Regulatory modules of human thermogenic adipocytes: functional genomics of large cohort and Meta-analysis derived marker-genes.

BACKGROUND: Recently, ProFAT and BATLAS studies identified brown and white adipocytes marker genes based on analysis of large databases. They offered scores to determine the thermogenic status of adipocytes using the gene-expression data of these markers. In this work, we investigated the functional context of these genes. RESULTS: Gene Set Enrichment Analyses (KEGG, Reactome) of the BATLAS and ProFAT marker-genes identified pathways deterministic in the formation of brown and white adipocytes. The collection of the annotated proteins of the defined pathways resulted in expanded white and brown characteristic protein-sets, which theoretically contain all functional proteins that could be involved in the formation of adipocytes. Based on our previously obtained RNA-seq data, we visualized the expression profile of these proteins coding genes and found patterns consistent with the two adipocyte phenotypes. The trajectory of the regulatory processes could be outlined by the transcriptional profile of progenitor and differentiated adipocytes, highlighting the importance of suppression processes in browning. Protein interaction network-based functional genomics by STRING, Cytoscape and R-Igraph platforms revealed that different biological processes shape the brown and white adipocytes and highlighted key regulatory elements and modules including GAPDH-CS, DECR1, SOD2, IL6, HRAS, MTOR, INS-AKT, ERBB2 and 4-NFKB, and SLIT-ROBO-MAPK. To assess the potential role of a particular protein in shaping adipocytes, we assigned interaction network location-based scores (betweenness centrality, number of bridges) to them and created a freely accessible platform, the AdipoNET ( https//adiponet.com ), to conveniently use these data. The Eukaryote Promoter Database predicted the response elements in the UCP1 promoter for the identified, potentially important transcription factors (HIF1A, MYC, REL, PPARG, TP53, AR, RUNX, and FoxO1). CONCLUSION: Our integrative approach-based results allowed us to investigate potential regulatory elements of thermogenesis in adipose tissue. The analyses revealed that some unique biological processes form the brown and white adipocyte phenotypes, which presumes the existence of the transitional states. The data also suggests that the two phenotypes are not mutually exclusive, and differentiation of thermogenic adipocyte requires induction of browning as well as repressions of whitening. The recognition of these simultaneous actions and the identified regulatory modules can open new direction in obesity research.

Draft genome of a biparental beetle species, Lethrus apterus.

BACKGROUND: The lack of an understanding about the genomic architecture underpinning parental behaviour in subsocial insects displaying simple parental behaviours prevents the development of a full understanding about the evolutionary origin of sociality. Lethrus apterus is one of the few insect species that has biparental care. Division of labour can be observed between parents during the reproductive period in order to provide food and protection for their offspring. RESULTS: Here, we report the draft genome of L. apterus, the first genome in the family Geotrupidae. The final assembly consisted of 286.93 Mbp in 66,933 scaffolds. Completeness analysis found the assembly contained 93.5% of the Endopterygota core BUSCO gene set. Ab initio gene prediction resulted in 25,385 coding genes, whereas homology-based analyses predicted 22,551 protein coding genes. After merging, 20,734 were found during functional annotation. Compared to other publicly available beetle genomes, 23,528 genes among the predicted genes were assigned to orthogroups of which 1664 were in species-specific groups. Additionally, reproduction related genes were found among the predicted genes based on which a reduction in the number of odorant- and pheromone-binding proteins was detected. CONCLUSIONS: These genes can be used in further comparative and functional genomic researches which can advance our understanding of the genetic basis and hence the evolution of parental behaviour.

Experimental manipulation of body size alters life history in hydra.

Body size has fundamental impacts on animal ecology and physiology but has been strongly influenced by recent climate change and human activities, such as size-selective harvesting. Understanding the ecological and life history consequences of body size has proved difficult due to the inseparability of direct effects of body size from processes connected to it (such as growth rate and individual condition). Here, we used the cnidarian Hydra oligactis to directly manipulate body size and understand its causal effects on reproduction and senescence. We found that experimentally reducing size delayed sexual development and lowered fecundity, while post-reproductive survival increased, implying that smaller individuals can physiologically detect their reduced size and adjust life history decisions to achieve higher survival. Our experiment suggests that ecological or human-induced changes in body size will have immediate effects on life history and population dynamics through a growth-independent link between body size, reproduction and senescence.

Social groups with diverse personalities mitigate physiological stress in a songbird.

