat blinding trachoma.     

Conspecific crop-weed introgression influences evolution of weedy rice (Oryza sativa f. spontanea) across a geographical range

Background

Introgression plays an important role in evolution of plant species via its influences on genetic diversity and differentiation. Outcrossing determines the level of introgression but little is known about the relationships of outcrossing rates, genetic diversity, and differentiation particularly in a weedy taxon that coexists with its conspecific crop.

Methodology/Principal Findings

Eleven weedy rice (Oryza sativa f. spontanea) populations from China were analyzed using microsatellite (SSR) fingerprints to study outcrossing rate and its relationship with genetic variability and differentiation. To estimate outcrossing, six highly polymorphic SSR loci were used to analyze >5500 progeny from 216 weedy rice families, applying a mixed mating model; to estimate genetic diversity and differentiation, 22 SSR loci were analyzed based on 301 weedy individuals. Additionally, four weed-crop shared SSR loci were used to estimate the influence of introgression from rice cultivars on weedy rice differentiation. Outcrossing rates varied significantly (0.4∼11.7%) among weedy rice populations showing relatively high overall Nei''s genetic diversity (0.635). The observed heterozygosity was significantly correlated with outcrossing rates among populations (r² = 0.783; P<0.001) although no obvious correlation between outcrossing rates and genetic diversity parameters was observed. Allelic introgression from rice cultivars to their coexisting weedy rice was detected. Weedy rice populations demonstrated considerable genetic differentiation that was correlated with their spatial distribution (r² = 0.734; P<0.001), and possibly also influenced by the introgression from rice cultivars.

Conclusions/Significance

Outcrossing rates can significantly affect heterozygosity of populations, which may shape the evolutionary potential of weedy rice. Introgression from the conspecific crop rice can influence the genetic differentiation and possibly evolution of its coexisting weedy rice populations.     

Environmental variation and rivers govern the structure of chimpanzee genetic diversity in a biodiversity hotspot

Background

The mechanisms that underlie the diversification of tropical animals remain poorly understood, but new approaches that combine geo-spatial modeling with spatially explicit genetic data are providing fresh insights on this topic. Data about the diversification of tropical mammals remain particularly sparse, and vanishingly few opportunities exist to study endangered large mammals that increasingly exist only in isolated pockets. The chimpanzees of Cameroon represent a unique opportunity to examine the mechanisms that promote genetic differentiation in tropical mammals because the region is home to two chimpanzee subspecies: Pan troglodytes ellioti and P. t. trogolodytes. Their ranges converge in central Cameroon, which is a geographically, climatically and environmentally complex region that presents an unparalleled opportunity to examine the roles of rivers and/or environmental variation in influencing the evolution of chimpanzee populations.

Results

We analyzed microsatellite genotypes and mtDNA HVRI sequencing data from wild chimpanzees sampled at a fine geographic scale across Cameroon and eastern Nigeria using a spatially explicit approach based upon Generalized Dissimilarity Modeling. Both the Sanaga River and environmental variation were found to contribute to driving separation of the subspecies. The importance of environmental variation differed among subspecies. Gene-environment associations were weak in P. t. troglodytes, whereas environmental variation was found to play a much larger role in shaping patterns of genetic differentiation in P. t. ellioti.

Conclusions

We found that both the Sanaga River and environmental variation likely play a role in shaping patterns of chimpanzee genetic diversity. Future studies using single nucleotide polymorphism (SNP) data are necessary to further understand how rivers and environmental variation contribute to shaping patterns of genetic variation in chimpanzees.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0274-0) contains supplementary material, which is available to authorized users.     

Gene bionetworks involved in the epigenetic transgenerational inheritance of altered mate preference: environmental epigenetics and evolutionary biology

Background

Mate preference behavior is an essential first step in sexual selection and is a critical determinant in evolutionary biology. Previously an environmental compound (the fungicide vinclozolin) was found to promote the epigenetic transgenerational inheritance of an altered sperm epigenome and modified mate preference characteristics for three generations after exposure of a gestating female.

Results

The current study investigated gene networks involved in various regions of the brain that correlated with the altered mate preference behavior in the male and female. Statistically significant correlations of gene clusters and modules were identified to associate with specific mate preference behaviors. This novel systems biology approach identified gene networks (bionetworks) involved in sex-specific mate preference behavior. Observations demonstrate the ability of environmental factors to promote the epigenetic transgenerational inheritance of this altered evolutionary biology determinant.

