Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae)

<p>Abstract</p> <p>Background</p> <p>The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the <it>pDo500 </it>sequence family in <it>Dolichopoda </it>cave crickets, have a catalytic hammerhead (HH) ribozyme structure and activity embedded within each repeat.</p> <p>Results</p> <p>We assessed the phylogenetic footprints of the HH ribozyme within the <it>pDo500 </it>sequences from 38 different populations representing 12 species of <it>Dolichopoda</it>. The HH region was significantly more conserved than the non-hammerhead (NHH) region of the <it>pDo500 </it>repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the <it>Dolichopoda </it>populations and species.</p> <p>Conclusions</p> <p>The phylogenetic footprints suggest that the HH region of the <it>pDo500 </it>sequence family is selected for function in <it>Dolichopoda </it>cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to <it>trans </it>cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in <it>Dolichopoda </it>is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.</p

Novel Genes from Formation to Function

The study of the evolution of novel genes generally focuses on the formation of new coding sequences. However, equally important in the evolution of novel functional genes are the formation of regulatory regions that allow the expression of the genes and the effects of the new genes in the organism as well. Herein, we discuss the current knowledge on the evolution of novel functional genes, and we examine in more detail the youngest genes discovered. We examine the existing data on a very recent and rapidly evolving cluster of duplicated genes, the Sdic gene cluster. This cluster of genes is an excellent model for the evolution of novel genes, as it is very recent and may still be in the process of evolving.Organismic and Evolutionary Biolog

Molecular evolution of the pDo500 satellite DNA family in Dolichopoda cave crickets (Rhaphidophoridae)

Background Non-coding satellite DNA (satDNA) usually has a high turn-over rate frequently leading to species specific patterns. However, some satDNA families evolve more slowly and can be found in several related species. Here, we analyzed the mode of evolution of the pDo500 satDNA family of Dolichopoda cave crickets. In addition, we discuss the potential of slowly evolving satDNAs as phylogenetic markers. Results We sequenced 199 genomic or PCR amplified satDNA repeats of the pDo500 family from 12 Dolichopoda species. For the 38 populations under study, 39 pDo500 consensus sequences were deduced. Phylogenetic analyses using Bayesian, Maximum Parsimony, and Maximum Likelihood approaches yielded largely congruent tree topologies. The vast majority of pDo500 sequences grouped according to species designation. Scatter plots and statistical tests revealed a significant correlation between genetic distances for satDNA and mitochondrial DNA. Sliding window analyses showed species specific patterns of variable and conserved regions. The evolutionary rate of the pDo500 satDNA was estimated to be 1.63-1.78% per lineage per million years. Conclusions The pDo500 satDNA evolves gradually at a rate that is only slightly faster than previously published rates of insect mitochondrial COI sequences. The pDo500 phylogeny was basically congruent with the previously published mtDNA phylogenies. Accordingly, the slowly evolving pDo500 satDNA family is indeed informative as a phylogenetic marker

Inside the clockwork of the ECHO factorial trial: A conceptual model with proposed mediators for prevention of emotional problems in children

Having interventions that are not only evidence-based and effective but also cost-effective and efficient is important for the prevention and treatment of child and adolescent emotional problems. A randomized clinical trial (RCT) tests the totalinterventions effect but does not address specific components of the intervention. In this article the hypothesis and a conceptual model of the ECHO study are presented and discussed. The ECHO intervention consists of three different components each containing two levels of intervention. By using a cluster randomized factorial design, children aged 8–12 at 40 schools across Norway will be randomized to eight different experimental conditions investigating the optimal balance between effect, cost-effectiveness, and efficiency. The article presents the design and the different components being tested and discusses how optimalization can be reached through this innovative design. The article also discusses how interventions can be improved by investigating and understanding the mechanisms of change within psychological interventions. For each of the three components in the study we consider the mediators that could be active within the intervention and how the study investigates such mediation. The results will contribute to a better understanding of how psychological interventions work and how we intend to optimize the EMOTION intervention

Inside the Clockwork of the ECHO Factorial Trial: A Conceptual Model With Proposed Mediators for Prevention of Emotional Problems in Children

