Pleiotropic effects of melanin pigmentation: haemoparasite infection intensity but not telomere length is associated with plumage morph in black sparrowhawks.

There is increasing recognition of the potential pleiotropic effects of melanin pigmentation, particularly on immunity, with reports of variation in haemoparasite infection intensity and immune responses between the morphs of colour-polymorphic bird species. In a population of the black sparrowhawk (Accipiter melanoleucus) in western South Africa, light morphs have a higher haemoparasite infection intensity, but no physiological effects of this are apparent. Here, we investigate the possible effects of haemoparasite infection on telomere length in this species and explore whether relative telomere length is associated with either plumage morph or sex. Using quantitative polymerase chain reaction analysis, we confirmed that dark morphs had a lower haemoparasite infection intensity than light morphs. However, we found no differences in telomere length associated with either the haemoparasite infection status or morph in adults, although males have longer telomeres than females. While differences in haemoparasite intensity between morphs are consistent with pleiotropic effects of melanin pigmentation in the black sparrowhawk, we found no evidence that telomere length was associated with haemoparasite infection. Further work is needed to investigate the implications of possible pleiotropic effects of plumage morph and their potential role in the maintenance of colour polymorphism in this species.

Defining predictors of responsiveness to advanced therapies in Crohn's disease and ulcerative colitis: protocol for the IBD-RESPONSE and nested CD-metaRESPONSE prospective, multicentre, observational cohort study in precision medicine.

INTRODUCTION: Characterised by chronic inflammation of the gastrointestinal tract, inflammatory bowel disease (IBD) symptoms including diarrhoea, abdominal pain and fatigue can significantly impact patient's quality of life. Therapeutic developments in the last 20 years have revolutionised treatment. However, clinical trials and real-world data show primary non-response rates up to 40%. A significant challenge is an inability to predict which treatment will benefit individual patients.Current understanding of IBD pathogenesis implicates complex interactions between host genetics and the gut microbiome. Most cohorts studying the gut microbiota to date have been underpowered, examined single treatments and produced heterogeneous results. Lack of cross-treatment comparisons and well-powered independent replication cohorts hampers the ability to infer real-world utility of predictive signatures.IBD-RESPONSE will use multi-omic data to create a predictive tool for treatment response. Future patient benefit may include development of biomarker-based treatment stratification or manipulation of intestinal microbial targets. IBD-RESPONSE and downstream studies have the potential to improve quality of life, reduce patient risk and reduce expenditure on ineffective treatments. METHODS AND ANALYSIS: This prospective, multicentre, observational study will identify and validate a predictive model for response to advanced IBD therapies, incorporating gut microbiome, metabolome, single-cell transcriptome, human genome, dietary and clinical data. 1325 participants commencing advanced therapies will be recruited from ~40 UK sites. Data will be collected at baseline, week 14 and week 54. The primary outcome is week 14 clinical response. Secondary outcomes include clinical remission, loss of response in week 14 responders, corticosteroid-free response/remission, time to treatment escalation and change in patient-reported outcome measures. ETHICS AND DISSEMINATION: Ethical approval was obtained from the Wales Research Ethics Committee 5 (ref: 21/WA/0228). Recruitment is ongoing. Following study completion, results will be submitted for publication in peer-reviewed journals and presented at scientific meetings. Publications will be summarised at www.ibd-response.co.uk. TRIAL REGISTRATION NUMBER: ISRCTN96296121.

Reviewing essential public health functions in the Eastern Mediterranean Region post COVID-19 pandemic: a foundation for system resilience.

The COVID-19 pandemic exposed vulnerabilities in many health systems worldwide with profound implications for health and society. The public health challenges experienced during the pandemic have highlighted the importance of resilient health systems, that can adapt and transform to meet the population's evolving health needs. Essential public health functions (EPHFs) offer a holistic, integrated and sustainable approach to public health by contributing to achieving several health priorities and goals. In recent years, there has been a focused effort to conceptualise and define the EPHFs. In this paper, we describe the collaborative approach undertaken by the WHO Eastern Mediterranean Region (EMR) and UK Health Security Agency and present the findings and results of the revised EPHFs, in view of lessons learnt from the COVID-19 pandemic and the current priorities for countries across the EMR. This included conducting a desktop review, a gap and bottleneck analysis and stakeholder consultation to arrive at the revised EPHF model including four enablers and nine core functions, including a new function: public health services. The EPHFs will offer countries a complementary and synergistic approach to strengthen health systems and public health capacities and contribute to the region's ability to effectively respond to future health challenges and emergencies. By focusing on the EPHFs, countries can work towards ensuring health security as an integral goal for the health system besides universal health coverage, thus strengthening and building more resilient and equitable health systems.