Social groups often consist of diverse phenotypes, including personality types, and this diversity is known to affect the functioning of the group as a whole. Social selection theory proposes that group composition (i.e. social environment) also influences the performance of individual group members. However, the effect of group behavioural composition on group members remains largely unexplored, and it is still contentious whether individuals benefit more in a social environment with homogeneous or diverse behavioural composition. We experimentally formed groups of house sparrows Passer domesticus with high and low diversity of personality (exploratory behaviour), and found that their physiological state (body condition, physiological stress and oxidative damage) improved with increasing group-level diversity of personality. These findings demonstrate that group personality composition affects the condition of group members and individuals benefit from social heterosis (i.e. associating with a diverse set of behavioural types). This aspect of the social life can play a key role in affiliation rules of social animals and might explain the evolutionary coexistence of different personalities in nature.

Phenotypic plasticity rather than genotype drives reproductive choices in Hydra populations.

Facultative clonality is associated with complex life cycles where sexual and asexual forms can be exposed to contrasting selection pressures. Facultatively clonal animals often have distinct developmental capabilities that depend on reproductive mode (e.g., negligible senescence and exceptional regeneration ability in asexual individuals, which are lacking in sexual individuals). Understanding how these differences in life history strategies evolved is hampered by limited knowledge of the population structure underlying sexual and asexual forms in nature. Here we studied genetic differentiation of coexisting sexual and asexual Hydra oligactis polyps, a freshwater cnidarian where reproductive mode-dependent life history patterns are observed. We collected asexual and sexual polyps from 13 Central European water bodies and used restriction-site associated DNA sequencing to infer population structure. We detected high relatedness among populations and signs that hydras might spread with resting eggs through zoochory. We found no genetic structure with respect to mode of reproduction (asexual vs. sexual). On the other hand, clear evidence was found for phenotypic plasticity in mode of reproduction, as polyps inferred to be clones differed in reproductive mode. Moreover, we detected two cases of apparent sex change (males and females found within the same clonal lineages) in this species with supposedly stable sexes. Our study describes population genetic structure in Hydra for the first time, highlights the role of phenotypic plasticity in generating patterns of life history variation, and contributes to understanding the evolution of reproductive mode-dependent life history variation in coexisting asexual and sexual forms.

Behavioural flexibility and reputation formation.

Limited flexibility in behaviour gives rise to behavioural consistency, so that past behaviour is partially predictive of current behaviour. The consequences of limits to flexibility are investigated in a population in which pairs of individuals play a game of trust. The game can either be observed by others or not. Reputation is based on trustworthiness when observed and acts as a signal of behaviour in future interactions with others. Individuals use the reputation of partner in deciding whether to trust them, both when observed by others and when not observed. We explore the effects of costs of exhibiting a difference in behaviour between when observed and when not observed (i.e. a cost of flexibility). When costs are low, individuals do not attempt to signal that they will later be trustworthy: their signal should not be believed since it will always pay them to be untrustworthy if trusted. When costs are high, their local optimal behaviour automatically acts as an honest signal. At intermediate costs, individuals are very trustworthy when observed in order to convince others of their trustworthiness when unobserved. It is hypothesized that this type of strong signalling might occur in other settings.

Environmental variability, reliability of information and the timing of migration.

The timing of migration and migratory steps is highly relevant for fitness. Because environmental conditions vary between years, the optimal time for migration varies accordingly. Therefore, migratory animals could clearly benefit from acquiring information as to when it is the best time to migrate in a specific year. Thus, environmental predictability and variability are fundamental characteristics of migration systems but their relationship and consequence for migratory progression has remained unexplored. We develop a simple dynamic model to identify the optimal migration behaviour in environments that differ in predictability, variability and the number of intermediate stop-over sites. Our results indicate that higher predictability along migration routes enables organisms to better time migration when phenology deviates from its long-term average and thus, increases fitness. Information is particularly valuable in highly variable environments and in the final migration-step, i.e. before the destination. Furthermore, we show that a general strategy for obtaining information in relatively uninformative but variable environments is using intermediate stop-over sites that enable migrants to better predict conditions ahead. Our study contributes to a better understanding of the relationship between animal movement and environmental predictability-an important, yet underappreciated factor that strongly influences migratory progression.

Consequences of rapid development owing to cohort splitting: just how costly is it to hurry?

