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opencc-by-4.0Apr 2020View details →

Multiplexed histology reveals phenotypic and spatial characteristics of human Innate Lymphoid Cells in chronic inflammation - Data tables

Data tables containing image-based, single cell information for a tonsil and a colon data-set analyzed in CellProfiler: cell numbers, MFI of all markers, annotated cell types and cell allocations (X, Y coordinates).

opencc-by-4.0May 2020View details →

Phenotypic modulation of biofilm formation in a Staphylococcus epidermidis orthopedic clinical isolate grown under different mechanical stimuli: contribution from a combined proteomic study

One of the major causes of prosthetic joint failure is infection. Recently, coagulase negative Staphylococcus epidermidis has been identified as an emergent, nosocomial pathogen involved in subclinical prosthetic join infections (PJIs). The diagnosis of PJIs mediated by S. epidermidis is usually complex and difficulties due to the absence of acute clinical signs derived from the host immune system response. Therefore, analysis of protein patterns in biofilm-producing S. epidermidis allows for the examination of the molecular basis of biofilm formation. Thus, in the present study, the proteome of a clinical isolate S. epidermidis was analyzed when cultured in its planktonic or sessile form to examine protein expression changes depending on culture conditions. After 24 hours of culture, sessile bacteria exhibited increased gene expression for ribosomal activity and for expression of proteins related to the initial attachment phase, involved in the capsular polysaccharide/adhesin, surface associated proteins and peptidoglycan biosynthesis. Likewise, planktonic S. epidermidis was able to aggregate after 24 hours, synthesizing the accumulation associate protein and cell-wall molecules through the activation of the YycFG and ArlRS, two component regulatory pathways. Prolonged culture under vigorous agitation generated a stressful growing environment triggering aggregation in a biofilm-like matrix as a mechanism to survive harsh conditions. Further studies will be essential to support these findings in order to further delineate the complex mechanisms of biofilm formation of S. epidermidis and they could provide the groundwork for the development of new drugs against biofilm-related infections, as well as the identification of novel biomarkers of subclinical or chronic infections mediated by these emerging, low virulence pathogens.

opencc-zeroJun 2020View details →

Multiple phenotypes conferred by a single insect symbiont are independent

Many microbial symbionts have multiple phenotypic consequences for their animal hosts. However, the ways in which different symbiont-mediated phenotypes combine to affect fitness are not well understood. We investigated whether there are correlations between different symbiont-mediated phenotypes. We used the symbiont Spiroplasma, a striking example of a bacterial symbiont conferring diverse phenotypes on insect hosts. We took 11 strains of Spiroplasma infecting pea aphids (Acyrthosiphon pisum) and assessed their ability to provide protection against the fungal pathogen Pandora neoaphidis and the parasitoids Aphidius ervi and Praon volucre. We also assessed effects on male offspring production for five of the Spiroplasma strains. All but one of the Spiroplasma strains provided very strong protection against the parasitoid P. volucre. As previously reported, variable protection against P. neoaphidis and A. ervi was also present; male-killing was likewise a variable phenotype. We find no evidence of any correlation, positive or negative, between the different phenotypes, nor was there any evidence of an effect of symbiont phylogeny on protective phenotype. We conclude that multiple symbiont-mediated phenotypes can evolve independently from one another without trade-offs between them.

opencc-zeroMar 2020View details →

Data from: Adaptive reshaping of the hormonal phenotype after social niche transition in adulthood

Phenotypic plasticity allows individuals to adjust traits to the environment. Whether long-term adjustments of the phenotype occur during later life stages is largely unknown. To address this question, we examined whether hormonal phenotypes that are shaped by the environment during adolescence can still be reshaped in full adulthood. For this, guinea pig males were either housed in mixed-sex colonies or in heterosexual pairs. In adulthood, males were individually transferred to pair housing with a female. This way, a social niche transition was induced in colony-housed males, but not in pair-housed males. Before transfer, corresponding to findings in adolescence, adult colony-housed males showed significantly higher baseline testosterone levels and lower cortisol responsiveness than pair-housed males. One month after transfer, the hormonal phenotype of colony-housed males was changed towards that of pair-housed males: animals showed comparable baseline testosterone levels and cortisol responsiveness was significantly increased in colony-housed males. This endocrine readjustment builds the basis for an adaptive behavioural tactic in the new social situation. Thus, an adaptive change of the behavioural phenotype may still occur in adulthood via modification of underlying mechanisms. This suggests a greater role for developmental plasticity in later life stages than commonly is presumed.

opencc-zeroJul 2020View details →

Data from: Genetic growth potential, rather than phenotypic size, predicts migration phenotype in Atlantic salmon