Only rare classical MHC-I alleles are highly expressed in the European house sparrow.

The exceptional polymorphism observed within genes of the major histocompatibility complex (MHC), a core component of the vertebrate immune system, has long fascinated biologists. The highly polymorphic classical MHC class-I (MHC-I) genes are maintained by pathogen-mediated balancing selection (PMBS), as shown by many sites subject to positive selection, while the more monomorphic non-classical MHC-I genes show signatures of purifying selection. In line with PMBS, at any point in time, rare classical MHC alleles are more likely than common classical MHC alleles to confer a selective advantage in host-pathogen interactions. Combining genomic and expression data from the blood of wild house sparrows Passer domesticus, we found that only rare classical MHC-I alleles were highly expressed, while common classical MHC-I alleles were lowly expressed or not expressed. Moreover, highly expressed rare classical MHC-I alleles had more positively selected sites, indicating exposure to stronger PMBS, compared with lowly expressed classical alleles. As predicted, the level of expression was unrelated to allele frequency in the monomorphic non-classical MHC-I alleles. Going beyond previous studies, we offer a fine-scale view of selection on classical MHC-I genes in a wild population by revealing differences in the strength of PMBS according to allele frequency and expression level.

A systematic review of interventions targeting physical activity and/or healthy eating behaviours in adolescents: practice and training.

Despite the many health benefits of physical activity (PA) and healthy eating (HE) most adolescents do not meet current guidelines which poses future health risks. This review aimed to (1) identify whether adolescent PA and HE interventions show promise at promoting behaviour change and maintenance, (2) identify which behaviour change techniques (BCTs) are associated with promising interventions, and (3) explore the optimal approaches to training deliverers of adolescent PA/HE interventions. Nine databases were searched for randomised controlled, or quasi-experimental, trials targeting 10-19 year olds, with a primary aim to increase PA/HE, measured at baseline and at least six months post-intervention, in addition to papers reporting training of deliverers of adolescent PA/HE interventions. Included were seven PA studies, three HE studies and four studies targeting both, with two training papers. For PA studies, two were promising post-intervention with two promising BCTs, and five were promising for maintenance with two promising BCTs. For HE studies, three were promising at post-intervention and four at maintenance, both with four promising BCTs. There is preliminary evidence that interventions support adolescents to improve their PA and HE behaviours over a period of at least six months.

Urbanisation impacts plumage colouration in a songbird across Europe: Evidence from a correlational, experimental and meta-analytical approach.

Urbanisation is accelerating across the globe, transforming landscapes, presenting organisms with novel challenges, shaping phenotypes and impacting fitness. Urban individuals are claimed to have duller carotenoid-based colouration, compared to their non-urban counterparts, the so-called 'urban dullness' phenomenon. However, at the intraspecific level, this generalisation is surprisingly inconsistent and often based on comparisons of single urban/non-urban populations or studies from a limited geographical area. Here, we combine correlational, experimental and meta-analytical data on a common songbird, the great tit Parus major, to investigate carotenoid-based plumage colouration in urban and forest populations across Europe. We find that, as predicted, urban individuals are paler than forest individuals, although there are large population-specific differences in the magnitude of the urban-forest contrast in colouration. Using one focal region (Malmö, Sweden), we reveal population-specific processes behind plumage colouration differences, which are unlikely to be the result of genetic or early-life conditions, but instead a consequence of environmental factors acting after fledging. Finally, our meta-analysis indicates that the urban dullness phenomenon is well established in the literature, for great tits, with consistent changes in carotenoid-based plumage traits, particularly carotenoid chroma, in response to anthropogenic disturbances. Overall, our results provide evidence for uniformity in the 'urban dullness' phenomenon but also highlight that the magnitude of the effect on colouration depends on local urban characteristics. Future long-term replicated studies, covering a wider range of species and feeding guilds, will be essential to further our understanding of the eco-evolutionary implications of this phenomenon.

Acute stroke CDS: automatic retrieval of thrombolysis contraindications from unstructured clinical letters.

