Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome

Background: Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata) transcriptome using 454 sequence reads, and we evaluate potential uses of this transcriptome, including detection of sex-specific transcripts and deployment as a reference for gene expression analysis in guppies and a related species. Guppies have been model organisms in ecology, evolutionary biology, and animal behaviour for over 100 years. An annotated transcriptome and other genomic tools will facilitate understanding the genetic and molecular bases of adaptation and variation in a vertebrate species with a uniquely well known natural history. Results: We generated approximately 336 Mbp of mRNA sequence data from male brain, male body, female brain, and female body. The resulting 1,162,670 reads assembled into 54,921 contigs, creating a reference transcriptome for the guppy with an average read depth of 28×. We annotated nearly 40% of this reference transcriptome by searching protein and gene ontology databases. Using this annotated transcriptome database, we identified candidate genes of interest to the guppy research community, putative single nucleotide polymorphisms (SNPs), and male-specific expressed genes. We also showed that our reference transcriptome can be used for RNA- sequencing-based analysis of differential gene expression. We identified transcripts that, in juveniles, are regulated differently in the presence and absence of an important predator, Rivulus hartii, including two genes implicated in stress response. For each sample in the RNA-seq study, >50% of high-quality reads mapped to unique sequences in the reference database with high confidence. In addition, we evaluated the use of the guppy reference transcriptome for gene expression analyses in a congeneric species, the sailfin molly (Poecilia latipinna). Over 40% of reads from the sailfin molly sample aligned to the guppy transcriptome. Conclusions: We show that next-generation sequencing provided a reliable and broad reference transcriptome. This resource allowed us to identify candidate gene variants, SNPs in coding regions, and sex-specific gene expression, and permitted quantitative analysis of differential gene expression

Amelogenesis Imperfecta caused by N-Terminal Enamelin Point Mutations in Mice and Men is driven by Endoplasmic Reticulum Stress

‘Amelogenesis imperfecta’ (AI) describes a group of inherited diseases of dental enamel that have major clinical impact. Here, we identify the aetiology driving AI in mice carrying a p.S55I mutation in enamelin; one of the most commonly mutated proteins underlying AI in humans. Our data indicate that the mutation inhibits the ameloblast secretory pathway leading to ER stress and an activated unfolded protein response (UPR). Initially, with the support of the UPR acting in pro-survival mode, Enam(p.S55I) heterozygous mice secreted structurally normal enamel. However, enamel secreted thereafter was structurally abnormal; presumably due to the UPR modulating ameloblast behaviour and function in an attempt to relieve ER stress. Homozygous mutant mice failed to produce enamel. We also identified a novel heterozygous ENAM(p.L31R) mutation causing AI in humans. We hypothesize that ER stress is the aetiological factor in this case of human AI as it shared the characteristic phenotype described above for the Enam(p.S55I) mouse. We previously demonstrated that AI in mice carrying the Amelx(p.Y64H) mutation is a proteinopathy. The current data indicate that AI in Enam(p.S55I) mice is also a proteinopathy, and based on comparative phenotypic analysis, we suggest that human AI resulting from the ENAM(p.L31R) mutation is another proteinopathic disease. Identifying a common aetiology for AI resulting from mutations in two different genes opens the way for developing pharmaceutical interventions designed to relieve ER stress or modulate the UPR during enamel development to ameliorate the clinical phenotype

Significant benefits of AIP testing and clinical screening in familial isolated and young-onset pituitary tumors

Context Germline mutations in the aryl hydrocarbon receptor-interacting protein (AIP) gene are responsible for a subset of familial isolated pituitary adenoma (FIPA) cases and sporadic pituitary neuroendocrine tumors (PitNETs). Objective To compare prospectively diagnosed AIP mutation-positive (AIPmut) PitNET patients with clinically presenting patients and to compare the clinical characteristics of AIPmut and AIPneg PitNET patients. Design 12-year prospective, observational study. Participants & Setting We studied probands and family members of FIPA kindreds and sporadic patients with disease onset ≤18 years or macroadenomas with onset ≤30 years (n = 1477). This was a collaborative study conducted at referral centers for pituitary diseases. Interventions & Outcome AIP testing and clinical screening for pituitary disease. Comparison of characteristics of prospectively diagnosed (n = 22) vs clinically presenting AIPmut PitNET patients (n = 145), and AIPmut (n = 167) vs AIPneg PitNET patients (n = 1310). Results Prospectively diagnosed AIPmut PitNET patients had smaller lesions with less suprasellar extension or cavernous sinus invasion and required fewer treatments with fewer operations and no radiotherapy compared with clinically presenting cases; there were fewer cases with active disease and hypopituitarism at last follow-up. When comparing AIPmut and AIPneg cases, AIPmut patients were more often males, younger, more often had GH excess, pituitary apoplexy, suprasellar extension, and more patients required multimodal therapy, including radiotherapy. AIPmut patients (n = 136) with GH excess were taller than AIPneg counterparts (n = 650). Conclusions Prospectively diagnosed AIPmut patients show better outcomes than clinically presenting cases, demonstrating the benefits of genetic and clinical screening. AIP-related pituitary disease has a wide spectrum ranging from aggressively growing lesions to stable or indolent disease course

Development and evaluation of CARIES-QC: a caries-specific measure of quality of life for children.