Having interventions that are not only evidence-based and effective but also cost-effective and efficient is important for the prevention and treatment of child and adolescent emotional problems. A randomized clinical trial (RCT) tests the total interventions effect but does not address specific components of the intervention. In this article the hypothesis and a conceptual model of the ECHO study are presented and discussed. The ECHO intervention consists of three different components each containing two levels of intervention. By using a cluster randomized factorial design, children aged 8–12 at 40 schools across Norway will be randomized to eight different experimental conditions investigating the optimal balance between effect, cost-effectiveness, and efficiency. The article presents the design and the different components being tested and discusses how optimalization can be reached through this innovative design. The article also discusses how interventions can be improved by investigating and understanding the mechanisms of change within psychological interventions. For each of the three components in the study we consider the mediators that could be active within the intervention and how the study investigates such mediation. The results will contribute to a better understanding of how psychological interventions work and how we intend to optimize the EMOTION intervention

Molecular evolution of the <it>pDo500 </it>satellite DNA family in <it>Dolichopoda </it>cave crickets (Rhaphidophoridae)

Abstract Background Non-coding satellite DNA (satDNA) usually has a high turn-over rate frequently leading to species specific patterns. However, some satDNA families evolve more slowly and can be found in several related species. Here, we analyzed the mode of evolution of the pDo500 satDNA family of Dolichopoda cave crickets. In addition, we discuss the potential of slowly evolving satDNAs as phylogenetic markers. Results We sequenced 199 genomic or PCR amplified satDNA repeats of the pDo500 family from 12 Dolichopoda species. For the 38 populations under study, 39 pDo500 consensus sequences were deduced. Phylogenetic analyses using Bayesian, Maximum Parsimony, and Maximum Likelihood approaches yielded largely congruent tree topologies. The vast majority of pDo500 sequences grouped according to species designation. Scatter plots and statistical tests revealed a significant correlation between genetic distances for satDNA and mitochondrial DNA. Sliding window analyses showed species specific patterns of variable and conserved regions. The evolutionary rate of the pDo500 satDNA was estimated to be 1.63-1.78% per lineage per million years. Conclusions The pDo500 satDNA evolves gradually at a rate that is only slightly faster than previously published rates of insect mitochondrial COI sequences. The pDo500 phylogeny was basically congruent with the previously published mtDNA phylogenies. Accordingly, the slowly evolving pDo500 satDNA family is indeed informative as a phylogenetic marker.</p

Development assistance for health: what criteria do multi- and bilateral funders use?

After years of unprecedented growth in development assistance for health (DAH), the system is challenged on several fronts: by the economic downturn and stagnation of DAH, by the epidemiological transition and increase in non-communicable diseases, and by the economic transition and rise of the middle-income countries. This raises questions about which countries should receive DAH and how much, and, fundamentally, what criteria that promote fair and effective allocation. Yet, no broad comparative assessment exists of the criteria used today. We reviewed the allocation criteria stated by five multilateral and nine bilateral funders of DAH. We found that several funders had only limited information about concrete criteria publicly available. Moreover, many funders not devoted to health lacked specific criteria for DAH or criteria directly related to health, and no funder had criteria directly related to inequality. National income per capita was emphasised by many funders, but the associated eligibility thresholds varied considerably. These findings and the broad overview of criteria can assist funders in critically examining and revising the criteria they use, and inform the wider debate about what the optimal criteria are

The Factor Structure of MASC Youth Report in Norwegian School Children

Identifying children with symptoms of anxiety before they develop clinical disorders is important. The objective of our study was to examine the latent factor structure of the MASC (youth report version) in a large self-selected sample of school children in 4th to 6th grade, and examine if the measure had a comparable factor structure for gender and age. Gender and age differences in anxiety symptoms were also examined. Children (N = 1686, 53.8% female) were recruited from schools during pretest of an ongoing randomized, controlled, indicative intervention. Latent variable modelling was used to determine the underlying concepts of the MASC. We found good model fit for the four-factor model, however some items on the Harm/Avoidance scale had low factor loadings. Invariance analysis indicated that the MASC had similar factor structure (comparable meaning) for boys and girls and for younger and older children in this sample. Girls scored significantly higher than boys on all subscales and on the Total Anxiety scale. Age differences were only found on the Separation Anxiety scale. Overall, the original four-factor structure of the MASC was confirmed within a large sample of school children and was invariant across gender and age. However, the Harm/avoidance scale warrants some attention. The MASC is a potentially useful measure to be used for screening purposes in a school setting