Knowledge of the relative importance of genetic versus environmental determinants of major developmental transitions is pertinent to understanding phenotypic evolution. In salmonid fishes, a major developmental transition enables a risky seaward migration that provides access to feed resources. In Atlantic salmon, initiation of the migrant phenotype, and thus age of migrants, is presumably controlled via thresholds of a quantitative liability, approximated by body size expressed long before the migration. However, how well size approximates liability, both genetically and environmentally, remains uncertain. We studied 32 Atlantic salmon families in two temperatures and feeding regimes (fully fed, temporarily restricted) to completion of migration status at age 1 year. We detected a lower migrant probability in the cold (0.42) than the warm environment (0.76), but no effects of male maturation status or feed restriction. By contrast, body length in late summer predicted migrant probability and its control reduced migrant probability heritability by 50–70%. Furthermore, migrant probability and length showed high heritabilities and between-environment genetic correlations, and were phenotypically highly correlated with stronger genetic than environmental contributions. Altogether, quantitative estimates for the genetic and environmental effects predicting the migrant phenotype indicate, for a given temperature, a larger importance of genetic than environmental size effects.

Detritus decorations as the extended phenotype deflect avian predator attack increasing fitness in an orb‐web spider

<ol> <li>A number of strategies that divert attacks of visually guided predators, such as birds, have evolved multiple times in animals. Detritus web decorations built by certain orb-web spider species are thought to deflect avian predator attacks away from spiders and towards their web decorations. Still, empirical evidence for this function and its adaptive significance is lacking. The orb-web spider, Cyclosa monticola, adorns its web using a linear detritus decoration consisting of moults, egg sacs, prey remains, and leaf litters.</li> <li>In the present study, we investigated whether detritus decorations constructed by C. monticola spiders divert attacks of avian predators away from spiders. We first employed colour modelling to compare spider bodies and detritus decoration colouration from the perspective of domestic chicks and blue tits. We then experimentally tested the deflection hypothesis in the laboratory using naïve chicks as predators. We put the chicks in a cage containing a web either with (S+) or without (S-) a spider and either with (D+) or without (D-) detritus decoration (a total of four types of webs: S+D+, S+D-, S-D+, and S-D-) under both natural habitat background and white background. </li> <li>We found that the colour of C. monticola spiders is indistinguishable from that of their detritus decorations for both chicks and blue tits with both backgrounds. Laboratory predation experiments showed that with both backgrounds, chicks attacked the spiders much less frequently when their decorations were present on the webs (S+D+; natural habitat: 20%, white background: 30%) than when their decorations were absent (S+D-; natural habitat: 95%, white background: 85%), resulting in greater spider survival advantage. </li> <li>We also found that the rate of attack of spiders and their decorations was not random; the decorations were more likely to be attacked than spiders, regardless of the ratio of surface area of decorations to spider bodies when both spiders and decorations were presented (S+D+). Therefore, our results support a deflection, rather than concealment hypothesis for web decorations.</li> <li>In conclusion, our study provides evidence that the extended phenotypes beyond the animal bodies, can divert avian predator attacks, therefore, may improve the fitness of animals.</li> </ol>

Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment

Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones. Our results thus demonstrate rapid trait refinement and adaptation to the new citrate niche, while also suggesting a recalcitrant mismatch between E. coli physiology and growth on citrate.

Data from: An experimental investigation of how intraspecific competition and phenotypic plasticity can promote the evolution of novel, complex phenotypes

Intraspecific competition has long been considered a key driver of evolutionary diversification, but whether it can also promote evolutionary innovation is less clear. We examined the interplay between competition and phenotypic plasticity in fueling the origins of a novel, complex phenotype––a distinctive carnivore morph found in spadefoot toad tadpoles (genus Spea) that specializes on fairy shrimp. We specifically sought to explore the possible origins of this phenotype by providing shrimp to Scaphiopus holbrookii tadpoles (the sister genus to Spea that does not produce carnivores) while subjecting them to competition for their standard diet of detritus. Previous research had shown that this species will eat shrimp when detritus is limited, and that these shrimp-fed individuals produce features that are redolent of a rudimentary Spea carnivore. In this study, we found that: 1) behavioral and morphological plasticity enabled some individuals to expand their diet to include shrimp; 2) there was heritable variation in this plasticity; and 3) individuals received a growth and development benefit by eating shrimp. Thus, novel resource use can arise via plasticity as an adaptive response to intraspecific competition. More generally, our results show how competition and plasticity may interact to pave the way for the evolution of complex, novel phenotypes, such as the distinctive carnivore morph in present-day Spea.

