Phenotypic plasticity affects the response of a sexually selected trait to anthropogenic noise

Sexually selected traits are shaped by an interaction between sexual selection and other natural selection pressures in the environment. However, there is little understanding of how recent anthropogenic environmental change affects the elaboration of sexually selected traits. Most sexually selected traits are complex displays comprising multiple components that interact in a functional way, thereby affecting overall trait expression. To understand how environmental change may shape the expression of sexually selected traits, we have to consider not only (i) the phenotypic plasticity of individual components of traits but also their (ii) phenotypic integration, that is, the correlations among trait components, as well as (iii) plasticity integration, that is, the correlations among the plasticities of trait components. Here, we show that background noise is a considerable pressure in shaping a sexually selected multicomponent acoustic signal, bird song. We compared singing behavior of European robins (Erithacus rubecula) in territories that differed in levels of anthropogenic noise and conducted noise-exposure experiments to test if behavioral plasticity caused immediate changes in song components, for example, minimum frequency, song complexity, and song length. We found that song components differed in their plasticity to background noise and that plasticity integration between components may further restrict the elaboration of song. Thus, the altered expression of song components under noise exposure leads to increased phenotypic integration, which is linked with reduced song complexity. Our findings demonstrate that plasticity integration restricts the elaboration of a sexually selected trait, which raises the question of how changing environments may modify sexual selection.

Are phenotypic traits useful for differentiating among a priori Coregonus taxa?

A key for three putative species apparently found in three geographic areas, i.e. Coregonus clupeoides (in Scotland), Coregonus stigmaticus (in England), and Coregonus pennantii (in Wales) given in a recent review was tested quantitatively using 544 individuals from nine populations. The classification success of the key was very low (27%). It was concluded that there is currently no robust evidence for the recognition of the three putative species. Furthermore, the use of phenotypic characters alone to distinguish putative species in postglacial fish species such as those of the genus Coregonus that show homoplasy in many of these traits is questioned. In the absence of further evidence, it was concluded that a single highly variable species best describes the pattern of phenotypic variation in these U.K. populations. On this basis it is argued that taxonomic subdivision of U.K. European coregonids is inappropriate and that Coregonus lavaretus should prevail as the species name applicable to all populations.

Has habitat heterogeneity promoted phenotypic and ecological sub-structuring among a Coregonus lavaretus population in a large Scottish lake?

Differences in stable-isotope values, morphology and ecology in whitefish Coregonus lavaretus were investigated between the three basins of Loch Lomond. The results are discussed with reference to a genetic investigation to elucidate any substructuring or spawning site fidelity. Foraging fidelity between basins of Loch Lomond was indicated by delta 13C and delta 15N values of C. lavaretus muscle tissue. There was, however, no evidence of the existence of sympatric morphs in the C. lavaretus population. A previous report of two C. lavaretus 'species' in Loch Lomond probably reflects natural variation between individuals within a single mixed population.

Is the phenotypic combination A1B8Cw7DR3 a marker for male longevity?

To study whether individual Human Leucocyte Antigens (HLA) at the HLA 1 or 11 loci or the phenotypic combination A1B8Cw7DR3 were associated with longevity.

Genotypic and phenotypic diversity of the noncapsulated Haemophilus influenzae:Adaptation and pathogenesis in the human airways

The human respiratory tract contains a highly adapted microbiota including commensal and opportunistic pathogens. Noncapsulated or nontypable Haemophilus influenzae (NTHi) is a human-restricted member of the normal airway microbiota in healthy carriers and an opportunistic pathogen in immunocompromised individuals. The duality of NTHi as a colonizer and as a symptomatic infectious agent is closely related to its adaptation to the host, which in turn greatly relies on the genetic plasticity of the bacterium and is facilitated by its condition as a natural competent. The variable genotype of NTHi accounts for its heterogeneous gene expression and variable phenotype, leading to differential host-pathogen interplay among isolates. Here we review our current knowledge of NTHi diversity in terms of genotype, gene expression, antigenic variation, and the phenotypes associated with colonization and pathogenesis. The potential benefits of NTHi diversity studies discussed herein include the unraveling of pathogenicity clues, the generation of tools to predict virulence from genomic data, and the exploitation of a unique natural system for the continuous monitoring of long-term bacterial evolution in human airways exposed to noxious agents. Finally, we highlight the challenge of monitoring both the pathogen and the host in longitudinal studies, and of applying comparative genomics to clarify the meaning of the vast NTHi genetic diversity and its translation to virulence phenotypes.