In cohort splitting, diverging sub-cohorts may show substantial differences in their growth and developmental rates. Although in the past, causes and adaptive value of cohort splitting were studied in detail, individual-level consequences of cohort splitting are still rather overlooked. Life history theory predicts that considerably increased growth and developmental rates should be traded off against other costly life history traits. However, it is not clear whether one should expect such associations in adaptive developmental plasticity scenarios, because natural selection might have promoted genotypes that mitigate those potential costs of rapid development. To address these contrasting propositions, we assessed life history traits in the wolf spider Pardosa agrestis, both collected from natural habitat and reared in laboratory. We found that some traits are negatively associated with developmental rates in spiders collected from the wild, but these associations were relaxed to a considerable extent in laboratory-reared specimens. In general, we observed no consistent trend for the presence of developmental costs, although some results might suggest higher relative fecundity costs in rapidly developing females. Our study provides a detailed approach to the understanding of individual-level consequences of cohort splitting, and to the associations between key life history traits in adaptive developmental plasticity scenarios.

Sex-dependent immune response in a semelparous spider.

Previous studies on arthropods showed that seasonality and parity in breeding considerably impact the direction of sex differences in immunocompetence, and it has been suggested that life span and the time window available for breeding play key roles in shaping sex-differences in immunity. One proposed mechanism behind this phenomenon is differential investment into life history traits in sexes. Here, we tested whether in a seasonally breeding semelparous arthropod sexes differ in their immunocompetence, predicting that females would show weaker immune response than males. We compared encapsulation efficiency (a well-established and widely used method for assessing immunocompetence) of freshly matured, virgin males and females of the lycosid spider Pardosa agrestis (Westring, 1861). On average, males mounted stronger immune response than females and the extent of encapsulation was positively associated with prosoma length in males, but not in females. Also, time until maturation was positively related to the extent of encapsulation in both sexes, but did not significantly affect adult prosoma length. We propose that sex-difference in encapsulation is likely shaped by combined effects of relatively higher costs of reproduction in females, narrow time window of reproductive activity, and the absence of trade-off between current and future reproduction.

Insulin/IGF Signaling and Life History Traits in Response to Food Availability and Perceived Density in the Cnidarian Hydra vulgaris.

Insulin/insulin-like growth factor signaling (IIS) is thought to be a central mediator of life history traits, but the generality of its role is not clear. Here, we investigated mRNA expression levels of three insulin-like peptide genes, the insulin-like receptor htk7, as well as several antioxidant genes, and the heat-shock protein hsp70 in the freshwater cnidarian Hydra vulgaris. Hydra polyps were exposed to a combination of different levels of food and perceived population density to manipulate life history traits (asexual reproduction and oxidative stress tolerance). We found that stress tolerance and the rate of asexual reproduction increased with food, and that these two effects were in significant interaction. Exposing animals to high perceived density resulted in increased stress tolerance or reduced reproduction only on lower food levels, but not on high food. The insulin-like receptor htk7 and the antioxidant gene catalase were significantly upregulated in the high density treatments. However, the expression level of insulin-like peptide genes, most antioxidant genes, and hsp70 were not affected by the experimental treatments. The higher expression level of htk7 may suggest that animals maintain a higher level of preparedness for insulin-like ligands at high population densities. However, the lack of difference between food levels suggests that IIS is not involved in regulating asexual reproduction and stress tolerance in hydra, or that its role is more subtle than a simple model of life history regulation would suggest.

Candida albicans isolates from a single hospital show low phenotypical specialization.

Candida albicans is the best-studied opportunistic human pathogenic yeast species, and its virulence factors, susceptibility to antimycotics, the diversity of its physiological properties and the determinative factors of these traits are interesting from a clinical as well as from an evolutionary perspective. By applying statistical modeling for the phenotypical differences observed among a collection of 63 C. albicans isolates originating from different clinical care units, from a diverse group of patients with or without mycosis, collected in a Hungarian clinic, we found that (i) host-related aspects like anatomical source, care unit of isolation, patients' age, sex, and disease severity, or ABC genotypes of the isolates had less effect on the phenotypic features of this opportunistic pathogen than host-independent aspects, for example, year or month of isolation; (ii) different phenotypic traits did not show any significant correlations with each other; and (iii) different genotypes displayed no anatomical specialization and rarely showed any significant correlation with parameters of isolation either. These results shed light on the dynamic nature and low specialization of the C. albicans populations observable in a narrow geographic range, namely in the patients hospitalized in the different care units of the clinic.

Social role specialization promotes cooperation between parents.