No, you go first: phenotype and social context affect house sparrow neophobia

Novel object trials are commonly used to assess aversion to novelty (neophobia), and previous work has shown neophobia can be influenced by the social environment, but whether the altered behaviour persists afterwards (social learning) is largely unknown in wild animals. We assessed house sparrow (Passer domesticus) novel object responses before, during, and after being paired with a conspecific of either similar or different behavioral phenotype. During paired trials, animals housed with a similar or more neophobic partner demonstrated an increased aversion to novel objects. This change did not persist a week after unpairing, but neophobia decreased after unpairing in birds previously housed with a less neophobic partner. We also compared novel object responses to non-object control trials to validate our experimental procedure. Our results provide evidence of social learning in a highly successful invasive species, and an interesting asymmetry in the effects of social environment on neophobia behavior depending on the animal's initial behavioral phenotype.

The roles of climate, geography and natural selection as drivers of genetic and phenotypic differentiation in a widespread amphibian Hyla annectans (Anura: Hylidae)

The role of geological events and Pleistocene climatic fluctuations as drivers of current patterns of genetic variation in extant species has been a topic of continued interest among evolutionary biologists. Nevertheless, comprehensive studies of widely distributed species are still rare, especially from Asia. Using geographically extensive sampling of many individuals and a large number of nuclear single nucleotide polymorphisms (SNPs), we studied the phylogeography and historical demography of Hyla annectans populations in southern China. Thirty-five sampled populations were grouped into seven clearly defined genetic clusters that closely match phenotype-based subspecies classification. These lineages diverged 2.32–5.23 million years ago, a timing that closely aligns with the rapid and drastic uplifting of the Qinghai-Tibet Plateau and adjacent southwest China. Demographic analyses and species distribution models indicate that different populations of this species have responded differently to past climatic changes. In the Hengduan Mountains, most populations experienced a bottleneck, whereas the populations located outside of the Hengduan Mountains have gradually declined in size since the end of the last glaciation. In addition, the levels of phenotypic and genetic divergence were strongly correlated across major clades. These results highlight the combined effects of geological events and past climatic fluctuations, as well as natural selection, as drivers of contemporary patterns of genetic and phenotypic variation in a widely distributed anuran in Asia.

opencc-zeroDec 2019View details →

Data from: Genotype and male sterility phenotype data for An. coluzzii x An. quadriannulatus backcross

The Anopheles gambiae complex is comprised of eight morphologically indistinguishable species and has emerged as a model system for the study of speciation genetics due to the rapid radiation of its member species over the past two million years. Male hybrids between most An. gambiae complex species pairs are sterile, and some genotype combinations in hybrid males cause inviability. We investigated the genetic basis of hybrid male inviability and sterility between An. coluzzii and An. quadriannulatus by measuring segregation distortion and performing a QTL analysis of sterility in a backcross population. Hybrid males were inviable if they inherited the An. coluzzii X chromosome and were homozygous at one or more loci in 18.9 Mb region of chromosome 3. The An. coluzzii X chromosome has a disproportionately large effect on hybrid sterility when introgressed into an An. quadriannulatus genetic background. Additionally, an epistatic interaction between the An. coluzzii X and a 1.12 Mb, pericentric region of the An. quadriannulatus 3L chromosome arm has a statistically significant contribution to the hybrid sterility phenotype. This same epistatic interaction occurs when the An. coluzzii X is introgressed into the genetic background of An. arabiensis, the sister species of An. quadriannulatus, suggesting that this may represent one of the first Dobzhansky–Muller incompatibilities to evolve early in the radiation of the Anopheles gambiae species complex. We describe the additive effects of each sterility QTL, epistatic interactions between them, and genes within QTL with protein functions related to mating behavior, reproduction, spermatogenesis, and microtubule morphogenesis, whose divergence may contribute to post-zygotic reproductive isolation between An. coluzzii and An. quadriannulatus.

opencc-by-4.0Aug 2020View details →

The Ubiquitin Ligase WWP1 Contributes to Shifts in Matrix Proteolytic Profiles and a Myocardial Aging Phenotype with Diastolic Heart Failure