Introduction: Thrombolysis treatment for acute ischaemic stroke can lead to better outcomes if administered early enough. However, contraindications exist which put the patient at greater risk of a bleed (e.g. recent major surgery, anticoagulant medication). Therefore, clinicians must check a patient's past medical history before proceeding with treatment. In this work we present a machine learning approach for accurate automatic detection of this information in unstructured text documents such as discharge letters or referral letters, to support the clinician in making a decision about whether to administer thrombolysis. Methods: We consulted local and national guidelines for thrombolysis eligibility, identifying 86 entities which are relevant to the thrombolysis decision. A total of 8,067 documents from 2,912 patients were manually annotated with these entities by medical students and clinicians. Using this data, we trained and validated several transformer-based named entity recognition (NER) models, focusing on transformer models which have been pre-trained on a biomedical corpus as these have shown most promise in the biomedical NER literature. Results: Our best model was a PubMedBERT-based approach, which obtained a lenient micro/macro F1 score of 0.829/0.723. Ensembling 5 variants of this model gave a significant boost to precision, obtaining micro/macro F1 of 0.846/0.734 which approaches the human annotator performance of 0.847/0.839. We further propose numeric definitions for the concepts of name regularity (similarity of all spans which refer to an entity) and context regularity (similarity of all context surrounding mentions of an entity), using these to analyse the types of errors made by the system and finding that the name regularity of an entity is a stronger predictor of model performance than raw training set frequency. Discussion: Overall, this work shows the potential of machine learning to provide clinical decision support (CDS) for the time-critical decision of thrombolysis administration in ischaemic stroke by quickly surfacing relevant information, leading to prompt treatment and hence to better patient outcomes.

Feather corticosterone reveals that urban great tits experience lower corticosterone exposure than forest individuals during dominance-rank establishment.

Although the consequences of urbanization for the physiological health of animals are the focus of much active research, an overlooked aspect is how physiology could be indirectly modulated by the urban environment via changes in intraspecific behavioural interactions, particularly among gregarious species. Both urbanization and the establishment, as well as maintenance, of hierarchical rank position are processes that could incur physiological stress. Measurements of glucocorticoids (GCs) in relation to urbanization, however, have yielded inconsistent results. In most cases, GCs have been measured in blood, offering only a 'snapshot' of an animal's current physiological state. Because circulating GCs are incorporated into growing feathers or hair, measurements of feather/hair GCs offer a longer term measure of stress exposure reflecting the whole period of feather/hair growth. During two calendar years, we collected tail feathers from 188 urban and forest great tits (P. major) across multiple sampling sites and analysed corticosterone (CORT-the main GC in birds) levels, reflecting CORT exposure during the extended period in late summer and early autumn when great tits moult and winter flocks are formed. Urban individuals exhibited consistently lower feather CORT (fCORT) levels than forest birds indicating lower overall exposure to CORT during this period. The lower fCORT levels in urban individuals could represent an adaptation to cope with the more challenging urban environment, physiological constraints on stress axis function or a trade-off between the ability to respond to stressors and predation risk during moult. Despite the expectation that CORT responses to urbanization are highly context-dependent, the spatial consistency of our results and agreement with a multi-population study of fCORT in European blackbirds (Turdus merula) suggests a generalization of the effect of urbanization on CORT exposure during post-breeding moult (i.e. not site- or species-specific).

Thermoregulatory costs of the innate immune response are modulated by winter food availability in a small passerine.

In winter, a challenge to the immune system could pose a major energetic trade-off for small endotherms, whereby increasing body temperature (Tb ; i.e. eliciting fever) may be beneficial to fight off invading pathogens yet incur a cost for vital energy-saving mechanisms. Having previously shown that the availability and acquisition of energy, through manipulation of food predictability, influences the depth of rest-phase hypothermia in a wild bird in winter, we expected that the nocturnal thermoregulatory component of the acute-phase immune response would also be modulated by food availability. By manipulating winter food availability in the wild for great tits Parus major, we created an area offering a "predictable" and constant supply of food at feeding stations, while an unmanipulated area was subject to naturally "unpredictable" food. Birds were subject to an immune challenge shortly after dusk, and the thermoregulatory response was quantified via continuous recording of nocturnal Tb , using subcutaneous thermo-sensitive transponders. In response to immune challenge, all birds increased Tb above the level maintained prior to immune challenge (i.e. baseline). However, birds experiencing a naturally unpredictable food supply elevated Tb more than birds subject to predictable food resources, during the period of expected peak response and for the duration of the night. Furthermore, "unpredictable-food" females took longer to return to their baseline Tb . Assuming baseline nocturnal Tb reflects an individual's optimum, based on their available energy budget, the metabolic cost of eliciting an acute-phase response for "unpredictable-food" birds was more than double that of "predictable-food" birds. The absence of differences in absolute Tb during the peak response could support the idea of an optimal Tb for immune system activation. Alternatively, "predictable-food" birds could have acquired tolerance to endotoxin as a result of using feeding stations, thus affording them reduced costs associated with a smaller Tb increase. These findings shed new light on the trade-offs associated with food acquisition, thermoregulation and immune function in small-bodied endotherms. This knowledge is of increasing importance, given the predicted elevated pathogen risks associated with changes in climate and anthropogenic activities.