Phenotypic subtypes of Stargardt macular:Dystrophy-fundus flavimaculatus

Objective: To determine if phenotypic subtypes exist in Stargardt macular dystrophy-fundus flavimaculatus (SMD-FFM). Methods: A cross-sectional study of 63 patients with autosomal recessive SMD-FFM was undertaken. The age of onset, duration of symptoms, visual acuity, and clinical features on fundus examination, color fundus photographs, and fundus autofluorescence images were recorded. Electrophysiological tests, including pattern, focal, and full-field electroretinogram (ERG), electro-oculogram, and color-contrast sensitivity measurement, were also performed. Results: Based on electrophysiological attributes (ERG), patients with SMD-FFM could be classified into 3 groups. In group 1, there was severe pattern ERG abnormality with normal scotopic and full-field ERGs. In group 2, there was additional loss of photopic function, and in group 3, there was loss of both photopic and scotopic function. Differences in scotopic or photopic function among groups were not explained on the basis of differences in age of onset or duration of disease. Conclusions: Patients with SMD-FFM can be classified into 3 groups based on the absence or presence of generalized loss of either photopic or photopic and scotopic function. It appears that these 3 groups may represent distinct phenotypic subtypes in SMD-FFM.

Counterphase modulation flicker photometry: phenotypic and genotypic associations

The OSCAR test, a clinical device that uses counterphase flicker photometry, is believed to be sensitive to the relative numbers of long-wavelength and middle-wavelength cones in the retina, as well as to individual variations in the spectral positions of the photopigments. As part of a population study of individual variations in perception, we obtained OSCAR settings from 1058 participants. We report the distribution characteristics for this cohort. A randomly selected subset of participants was tested twice at an interval of at least one week: the test-retest reliability (Spearman's rho) was 0.80. In a whole-genome association analysis we found a provisional association with a single nucleotide polymorphism (rs16844995). This marker is close to the gene RXRG, which encodes a nuclear receptor, retinoid X receptor γ. This nuclear receptor is already known to have a role in the differentiation of cones during the development of the eye, and we suggest that polymorphisms in or close to RXRG influence the relative probability with which long-wave and middle-wave opsin genes are expressed in human cones.

Characterization of nontypable Haemophilus influenzae isolates recovered from adult patients with underlying chronic lung disease reveals genotypic and phenotypic traits associated with persistent infection

Nontypable Haemophilus influenzae (NTHi) has emerged as an important opportunistic pathogen causing infection in adults suffering obstructive lung diseases. Existing evidence associates chronic infection by NTHi to the progression of the chronic respiratory disease, but specific features of NTHi associated with persistence have not been comprehensively addressed. To provide clues about adaptive strategies adopted by NTHi during persistent infection, we compared sequential persistent isolates with newly acquired isolates in sputa from six patients with chronic obstructive lung disease. Pulse field gel electrophoresis (PFGE) identified three patients with consecutive persistent strains and three with new strains. Phenotypic characterisation included infection of respiratory epithelial cells, bacterial self-aggregation, biofilm formation and resistance to antimicrobial peptides (AMP). Persistent isolates differed from new strains in showing low epithelial adhesion and inability to form biofilms when grown under continuous-flow culture conditions in microfermenters. Self-aggregation clustered the strains by patient, not by persistence. Increasing resistance to AMPs was observed for each series of persistent isolates; this was not associated with lipooligosaccharide decoration with phosphorylcholine or with lipid A acylation. Variation was further analyzed for the series of three persistent isolates recovered from patient 1. These isolates displayed comparable growth rate, natural transformation frequency and murine pulmonary infection. Genome sequencing of these three isolates revealed sequential acquisition of single-nucleotide variants in the AMP permease sapC, the heme acquisition systems hgpB, hgpC, hup and hxuC, the 3-deoxy-D-manno-octulosonic acid kinase kdkA, the long-chain fatty acid transporter ompP1, and the phosphoribosylamine glycine ligase purD. Collectively, we frame a range of pathogenic traits and a repertoire of genetic variants in the context of persistent infection by NTHi.