Biparental care of offspring is a widespread social behavior, and various ecological, life-history, and demographic factors have been proposed to explain its evolution and maintenance. Raising offspring generally requires several types of care (e.g., feeding, brooding, and defense), and males and females often specialize in providing different types of care. However, theoretical models of care often assume that care is a single variable and hence that a unit of care by the mother is interchangeable with a unit of care by the father. We hypothesize that the ability of one parent to provide all types of care may be limited by nonadditive costs or by sex-based asymmetries in the costs of particular care types. Using an individual-based simulation, we show that synergistic costs of investing in two tasks or negligible sex-based cost asymmetries select for task specialization and biparental care. Biparental care persists despite intense sexual selection and sex-biased mortality, suggesting that previous models make overly restrictive predictions of the conditions under which cooperation can be maintained. Our model provides a mechanistic underpinning for published models that show that the synergistic benefits of individuals cooperating can stabilize cooperation, both in the context of parental care and in other social scenarios.

The coevolution of choosiness and cooperation.

Explaining the rise and maintenance of cooperation is central to our understanding of biological systems and human societies. When an individual's cooperativeness is used by other individuals as a choice criterion, there can be competition to be more generous than others, a situation called competitive altruism. The evolution of cooperation between non-relatives can then be driven by a positive feedback between increasing levels of cooperativeness and choosiness. Here we use evolutionary simulations to show that, in a situation where individuals have the opportunity to engage in repeated pairwise interactions, the equilibrium degree of cooperativeness depends critically on the amount of behavioural variation that is being maintained in the population by processes such as mutation. Because our model does not invoke complex mechanisms such as negotiation behaviour, it can be applied to a wide range of species. The results suggest an important role of lifespan in the evolution of cooperation.

Mowing wet meadows reduces the health of their snail communities.

Wet meadows harbor rich biodiversity, making them pivotal ecosystems worldwide. These habitats are commonly used for grazing or hay production for livestock. However, regular mowing can influence these habitats, potentially leading to significant repercussions for the animals residing within them. In order to investigate the effects of land management practices, we conducted an experimental study to compare snail communities in mowed and unmowed wet meadows in northern Hungary. We found that overall, mowing decreases snail populations, as well as species richness and diversity. Thus, our results suggest that routine mowing of wet meadows is deleterious to their snail communities. Based on these results, we suggest that designated patches of meadows that are regularly managed should be left uncultivated in their natural state. These patches can serve as potential colonization sites, facilitating the restoration of the entire meadow's ecological balance.

Ventriculosubgaleal shunt in the treatment of posthemorrhagic and postinfectious hydrocephalus of premature infants.

PURPOSE: The aim of the study was to compare the characteristics of ventriculosubgaleal shunts during the clinical course of posthemorrhagic and postinfectious hydrocephalus in the neonatal period. PATIENTS AND METHODS: The study comprised 102 premature babies in whom subgaleal shunt was consecutively inserted between 2006 and 2011. Seventy-two patients had posthemorrhagic hydrocephalus (mean gestational age 27.3 ± 2.1 weeks, mean birth weight 1,036.9 ± 327.7 g, mean age at insertion 51.4 ± 56.2 days) and 30 patients were operated postinfectiously (27.5 ± 2.2 weeks, 1,064.7 g ± 310.7 g, 115.9 ± 47.8 days). RESULTS: The mean survival of subgaleal shunts was 87.9 days for the posthemorrhagic group and 75.6 days for the postinfectious group. Only six infants (8.3 %) did not need ventriculoperitoneal shunts later, all posthemorrhagic. There were meaningful differences between two groups with regard to ventriculosubgaleal shunt-related infections (8.3 % in posthemorrhagic versus 20.0 % in postinfectious) and shunt revision rate (6.9 % in posthemorrhagic versus 13.3 % in postinfectious), but these were not statistically significant. The need of ventriculoscopic procedures was notably more frequent in postinfectious group (1.4 versus 23.3 %). CONCLUSION: In premature infants with ventriculomegaly, the subgaleal shunt is an effective temporary diversion tool. The complications were less with posthemorrhagic than with postinfectious hydrocephalus. With previous severe infections of prematures, the risk for complications regarding infection and obstruction will be 2.75 and 2.06 (odds ratios) times higher and more frequent need of ventriculoscopic procedures should be considered (odds ratio 21.6).

Deep learning in terrestrial conservation biology.

Biodiversity is being lost at an unprecedented rate on Earth. As a first step to more effectively combat this process we need efficient methods to monitor biodiversity changes. Recent technological advance can provide powerful tools (e.g. camera traps, digital acoustic recorders, satellite imagery, social media records) that can speed up the collection of biological data. Nevertheless, the processing steps of the raw data served by these tools are still painstakingly slow. A new computer technology, deep learning based artificial intelligence, might, however, help. In this short and subjective review I oversee recent technological advances used in conservation biology, highlight problems of processing their data, shortly describe deep learning technology and show case studies of its use in conservation biology. Some of the limitations of the technology are also highlighted.