Interactive effects of rising temperatures and urbanisation on birds across different climate zones: A mechanistic perspective.

Climate change and urbanisation are among the most pervasive and rapidly growing threats to biodiversity worldwide. However, their impacts are usually considered in isolation, and interactions are rarely examined. Predicting species' responses to the combined effects of climate change and urbanisation, therefore, represents a pressing challenge in global change biology. Birds are important model taxa for exploring the impacts of both climate change and urbanisation, and their behaviour and physiology have been well studied in urban and non-urban systems. This understanding should allow interactive effects of rising temperatures and urbanisation to be inferred, yet considerations of these interactions are almost entirely lacking from empirical research. Here, we synthesise our current understanding of the potential mechanisms that could affect how species respond to the combined effects of rising temperatures and urbanisation, with a focus on avian taxa. We discuss potential interactive effects to motivate future in-depth research on this critically important, yet overlooked, aspect of global change biology. Increased temperatures are a pronounced consequence of both urbanisation (through the urban heat island effect) and climate change. The biological impact of this warming in urban and non-urban systems will likely differ in magnitude and direction when interacting with other factors that typically vary between these habitats, such as resource availability (e.g. water, food and microsites) and pollution levels. Furthermore, the nature of such interactions may differ for cities situated in different climate types, for example, tropical, arid, temperate, continental and polar. Within this article, we highlight the potential for interactive effects of climate and urban drivers on the mechanistic responses of birds, identify knowledge gaps and propose promising future research avenues. A deeper understanding of the behavioural and physiological mechanisms mediating species' responses to urbanisation and rising temperatures will provide novel insights into ecology and evolution under global change and may help better predict future population responses.

Urban tree composition is associated with breeding success of a passerine bird, but effects vary within and between years.

Birds breeding in urban environments have lower reproductive output compared to rural conspecifics, most likely because of food limitation. However, which characteristics of urban environments may cause this deficiency is not clear. Here, we investigated how tree composition within urban territories of passerine birds is associated with breeding probability and reproductive success. We used 7 years of data of breeding occupancy for blue and great tits (Cyanistes caeruleus; Parus major) and several reproductive traits for great tits, from 400 urban nest boxes located in 5 parks within the city of Malmö, Sweden. We found that tits, overall, were less likely to breed in territories dominated by either non-native trees or beech trees. Great tit chicks reared in territories dominated by non-native trees weighed significantly less, compared to territories with fewer non-native trees. An earlier onset of breeding correlated with increased chick weight in great tits. Increasing number of common oak trees (Quercus robur) was associated with delayed onset of breeding in great tits. Notably, as offspring survival probability generally increased by breeding earlier, in particular in oak-dominated territories, our results suggest that delayed onset of breeding induced by oak trees may be maladaptive and indicate a mismatch to this food source. Our results demonstrate that tree composition may have important consequences on breeding success of urban birds, but some of these effects are not consistent between years, highlighting the need to account for temporal effects to understand determinants of breeding success and inform optimal management in urban green spaces.

Caudal foot placement superior to toe elevation for navicular palmaroproximal-palmarodistal-oblique image quality.