Phenotypic characterization of an international Pseudomonas aeruginosa reference panel: strains of cystic fibrosis (CF) origin show less in vivo virulence than non-CF strains

Pseudomonas aeruginosa causes chronic lung infections in people with cystic fibrosis (CF) and acute opportunistic infections in people without CF. Forty two P. aeruginosa strains from a range of clinical and environmental sources were collated into a single reference strain panel to harmonise research on this diverse opportunistic pathogen. To facilitate further harmonized and comparable research on P. aeruginosa, we characterised the panel strains for growth rates, motility, virulence in the Galleria mellonella infection model, pyocyanin and alginate production, mucoid phenotype, lipopolysaccharide (LPS) pattern, biofilm formation, urease activity, antimicrobial and phage susceptibilities. Phenotypic diversity across the P. aeruginosa panel was apparent for all phenotypes examined agreeing with the marked variability seen in this species. However, except for growth rate, the phenotypic diversity among strains from CF versus non-CF sources was comparable. CF strains were less virulent in the G. mellonella model than non-CF strains (p=0.037). Transmissible CF strains generally lacked O antigen, produced less pyocyanin, and had low virulence in G. mellonella. Further, in the three sets of sequential CF strains, virulence, O-antigen expression and pyocyanin production were higher in the earlier isolate compared to the isolate obtained later in infection. Overall, full phenotypic characterization of the defined panel of P. aeruginosa strains increases our understanding of the virulence and pathogenesis of P. aeruginosa and may provide a valuable resource for the testing of novel therapies against this problematic pathogen.