Aims. Ubiquitylation is a key event that regulates protein turnover, and induction of the ubiquitin ligase E3 WWP1 has been associated with age. Left ventricular hypertrophy (LVH) commonly occurs as a function of age and can cause heart failure with a preserved ejection fraction (EF; HFpEF). We hypothesized that overexpression (O/E) of WWP1 in the heart would cause LVH as well as functional and structural changes consistent with the aging HFpEF phenotype. Methods and Results. Global WWP1 O/E was achieved in mice (n=11) and echocardiography (40 MHz) performed to measure LV mass, EF, Doppler velocities (early-E, late/atrial-A), myocardial relaxation (E’), and isovolumetric relaxation time (IVRT) at 4, 6, and 8 weeks. Age matched wild type animals (n=15) were included as referent controls. LV EF was identical (60+1% vs 60+1%, p>0.90) with no difference in LV mass (67+3 vs 75+5, p>0.25) at 4 weeks. However, at 8 weeks of age, LV mass increased by over two-fold, E/A fell (impaired passive filling), and E/E’ was lower and IVRT prolonged (impaired LV relaxation) - all p<0.05. Collagen percent area increased by over two-fold and fibrillar collagen expression (rtPCR) by over 1.5 fold (p<0.05) with WWP1 O/E. WWP1 with an anti-WWP1 antibody could be identified in isolated cardiac fibroblasts with WWP1 increased by over two-fold in O/E fibroblasts (p<0.05). Conclusion. Inducing WWP1 expression caused LVH, preserved systolic function, but impaired diastolic dysfunction, consistent with the HFpEF phenotype. Targeting the WWP1 pathway may be a novel therapeutic target for this intractable form of HF associated with aging.

Genotype and phenotype data for Columbia River steelhead.

As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding the genetic basis of those life history variations is important for conservation management. However, effective application requires a robust understanding of the strength and universality of genetic associations. Here, we examine genetic variation of single nucleotide polymorphisms in genomic regions previously associated with migration phenology and age-at-maturity in steelhead (Oncorhynchus mykiss) from the Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance in migration timing in both coastal and inland steelhead. However, strength of association was much greater in coastal than inland steelhead (R2 0.51 vs 0.08), suggesting that genomic background and challenging inland migration pathways may act to moderate effects of this region. Further, we found that chromosome 25 candidate markers (SIX6 gene) were significantly associated with age and size at first return migration for inland steelhead, and this pattern was mediated by sex in a predictable pattern (males R2 = 0.139-0.170; females R2 = 0.096-0.111). While this encourages using these candidate regions in predicting life history characteristics, we suggest that stock specific associations and haplotype frequencies will be useful in guiding implementation of genetic assays to inform management.

opencc-zeroDec 2017View details →

Data from: Convergent shifts in host-associated microbial communities across environmentally elicited phenotypes

Morphological plasticity is a genotype-by-environment interaction that enables organisms to increase fitness across varying environments. Symbioses with diverse microbiota may aid in acclimating to this variation, but whether the associated bacteria community is phenotype-specific remains unstudied. Here we induce morphological plasticity in three species of sea urchins and measure changes in the associated bacterial community. While each host species had unique microbial communities, the expression of morphological plasticity resulted in the convergence for a phenotype-specific microbiome that was, in part, driven by differentially associating with α- and γ-proteobacteria. Furthermore, these results suggest that phenotype-specific signatures were the product of the environment, and are correlated with ingestive and digestive structures. By manipulating diet quantity over time, we also support that differentially associating with microbiota along a phenotypic continuum is bidirectional. Taken together, our data support the idea of a phenotype-specific microbial community and that phenotypic plasticity extends beyond a genotype-by-environment interaction.

Domestication phenotype linked to vocal behavior in marmoset monkeys

The domestication syndrome refers to a set of traits that are the incidental by-products of artificial selection for increased tolerance towards humans. One hypothesis is that some species like humans and bonobos "self domesticated", that they have been under selection for that same suite of domesticated phenotypes. However, the evidence for this has been largely circumstantial. Here, we provide evidence that in marmoset monkeys, the size of a domestication phenotype—a white facial fur patch—is linked to their degree of affiliative vocal responses. During development, the amount of parental vocal feedback experienced by influences the rate of growth of this facial white patch and this suggests a mechanistic link between the two phenotypes, possibly neural crest cells. Our study provides evidence for links between vocal behavior and the development of morphological phenotypes associated with domestication in a nonhuman primate.