BACKGROUND: Palmaroproximal-palmarodistal oblique (PaPr-PaDiO) radiographs are regularly obtained for a full evaluation of the navicular bone (NB). Despite their routine use, different acquisition techniques are described. OBJECTIVES: To determine optimal foot placement and beam angle for obtaining PaPr-PaDiO views. STUDY DESIGN: In vitro experiment. METHODS: A convenience sample of 26 disarticulated forelimbs were placed in six different positions using a leg press to mimic the weight-bearing position. In each position, navicular PaPr-PaDiO images were obtained with eight different beam angles. The resulting 1248 radiographs were graded for their diagnostic quality and the compacta spongiosa demarcation of the NB. RESULTS: Diagnostic quality and compacta-spongiosa demarcation was graded higher for feet positioned caudally and angle between 40° and 45°. Elevation of the toe significantly decreased the NB palmar border angle (elevated mean: 40.66, SD: 4.46, non-elevated mean: 42.06, SD: 4.70) (P < .01), but seemed to have no obvious positive influence on radiographs. MAIN LIMITATIONS: Using disarticulated legs could only mimic positions but, using a press, weight-bearing positions were replicated as closely as possible. The use of a convenience sample makes the results of the study exploratory only. CONCLUSIONS: Caudal foot placement seems to improve the image quality of the navicular PaPr-PaDiO view. The widely used standard beam angle of 45° appears to be the favourable angle for acquisition with a varied range of -5°. Elevation of the toe, standard in most commercially available navicular skyline cassette holders, does not influence the obtained image quality.

Evaluating the Impact on Clinical Task Efficiency of a Natural Language Processing Algorithm for Searching Medical Documents: Prospective Crossover Study.

BACKGROUND: Information retrieval (IR) from the free text within electronic health records (EHRs) is time consuming and complex. We hypothesize that natural language processing (NLP)-enhanced search functionality for EHRs can make clinical workflows more efficient and reduce cognitive load for clinicians. OBJECTIVE: This study aimed to evaluate the efficacy of 3 levels of search functionality (no search, string search, and NLP-enhanced search) in supporting IR for clinical users from the free text of EHR documents in a simulated clinical environment. METHODS: A clinical environment was simulated by uploading 3 sets of patient notes into an EHR research software application and presenting these alongside 3 corresponding IR tasks. Tasks contained a mixture of multiple-choice and free-text questions. A prospective crossover study design was used, for which 3 groups of evaluators were recruited, which comprised doctors (n=19) and medical students (n=16). Evaluators performed the 3 tasks using each of the search functionalities in an order in accordance with their randomly assigned group. The speed and accuracy of task completion were measured and analyzed, and user perceptions of NLP-enhanced search were reviewed in a feedback survey. RESULTS: NLP-enhanced search facilitated more accurate task completion than both string search (5.14%; P=.02) and no search (5.13%; P=.08). NLP-enhanced search and string search facilitated similar task speeds, both showing an increase in speed compared to the no search function, by 11.5% (P=.008) and 16.0% (P=.007) respectively. Overall, 93% of evaluators agreed that NLP-enhanced search would make clinical workflows more efficient than string search, with qualitative feedback reporting that NLP-enhanced search reduced cognitive load. CONCLUSIONS: To the best of our knowledge, this study is the largest evaluation to date of different search functionalities for supporting target clinical users in realistic clinical workflows, with a 3-way prospective crossover study design. NLP-enhanced search improved both accuracy and speed of clinical EHR IR tasks compared to browsing clinical notes without search. NLP-enhanced search improved accuracy and reduced the number of searches required for clinical EHR IR tasks compared to direct search term matching.

Causal machine learning for healthcare and precision medicine.

Causal machine learning (CML) has experienced increasing popularity in healthcare. Beyond the inherent capabilities of adding domain knowledge into learning systems, CML provides a complete toolset for investigating how a system would react to an intervention (e.g. outcome given a treatment). Quantifying effects of interventions allows actionable decisions to be made while maintaining robustness in the presence of confounders. Here, we explore how causal inference can be incorporated into different aspects of clinical decision support systems by using recent advances in machine learning. Throughout this paper, we use Alzheimer's disease to create examples for illustrating how CML can be advantageous in clinical scenarios. Furthermore, we discuss important challenges present in healthcare applications such as processing high-dimensional and unstructured data, generalization to out-of-distribution samples and temporal relationships, that despite the great effort from the research community remain to be solved. Finally, we review lines of research within causal representation learning, causal discovery and causal reasoning which offer the potential towards addressing the aforementioned challenges.

Morphine versus methadone for neonatal opioid withdrawal syndrome: a randomized controlled pilot study.