Nucella lapillus: imposex transcriptome analysis and phenotypic plasticity

O conhecimento de mecanismos de genómica funcional tem sido maioritariamente adquirido pela utilização de organismos modelo que são mantidos em condições laboratoriais. Contudo, estes organismos não reflectem as respostas a alterações ambientais. Por outro lado, várias espécies, ecologicamente bem estudadas, reflectem bem as interacções entre genes e ambiente mas que, das quais não existem recursos genéticos disponíveis. O imposex, caracterizado pela superimposição de caracteres sexuais masculinos em fêmeas, é induzido pelo tributilestanho (TBT) e trifenilestanho (TPT) e representa um dos melhores exemplos de disrupção endócrina com causas antropogénicas no ambiente aquático. Com o intuito de elucidar as bases moleculares deste fenómeno, procedeu-se à combinação das metodologias de pirosequenciação (sequenciação 454 da Roche) e microarrays (Agilent 4*180K) de forma a contribuir para um melhor conhecimento desta interacção gene-ambiente no gastrópode Nucella lapillus, uma espécie sentinela para imposex. O trancriptoma de N. lapillus foi sequenciado, reconstruído e anotado e posteriormente utilizado para a produção de um “array” de nucleótidos. Este array foi então utilizado para explorar níveis de expressão génica em resposta à contaminação por TBT. Os resultados obtidos confirmaram as hipóteses anteriormente propostas (esteróidica, neuroendócrina, retinóica) e adicionalmente revelou a existência de potenciais novos mecanismos envolvidos no fenómeno imposex. Evidência para alvos moleculares de disrupção endócrina não relacionados com funções reprodutoras, tais como, sistema imunitário, apoptose e supressores de tumores, foram identificados. Apesar disso, tendo em conta a forte componente reprodutiva do imposex, esta componente funcional foi a mais explorada. Assim, factores de transcrição e receptores nucleares lipofílicos, funções mitocondriais e actividade de transporte celular envolvidos na diferenciação de géneros estão na base de potenciais novos mecanismos associados ao imposex em N. lapillus. Em particular, foi identificado como estando sobre-expresso, um possível homólogo do receptor nuclear “peroxisome proliferator-activated receptor gamma” (PPARγ), cuja função na indução de imposex foi confirmada experimentalmente in vivo após injecção dos animais com Rosiglitazone, um conhecido ligando de PPARγ em vertebrados. De uma forma geral, os resultados obtidos mostram que o fenómeno imposex é um mecanismo complexo, que possivelmente envolve a cascata de sinalização envolvendo o receptor retinoid X (RXR):PPARγ “heterodimer” que, até à data não foi descrito em invertebrados. Adicionalmente, os resultados obtidos apontam para alguma conservação de mecanismos de acção envolvidos na disrupção endócrina em invertebrados e vertebrados. Finalmente, a informação molecular produzida e as ferramentas moleculares desenvolvidas contribuem de forma significativa para um melhor conhecimento do fenómeno imposex e constituem importantes recursos para a continuação da investigação deste fenómeno e, adicionalmente, poderão vir a ser aplicadas no estudo de outras respostas a alterações ambientais usando N. lapillus como organismo modelo. Neste sentido, N. lapillus foi também utilizada para explorar a adaptação na morfologia da concha em resposta a alterações naturais induzidas por acção das ondas e pelo risco de predação por caranguejos. O contributo da componente genética, plástica e da sua interacção para a expressão fenotípica é crucial para compreender a evolução de caracteres adaptativos a ambientes heterogéneos. A contribuição destes factores na morfologia da concha de N. lapillus foi explorada recorrendo a transplantes recíprocos e experiências laboratoriais em ambiente comum (com e sem influência de predação) e complementada com análises genéticas, utilizando juvenis provenientes de locais representativos de costas expostas e abrigadas da acção das ondas. As populações estudadas são diferentes geneticamente mas possuem o mesmo cariótipo. Adicionalmente, análises morfométricas revelaram plasticidade da morfologia da concha em ambas as direcções dos transplantes recíprocos e também a retenção parcial, em ambiente comum, da forma da concha nos indivíduos da F2, indicando uma correlação positiva (co-gradiente) entre heritabilidade e plasticidade. A presença de estímulos de predação por caranguejos estimulou a produção de conchas com labros mais grossos, de forma mais evidente em animais recolhidos de costas expostas e também provocou alterações na forma da concha em animais desta proveniência. Estes dados sugerem contra-gradiente em alterações provocadas por predação na morfologia da concha, na produção de labros mais grossos e em níveis de crescimento. O estudo das interacções gene-ambiente descritas acima demonstram a actual possibilidade de produzir recursos e conhecimento genómico numa espécie bem caracterizada ecologicamente mas com limitada informação genómica. Estes recursos permitem um maior conhecimento biológico desta espécie e abrirão novas oportunidades de investigação, que até aqui seriam impossíveis de abordar.