Fine-scale collective movements reveal present, past and future dynamics of a multilevel society in Przewalski's horses.

Studying animal societies needs detailed observation of many individuals, but technological advances offer new opportunities in this field. Here, we present a state-of-the-art drone observation of a multilevel herd of Przewalski's horses, consisting of harems (one-male, multifemale groups). We track, in high spatio-temporal resolution, the movements of 238 individually identified horses on drone videos, and combine movement analyses with demographic data from two decades of population monitoring. Analysis of collective movements reveals how the structure of the herd's social network is related to kinship and familiarity of individuals. The network centrality of harems is related to their age and how long the harem stallions have kept harems previously. Harems of genetically related stallions are closer to each other in the network, and female exchange is more frequent between closer harems. High movement similarity of females from different harems predicts becoming harem mates in the future. Our results show that only a few minutes of fine-scale movement tracking combined with high throughput data driven analysis can reveal the structure of a society, reconstruct past group dynamics and predict future ones.

Publication games: In the web of reciprocity.

The present processes of research assessment, i.e. focusing on one or a few, related, scientometrics, foster questionable authorship practices, like gifting authorship to non-contributing people. An especially harmful one of these unethical practices is the formation of publication cartels, where authors offer gift authorship to each other reciprocally. Here, by developing a simple model and a simulation of the publication process I investigate how beneficial cartels can be and what measure can be used to restrict them. My results indicate that publication cartels can significantly boost members' productivity even if paper counts are weighted by the inverse of author number (the 1/n rule). Nevertheless, applying the 1/n rule generates conflicts of interest both among cartel members themselves and between cartel members and non-members which might lead to the self-purification of the academic publishing industry.

Seasonal variation of genotypes and reproductive plasticity in a facultative clonal freshwater invertebrate animal (Hydra oligactis) living in a temperate lake.

Facultative sexual organisms combine sexual and asexual reproduction within a single life cycle, often switching between reproductive modes depending on environmental conditions. These organisms frequently inhabit variable seasonal environments, where favorable periods alternate with unfavorable periods, generating temporally varying selection pressures that strongly influence life history decisions and hence population dynamics. Due to the rapidly accelerating changes in our global environment today, understanding the population dynamics and genetic changes in facultative sexual populations inhabiting seasonal environments is critical to assess and prepare for additional challenges that will affect such ecosystems. In this study, we aimed at obtaining insights into the seasonal population dynamics of the facultative sexual freshwater cnidarian Hydra oligactis through a combination of restriction site-associated sequencing (RAD-Seq) genotyping and the collection of phenotypic data on the reproductive strategy of field-collected hydra strains in a standard laboratory environment. We reliably detected 42 MlGs from the 121 collected hydra strains. Most of MLGs (N = 35, 83.3%) were detected in only one season. Five MLGs (11.9%) were detected in two seasons, one (2.4%) in three seasons and one (2.4%) in all four seasons. We found no significant genetic change during the 2 years in the study population. Clone lines were detected between seasons and even years, suggesting that clonal lineages can persist for a long time in a natural population. We also found that distinct genotypes differ in sexual reproduction frequency, but these differences did not affect whether genotypes reappeared across samplings. Our study provides key insights into the biology of natural hydra populations, while also contributing to understanding the population biology of facultative sexual species inhabiting freshwater ecosystems.

Range-wide phylogeography of the flightless steppe beetle Lethrus apterus (Geotrupidae) reveals recent arrival to the Pontic Steppes from the west.

The Eurasian Steppe belt is one of the largest biomes in the Northern Hemisphere. We provide here a range-wide phylogeography of the flightless steppe beetle Lethrus apterus that inhabits the western part of the Steppe belt through the study of population-level variance of mitochondrial cytochrome oxidase I sequences and nuclear microsatellites. We detected a concordant geographic structure of genetic data with a significant isolation-by-distance pattern. We found more genetic variation in the western part of the area and identified Northern Bulgaria and the Pannonian Basin as possible refugia. Genetic clusters were separated by main rivers in the eastern part of the area. This implies west-to-east colonisation and argues for an evolutionarily recent arrival of this species to its current main distribution area, the Pontic Steppes. This contradicts the classical biogeographical wisdom that assumed an east-to-west colonisation pattern.