Conclusions

Combined observations elucidate the potential molecular control of mate preference behavior and suggests environmental epigenetics can have a role in evolutionary biology.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-377) contains supplementary material, which is available to authorized users.     

Genetic adaptation of the human circadian clock to day-length latitudinal variations and relevance for affective disorders

Background

The temporal coordination of biological processes into daily cycles is a common feature of most living organisms. In humans, disruption of circadian rhythms is commonly observed in psychiatric diseases, including schizophrenia, bipolar disorder, depression and autism. Light therapy is the most effective treatment for seasonal affective disorder and circadian-related treatments sustain antidepressant response in bipolar disorder patients. Day/night cycles represent a major circadian synchronizing signal and vary widely with latitude.

Results

We apply a geographically explicit model to show that out-of-Africa migration, which led humans to occupy a wide latitudinal area, affected the evolutionary history of circadian regulatory genes. The SNPs we identify using this model display consistent signals of natural selection using tests based on population genetic differentiation and haplotype homozygosity. Signals of natural selection driven by annual photoperiod variation are detected for schizophrenia, bipolar disorder, and restless leg syndrome risk variants, in line with the circadian component of these conditions.

Conclusions

Our results suggest that human populations adapted to life at different latitudes by tuning their circadian clock systems. This process also involves risk variants for neuropsychiatric conditions, suggesting possible genetic modulators for chronotherapies and candidates for interaction analysis with photoperiod-related environmental variables, such as season of birth, country of residence, shift-work or lifestyle habits.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0499-7) contains supplementary material, which is available to authorized users.     

Distribution and Prevalence of the Australian Non-Pathogenic Rabbit Calicivirus Is Correlated with Rainfall and Temperature

Background

Australia relies heavily on rabbit haemorrhagic disease virus (RHDV) for the biological control of introduced European wild rabbits Oryctolagus cuniculus, which are significant economic and environmental pests. An endemic non-pathogenic rabbit calicivirus termed RCV–A1 also occurs in wild rabbits in Australian and provides partial protection against lethal RHDV infection, thus interfering with effective rabbit control. Despite its obvious importance for rabbit population management, little is known about the epidemiology of this benign rabbit calicivirus.

Methods

We determined the continent-wide distribution and prevalence of RCV-A1 by analysing 1,805 serum samples from wild rabbit populations at 78 sites across Australia for the presence of antibodies to RCV-A1 using a serological test that specifically detects RCV-A1 antibodies and does not cross-react with co-occurring RHDV antibodies. We also investigated possible correlation between climate variables and prevalence of RCV-A1 by using generalised linear mixed effect models.

Results

Antibodies to RCV-A1 were predominantly detected in rabbit populations in cool, high rainfall areas of the south-east and south-west of the continent. There was strong support for modelling RCV-A1 prevalence as a function of average annual rainfall and minimum temperature. The best ranked model explained 26% of the model structural deviance. According to this model, distribution and prevalence of RCV-A1 is positively correlated with periods of above average rainfall and negatively correlated with periods of drought.

Implications

Our statistical model of RCV-A1 prevalence will greatly increase our understanding of RCV-A1 epidemiology and its interaction with RHDV in Australia. By defining the environmental conditions associated with the prevalence of RCV-A1, it also contributes towards understanding the distribution of similar viruses in New Zealand and Europe.     

Identifying ontogenetic, environmental and individual components of forest tree growth

Background and Aims

This study aimed to identify and characterize the ontogenetic, environmental and individual components of forest tree growth. In the proposed approach, the tree growth data typically correspond to the retrospective measurement of annual shoot characteristics (e.g. length) along the trunk.

Methods

Dedicated statistical models (semi-Markov switching linear mixed models) were applied to data sets of Corsican pine and sessile oak. In the semi-Markov switching linear mixed models estimated from these data sets, the underlying semi-Markov chain represents both the succession of growth phases and their lengths, while the linear mixed models represent both the influence of climatic factors and the inter-individual heterogeneity within each growth phase.

Key Results

On the basis of these integrative statistical models, it is shown that growth phases are not only defined by average growth level but also by growth fluctuation amplitudes in response to climatic factors and inter-individual heterogeneity and that the individual tree status within the population may change between phases. Species plasticity affected the response to climatic factors while tree origin, sampling strategy and silvicultural interventions impacted inter-individual heterogeneity.

Conclusions

The transposition of the proposed integrative statistical modelling approach to cambial growth in relation to climatic factors and the study of the relationship between apical growth and cambial growth constitute the next steps in this research.