Phenotypic consequences of genome mistranslation in Candida albicans

Várias espécies do género Candida traduzem o codão CUG de leucine como serina. Em C. albicans este codão é traduzido pelo tRNACAG Ser de serina que é reconhecido por leucil- e seril-tRNA sintetases (LeuRS e SerRS), permitindo a incorporação de leucina ou serina em posições com CUG. Em condições padrão de crescimento os codões CUG é incorporam 3% de leucina e 97% de serina, no entanto estes valores são flexíveis uma vez que a incorporação de serina pode variar entre 0.6% e 5% em resposta a condições de stress. Estudos anteriores realizados in vivo em Escherichia coli sugeriram que a ambiguidade em codões CUG é regulada pela SerRS. De facto, o gene da SerRS de C. albicans tem um codão CUG na posição 197 (Ser197) cuja descodificação ambígua resulta na produção de duas isoformas de SerRS. A isoforma SerRS_Leu197 é mais ativa, apesar de menos estável, que a isoforma SerRS_Ser197, suportando a ideia da existência de um feedback loop negativo, envolvendo estas duas isoformas de SerRS, a enzima LeuRS e o tRNACAG Ser, que mantem os níveis de incorporação de leucina no codões CUG baixos. Nesta tese demonstramos que tal mecanismo não é operacional nas células de C. albicans. De facto, os níveis de incorporação de leucina em codões CUG flutuam drasticamente em resposta a alterações ambientais. Por exemplo, a incorporação de leucina pode chegar a níveis de 49.33% na presença de macrófagos e anfotericina B, mostrando a notória tolerância de C. albicans à ambiguidade. Para compreender a relevância biológica da ambiguidade do código genético em C. albicans construímos estirpes que incorporam serina em vários codões. Apesar da taxa crescimento ter sido negativamente afetada em condições padrão de crescimento, as estirpes construídas crescem favoravelmente em várias condições de stresse, sugerindo que a ambiguidade desempenha um papel importante na adaptação a novos nichos ecológicos. O transcriptoma das estirpes construídas de C. albicans e Saccharomyces. cerevisiae mostram que as leveduras respondem à ambiguidade dos codões de modo distinto. A ambiguidade induziu uma desregulação moderada da expressão génica de C. albicans, mas ativou uma resposta comum ao stresse em S. cerevisiae. O único processo celular que foi induzido na maioria das estirpes foi a oxidação redução. De salientar, que enriquecimento em elementos cis de fatores de transcrição que regulam a resposta à ambiguidade em ambas as leveduras foi distinta, sugerindo que ambas respondem ao stresse de modo diferente. Na globalidade, o nosso estudo aprofunda o conhecimento da elevada tolerância à ambiguidade de codões em C. albicans. Os resultados sugerem que este fungo usa a ambiguidade do codão CUG durante infeção, possivelmente para modular a sua interação com o hospedeiro e a resposta a drogas antifúngicas.

Detailed phenotypic and genotypic characterization of bietti crystalline dystrophy

OBJECTIVE: To provide a detailed phenotype/genotype characterization of Bietti crystalline dystrophy (BCD). DESIGN: Observational case series. PARTICIPANTS: Twenty patients from 17 families recruited from a multiethnic British population. METHODS: Patients underwent color fundus photography, near-infrared (NIR) imaging, fundus autofluorescence (FAF) imaging, spectral domain optical coherence tomography (SD-OCT), and electroretinogram (ERG) assessment. The gene CYP4V2 was sequenced. MAIN OUTCOME MEASURES: Clinical, imaging, electrophysiologic, and molecular genetics findings. RESULTS: Patients ranged in age from 19 to 72 years (median, 40 years), with a visual acuity of 6/5 to perception of light (median, 6/12). There was wide intrafamilial and interfamilial variability in clinical severity. The FAF imaging showed well-defined areas of retinal pigment epithelium (RPE) loss that corresponded on SD-OCT to well-demarcated areas of outer retinal atrophy. Retinal crystals were not evident on FAF imaging and were best visualized with NIR imaging. Spectral domain OCT showed them to be principally located on or in the RPE/Bruch's membrane complex. Disappearance of the crystals, revealed by serial recording, was associated with severe disruption and thinning of the RPE/Bruch's membrane complex. Cases with extensive RPE degeneration (N = 5) had ERGs consistent with generalized rod and cone dysfunction, but those with more focal RPE atrophy showed amplitude reduction without delay (N = 3), consistent with restricted loss of function, or that was normal (N = 2). Likely disease-causing variants were identified in 34 chromosomes from 17 families. Seven were novel, including p.Met66Arg, found in all 11 patients from 8 families of South Asian descent. This mutation appears to be associated with earlier onset (median age, 30 years) compared with other substitutions (median age, 41 years). Deletions of exon 7 were associated with more severe disease. CONCLUSIONS: The phenotype is highly variable. Several novel variants are reported, including a highly prevalent substitution in patients of South Asian descent that is associated with earlier-onset disease. Autofluorescence showed sharply demarcated areas of RPE loss that coincided with abrupt edges of outer retinal atrophy on SD-OCT; crystals were generally situated on or in the RPE/Bruch's complex but could disappear over time with associated RPE disruption. These results support a role for the RPE in disease pathogenesis.