BACKGROUND: Neonatal Opioid Withdrawal Syndrome (NOWS) is a significant public health issue and while millions of neonates are affected each year, an optimal pharmacologic weaning protocol has yet to be demonstrated. In this study, we compare hospital length of stay (LOS) and length of treatment (LOT) for treatment of neonatal opioid withdrawal (NOWS) with morphine versus methadone. METHODS: This was a single-site, open-label, randomized controlled pilot study conducted from October 2016-September 2018. Infants were eligible if their primary in-utero drug exposure was heroin, oral opioids, or methadone and they were born at greater than or equal to 34 weeks gestation. Infants were excluded for serious medical comorbidities and primary in-utero exposure to buprenorphine. RESULTS: Sixty-one infants were enrolled; 30 were randomized to methadone treatment, and 31 to morphine treatment. Overall 46% of infants required treatment for NOWS. LOS and LOT for infants treated with morphine was 17.9 days and 14.7 days respectively, compared to 16.1 days and 12.8 days for babies treated with methadone (p = 0.5, p = 0.54). Infants treated with morphine received lower total morphine equivalents than those treated with methadone (9.7 vs. 33, p < 0.01). Three treated infants in the methadone group required transfer to the Neonatal Intensive Care Unit, versus no infants in the morphine group. CONCLUSIONS: Infants treated with morphine versus methadone had no significant differences in LOS or LOT in this pilot study. Infants treated with methadone received up to 3 times the opioid based on morphine equivalents as infants treated with morphine and had more transfers to the NICU for over sedation. CLINICAL TRIAL REGISTRATION: Morphine Versus Methadone for Opiate Exposed Infants With Neonatal Abstinence Syndrome NCT02851303 , initiated 01/08/2016.

Effects of human disturbance on postnatal growth and baseline corticosterone in a long-lived bird.

Prolonged or repeated episodes of environmental stress could be especially detrimental for developing young, via impaired growth or development. Despite this, most studies investigating the effects of human recreational and tourism activities have focused on adults. An increasing demand for nature-based tourism in remote locations means that many seabirds, which have evolved largely in the absence of predators and humans, are being exposed to novel pressures. The slow-growing semi-precocial nestlings of the European storm petrel Hydrobates pelagicus experience higher mortality rates in nests exposed to human recreational disturbance. Here, we examine whether surviving nestlings reared in disturbed areas are also affected via changes in growth trajectories and baseline circulating glucocorticoids. Nestlings reared in high-disturbance areas displayed delayed mass growth, and we found weak evidence for slower rates of mass gain and tarsus growth, compared with nestlings reared in undisturbed areas. There were no differences in wing growth, consistent with prioritization of long wings, important for post-fledging survival. A tendency for a less marked age-related decline in corticosterone (CORT) in disturbed nestlings offers limited evidence that changes in growth trajectories were mediated by baseline CORT. However, disturbed nestlings could have experienced overall higher GC exposure if the acute GC response was elevated. 'Catch-up' growth enabled high-disturbance nestlings to overcome early constraints and achieve a similar, or even larger, asymptotic body size and mass as low-disturbance nestlings. While catch-up growth has been shown to carry costs for parents and offspring, the effects of disturbance were slight and considerably smaller than growth alterations driven by variation in environmental conditions between years. Nonetheless, effects of human recreational activities could be exacerbated under higher levels of human disturbance or in the presence of multiple pressures, as imposed by present rapid rates of environmental change.

Exposure to artificial light at night alters innate immune response in wild great tit nestlings.

The large-scale impact of urbanization on wildlife is rather well documented; however, the mechanisms underlying the effects of urban environments on animal physiology and behaviour are still poorly understood. Here, we focused on one major urban pollutant - artificial light at night (ALAN) - and its effects on the capacity to mount an innate immune response in wild great tit (Parus major) nestlings. Exposure to ALAN alters circadian rhythms of physiological processes, by disrupting the nocturnal production of the hormone melatonin. Nestlings were exposed to a light source emitting 3 lx for seven consecutive nights. Subsequently, nestlings were immune challenged with a lipopolysaccharide injection, and we measured haptoglobin and nitric oxide levels pre- and post-injection. Both haptoglobin and nitric oxide are important markers for innate immune function. We found that ALAN exposure altered the innate immune response, with nestlings exposed to ALAN having lower haptoglobin and higher nitric oxide levels after the immune challenge compared with dark-night nestlings. Unexpectedly, nitric oxide levels were overall lower after the immune challenge than before. These effects were probably mediated by melatonin, as ALAN-treated birds had on average 49% lower melatonin levels than the dark-night birds. ALAN exposure did not have any clear effects on nestling growth. This study provides a potential physiological mechanism underlying the documented differences in immune function between urban and rural birds observed in other studies. Moreover, it gives evidence that ALAN exposure affects nestling physiology, potentially causing long-term effects on physiology and behaviour, which ultimately can affect their fitness.