Data from: Genome-wide diversity and habitat underlie fine-scale phenotypic differentiation in the rainbow darter (Etheostoma caeruleum)

Adaptation to environmental change requires that populations harbor the necessary genetic variation to respond to selection. However, dispersal-limited species with fragmented populations and reduced genetic diversity may lack this variation and are at an increased risk of local extinction. In freshwater fish species, environmental change in the form of increased stream temperatures places many cold-water species at-risk. We present a study of rainbow darters (Etheostoma caeruleum) in which we evaluated the importance of genetic variation on adaptive potential and determined responses to extreme thermal stress. We compared fine-scale patterns of morphological and thermal tolerance differentiation across eight sites, including a unique lake habitat. We also inferred contemporary population structure using genomic data and characterized the relationship between individual genetic diversity and stress tolerance. We found site-specific variation in thermal tolerance that generally matched local conditions and morphological differences associated with lake-stream divergence. We detected patterns of population structure on a highly local spatial scale that could not be explained by isolation by distance or stream connectivity. Finally, we showed that individual thermal tolerance was positively correlated with genetic variation, suggesting that sites with increased genetic diversity may be better at tolerating novel stress. Our results highlight the importance of considering intraspecific variation in understanding population vulnerability and stress response.

opencc-by-4.0Jul 2020View details →

Supplementary information to the article by van Beijnum et al. "Integrating phenotypic search and phosphoproteomic profiling of active kinases for optimization of drug mixtures for RCC treatment"

Supplementary information to the article "Integrating phenotypic search and phosphoproteomic profiling of active kinases for optimization of drug mixtures for RCC treatment". Judy R. van Beijnum1, Andrea Weiss2, 3, Robert H. Berndsen1,2 , Tse J. Wong1, Louise C. Reckman1, Sander R. Piersma4,5, Marloes Zoetemelk2,3, Richard de Haas1,4,5, Olivier Dormond6, Axel Bex7,8, Alexander A. Henneman4,5, Connie R. Jimenez4,5, Arjan W. Griffioen1, Patrycja Nowak-Sliwinska2,3,9*   1    Angiogenesis Laboratory, Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands; 2    Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland*; 3   Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland 4   Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands 5    OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands 6    Department of Visceral surgery, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland               7   Royal Free London NHS Foundation Trust, Renal Cancer Centre, UCL Division of Surgical and Interventional Science, London, UK 8   Netherlands Cancer Institute, Amsterdam, The Netherlands 9  Translational Research Centre in Oncohaematology, Geneva, Switzerland  Correspondence: <a href="mailto:Patrycja.Nowak-Sliwinska@unige.ch">Patrycja.Nowak-Sliwinska@unige.ch</a>

opencc-zeroOct 2020View details →

Data from: Phenotypic flexibility in background-mediated color change in sticklebacks

Phenotypic flexibility may incur a selective advantage in changing and heterogeneous environments, and is increasingly recognized as an integral aspect of organismal adaptation. Despite the widespread occurrence and potential importance of rapid and reversible background-mediated color change for predator avoidance, knowledge gaps remain regarding its adaptive value, repeatability within individuals, phenotypic correlates, and whether its expression is context dependent. We used manipulative experiments to investigate these issues in two fish species, the three-spined (Gasterosteus aculeatus) and nine-spined stickleback (Pungitius pungitius). We sequentially exposed individuals to dark and light visual background treatments, quantified color change from video recordings, and examined associations of color change with phenotypic dimensions that can influence the outcome of predator-prey interactions. G. aculeatus expressed a greater degree of color change compared to P. pungitius. In G. aculeatus, the color change response was repeatable within individuals. Moreover, the color change response was independent of body size but affected by sex and boldness, with males and bolder individuals changing less. Infection by the parasite Schistocephalus solidus did not affect the degree of color change, but it did modulate its association with sex and boldness. G. aculeatus adjusted the expression of color change in response to predation risk, with enhanced color change expression in individuals exposed to either simulated attacks, or olfactory cues from a natural predator. These results provide novel evidence on repeatability, correlated traits, and context dependence in the color change response and highlight how a suite of factors can contribute to individual variation in phenotypic flexibility.

opencc-zeroOct 2020View details →

Data from: Metabolic rate shapes phenotypic covariance among physiological, behavioural, and life history traits in honeybees

Metabolic rate is often cited as the fundamental rate that determines the rate of all biological processes by shaping energetic availability for the various behavioral and life history traits that contribute to performance. It has therefore been suggested that metabolic rate drives the widely observed covariance among these different levels of phenotypic traits. However, much of the work on this topic has relied on pairwise correlational analysis, thereby leaving an important gap in our understanding regarding the functional links that shape this phenotypic covariance, often referred to as pace-of-life. Using honeybees as an experimental model, we measured a large number of behavioural, life history and physiological traits in individual bees and used a structural equation model to characterize the phenotypic covariance structure among these traits. Following this with a path analysis, we demonstrate that variation in metabolic rate plays a fundamental proximate role in driving this phenotypic covariance structure in honeybees. We discuss the importance of these findings in the context of how interindividual variation in terms of slow-fast phenotypes may drive the phenotype of a group and the functional role metabolic rate might play in shaping division of labour and social evolution.