BACKGROUND: Existing paediatric oral health-related quality of life (OHRQoL) measures are generic instruments designed to evaluate a range of oral conditions. It has been found that disease-specific measures may be more adept at detecting subtle changes which occur following treatment of the condition in question. Furthermore, existing self-report OHRQoL measures have not involved children at all stages of development of the measure. The aim of this study was to develop a caries-specific measure of quality of life for children. METHODS: The first stage of the study involved a qualitative enquiry with children, aged 5-16 years, to inform the development of the measure. Children generated the potential items, contributed to item reduction and questionnaire design and participated in the testing of face and content validity. The resulting measure was evaluated in a cross-sectional validation study. Ethical approval was granted for the study. RESULTS: The qualitative study found that children discussed a number of caries-related impacts which affected their daily lives. These were incorporated into a draft measure which was further refined following testing of face and content validity. This resulted in the production of the Caries Impacts and Experiences Questionnaire for Children (CARIES-QC), comprising 16 items and one global question. Two hundred participants with a mean (range) age of 8.1 (5-16) years took part in the further evaluation of CARIES-QC. Four items, which did not fit the Rasch model, were removed from further analysis. The remaining 12 items demonstrated good internal consistency (alpha = 0.9) and the total score showed significant correlations with the number of decayed teeth, presence of pain, pulpal involvement, the Child Perceptions Questionnaire (16-item short form) and the global score (p < 0.01, Spearman's rho). CONCLUSION: In conclusion, children's input allowed the development of a valid and reliable child-centred caries-specific quality of life measure. CARIES-QC can now be used to evaluate which interventions for dental caries are most effective in reducing impacts from the child's perspective

Assessment of the quality of measures of child oral health-related quality of life

Background Several measures of oral health-related quality of life have been developed for children. The most frequently used are the Child Perceptions Questionnaire (CPQ), the Child Oral Impacts on Daily Performances (C-OIDP) and the Child Oral Health Impact Profile (COHIP). The aim of this study was to assess the methodological quality of the development and testing of these three measures. Methods A systematic search strategy was used to identify eligible studies published up to December 2012, using both MEDLINE and Web of Science. Titles and abstracts were read independently by two investigators and full papers retrieved where the inclusion criteria were met. Data were extracted by two teams of two investigators using a piloted protocol. The data were used to describe the development of the measures and their use against existing criteria. The methodological quality and measurement properties of the measures were assessed using standards proposed by the Consensus-based Standards for the Selection of Health Measurement Instruments (COSMIN) group. Results The search strategy yielded 653 papers, of which 417 were duplicates. Following analysis of the abstracts, 119 papers met the inclusion criteria. The majority of papers reported cross-sectional studies (n = 117) with three of longitudinal design. Fifteen studies which had used the original version of the measures in their original language were included in the COSMIN analysis. The most frequently used measure was the CPQ. Reliability and construct validity appear to be adequate for all three measures. Children were not fully involved in item generation which may compromise their content validity. Internal consistency was measured using classic test theory with no evidence of modern psychometric techniques being used to test unidimensionality of the measures included in the COSMIN analysis. Conclusion The three measures evaluated appear to be able to discriminate between groups. CPQ has been most widely tested and several versions are available. COHIP employed a rigorous development strategy but has been tested in fewer populations. C-OIDP is shorter and has been used successfully in epidemiological studies. Further testing using modern psychometric techniques such as item response theory is recommended. Future developments should also focus on the development of measures which can evaluate longitudinal change

Mating Success in Ambush Bugs

Cross-sectional mating success data for Phymata americana in 2003 and 2004. Sampling was conducted at the Koffler Scientific Reserve at Joker's Hill (S. Ontario, Canada

Regulation of breeding density in Microtus pennsylvanicus

(1) This study tests the hypothesis that breeding density in polygamous microtines is determined by breeding females, which compete for space to rear young. Males compete for access to females directly, not for access initially to territories. (2) To test these predictions, we live-trapped three populations from 1978 to 1981: a Control grid; a Female grid, from which all breeding males were continuously removed; and a Male grid, from which all breeding females were continuously removed. (3) In every spring, the number of breeding males on the Male grid declined for approximately 2 months after the onset of the breeding season, the number on the Female grid increased markedly through immigration, and the number on the Control grid remained constant or increased slightly. The number of breeding females remained constant or increased slightly on the Control and Female grids, while the number on the Male grid increased markedly through immigration. (4) Adult males on the Control grid always had higher survival rates and longer expectations of life than did those on the Male grid throughout the breeding season. Adult females on the Control and Female grids had similar survival rates and expectations of life. Adult male survival was strongly related to the density of breeding females. Adult female survival was not related to the density of either sex. (5) Resident breeding males restricted recruitment of other breeding males in the presence of breeding female residents, but in their absence, resident males only partially restricted other breeding males. Resident breeding females restricted recruitment of other breeding females independently of male presence. (6) These results support the hypothesis that breeding female microtines regulate breeding density. We propose that males form dominance hierarchies to gain access to females

Effects of adult meadow voles, Microtus pennsylvanicus, on young conspecifics in field populations

(1) We investigated the influence of Microtus pennsylvanicus adults on young conspecifics by manipulating the density or sex ratio of the adult segment of several experimental populations. (2) Adults were removed from four experimental grids as follows: (i) all breeding males (female grid); (ii) all breeding females (male grid); (iii) most adults throughout the autumn, winter and spring (autumn-removal grid); and (iv) most adults throughout the spring (spring-removal grid). All manipulations were repeated the following year. (3) Survival, ages at sexual maturity, and reproductive rates were significantly improved in young individuals, especially young females, on all experimental grids except the female grid. The demography of young animals on the female grid was either similar to that on the control grid or intermediate between that on the control grid and that on the other experimental grids. For young females, there was a significant, negative relationship between adult density and each of these parameters; for young males, only survival rates of very young animals were negatively related to adult density. Individual growth rates were not influenced by any of the manipulations. (4) Therefore, adult animals, especially adult females, play a major role in limiting the density and fitness of young individuals