Urbanization is associated with modifications in DNA methylation in a small passerine bird.

Urbanization represents a fierce driver of phenotypic change, yet the molecular mechanisms underlying observed phenotypic patterns are poorly understood. Epigenetic changes are expected to facilitate more rapid adaption to changing or novel environments, such as our towns and cities, compared with slow changes in gene sequence. A comparison of liver and blood tissue from great tits Parus major originating from an urban and a forest site demonstrated that urbanization is associated with variation in genome-wide patterns of DNA methylation. Combining reduced representation bisulphite sequencing with transcriptome data, we revealed habitat differences in DNA methylation patterns that suggest a regulated and coordinated response to the urban environment. In the liver, genomic sites that were differentially methylated between urban- and forest-dwelling birds were over-represented in regulatory regions of the genome and more likely to occur in expressed genes. DNA methylation levels were also inversely correlated with gene expression at transcription start sites. Furthermore, differentially methylated CpG sites, in liver, were over-represented in pathways involved in (i) steroid biosynthesis, (ii) superoxide metabolism, (iii) secondary alcohol metabolism, (iv) chylomicron remodelling, (v) cholesterol transport, (vi) reactive oxygen species (ROS) metabolic process and (vii) epithelial cell proliferation. This corresponds with earlier studies identifying diet and exposure to ROS as two of the main drivers of divergence between organisms in urban and nonurban environments. Conversely, in blood, sites that were differentially methylated between urban- and forest-dwelling birds were under-represented in regulatory regions, more likely to occur in nonexpressed genes and not over-represented in specific biological pathways. It remains to be determined whether diverging patterns of DNA methylation represent adaptive evolutionary responses and whether the conclusions can be more widely attributed to urbanization.

Predictability of food supply modulates nocturnal hypothermia in a small passerine.

The combination of short days and long cold winter nights, in temperate regions, presents a major challenge for small diurnal birds. Small birds regularly employ heterothermy and enter rest-phase hypothermia during winter nights to conserve energy. However, we know little about how environmental conditions, such as food availability, shape these strategies. We experimentally manipulated food availability in winter to free-living great tits Parus major. A 'predictable' and constant food supply was provided to birds in one area of a forest, while birds in another area did not have access to a reliable supplementary food source. We found that predictability of food affected the extent of nocturnal hypothermia, but the response differed between the sexes. Whereas male nocturnal body temperature was similar regardless of food availability, females exposed to a naturally 'unpredictable' food supply entered deeper hypothermia at night, compared with females that had access to predictable food and compared with males in both treatment groups. We suggest that this response is likely a consequence of dominance, and subdominant females subject to unpredictable food resources cannot maintain sufficient energy intake, resulting in a higher demand for energy conservation at night.

Will urbanisation affect the expression level of genes related to cancer of wild great tits?

Recent studies suggest that oncogenic processes (from precancerous lesions to metastatic cancers) are widespread in wild animal species, but their importance for ecosystem functioning is still underestimated by evolutionary biologists and animal ecologists. Similar to what has been observed in humans, environmental modifications that often place wild organisms into an evolutionary trap and/or exposes them to a cocktail of mutagenic and carcinogenic pollutants might favor cancer emergence and progression, if animals do not up-regulate their defenses against these pathologies. Here, we compared, for the first time, the expression of 59 tumor-suppressor genes in blood and liver tissues of urban and rural great tits (Parus major); urban conditions being known to favor cancer progression due to, among other things, exposure to chemical or light pollution. Contrary to earlier indications, once we aligned the transcriptome to the great tit genome, we found negligible differences in the expression of anti-cancer defenses between urban and rural birds in blood and liver. Our results indicate the higher expression of a single caretaker gene (i.e. BRCA1) in livers of rural compared to urban birds. We conclude that, while urban birds might be exposed to an environment favoring the development of oncogenic processes, they seem to not upregulate their cancer defenses accordingly and future studies should confirm this result by assessing more markers of cancer defenses. This may result in a mismatch that might predispose urban birds to higher cancer risk and future studies in urban ecology should take into account this, so far completely ignored, hazard.