Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells.

BACKGROUND: Conserved non-coding sequences in the human genome are approximately tenfold more abundant than known genes, and have been hypothesized to mark the locations of cis-regulatory elements. However, the global contribution of conserved non-coding sequences to the transcriptional regulation of human genes is currently unknown. Deeply conserved elements shared between humans and teleost fish predominantly flank genes active during morphogenesis and are enriched for positive transcriptional regulatory elements. However, such deeply conserved elements account for <1% of the conserved non-coding sequences in the human genome, which are predominantly mammalian. RESULTS: We explored the regulatory potential of a large sample of these 'common' conserved non-coding sequences using a variety of classic assays, including chromatin remodeling, and enhancer/repressor and promoter activity. When tested across diverse human model cell types, we find that the fraction of experimentally active conserved non-coding sequences within any given cell type is low (approximately 5%), and that this proportion increases only modestly when considered collectively across cell types. CONCLUSIONS: The results suggest that classic assays of cis-regulatory potential are unlikely to expose the functional potential of the substantial majority of mammalian conserved non-coding sequences in the human genome.

Identifying protein-coding genes in genomic sequences.

The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets.

Mapping of the genes coding for the two major vaccinia virus core polypeptides.

We have mapped the genes coding for two major structural polypeptides of the vaccinia virus core by hybrid selection and transcriptional mapping. First, RNA was selected by hybridization to restriction fragments of the vaccinia virus genome, translated in vitro and the products were immunoprecipitated with antibodies against the two polypeptides. This approach allowed us to map the genes to the left hand end of the largest Hind III restriction fragment of 50 kilobase pairs. Second, transcriptional mapping of this region of the genome revealed the presence of the two expected RNAs. Both RNAs are transcribed from the leftward reading strand and the 5'-ends of the genes are separated by about 7.5 kilobase pairs of DNA. Thus, two genes encoding structural polypeptides with a similar location in the vaccinia virus particle are clustered at approximately 105 kilobase pairs from the left hand end of the 180 kilobase pair vaccinia virus genome.

Associationism and electoral participation: A multilevel study of 2000 Spanish general election

This work presents an application of the multilevel analysis techniques tothe study of the abstention in the 2000 Spanish general election. Theinterest of the study is both, substantive and methodological. From thesubstantive point of view the article intends to explain the causes ofabstention and analyze the impact of associationism on it. From themethodological point of view it is intended to analyze the interaction betweenindividual and context with a modelisation that takes into account thehierarchical structure of data. The multilevel study of this paper validatesthe one level results obtained in previous analysis of the abstention andshows that only a fraction of the differences in abstention are explained bythe individual characteristics of the electors. Another important fraction ofthese differences is due to the political and social characteristics of thecontext. Relating to associationism, the data suggest that individualparticipation in associations decrease the probability of abstention. However,better indicators are needed in order to catch more properly the effect ofassociationism in electoral behaviour.

Fuzzy coding in constrained ordinations

Canonical correspondence analysis and redundancy analysis are two methods of constrained ordination regularly used in the analysis of ecological data when several response variables (for example, species abundances) are related linearly to several explanatory variables (for example, environmental variables, spatial positions of samples). In this report I demonstrate the advantages of the fuzzy coding of explanatory variables: first, nonlinear relationships can be diagnosed; second, more variance in the responses can be explained; and third, in the presence of categorical explanatory variables (for example, years, regions) the interpretation of the resulting triplot ordination is unified because all explanatory variables are measured at a categorical level.

A multilevel analysis on the determinants of regional health care expenditure. A note

We apply a multilevel hierarchical model to explore whether anaggregation fallacy exists in estimating the income elasticity of healthexpenditure by ignoring the regional composition of national healthexpenditure figures. We use data for 110 regions in eight OECD countriesin 1997: Australia, Canada, France, Germany, Italy, Spain, Sweden andUnited Kingdom. In doing this we have tried to identify two sources ofrandom variation: within countries and between-countries. Our resultsshow that: 1- Variability between countries amounts to (SD) 0.5433, andjust 13% of that can be attributed to income elasticity and the remaining87% to autonomous health expenditure; 2- Within countries, variabilityamounts to (SD) 1.0249; and 3- The intra-class correlation is 0.5300. Weconclude that we have to take into account the degree of fiscaldecentralisation within countries in estimating income elasticity ofhealth expenditure. Two reasons lie behind this: a) where there isdecentralisation to the regions, policies aimed at emulating diversitytend to increase national health care expenditure; and b) without fiscaldecentralisation, central monitoring of finance tends to reduce regionaldiversity and therefore decrease national health expenditure.

A zero-delay sequential scheme for lossy coding of individual sequences

We consider adaptive sequential lossy coding of bounded individual sequences when the performance is measured by the sequentially accumulated mean squared distortion. Theencoder and the decoder are connected via a noiseless channel of capacity $R$ and both are assumed to have zero delay. No probabilistic assumptions are made on how the sequence to be encoded is generated. For any bounded sequence of length $n$, the distortion redundancy is defined as the normalized cumulative distortion of the sequential scheme minus the normalized cumulative distortion of the best scalarquantizer of rate $R$ which is matched to this particular sequence. We demonstrate the existence of a zero-delay sequential scheme which uses common randomization in the encoder and the decoder such that the normalized maximum distortion redundancy converges to zero at a rate $n^{-1/5}\log n$ as the length of the encoded sequence $n$ increases without bound.

Change of individual BMI in Switzerland and the USA: a multilevel model for growth

Objective The aim is to analyze and compare individual BMI growth patterns of adults from Switzerland and the U.S. Methods The analyses are based on data from two population representative longitudinal household surveys, one from Switzerland, the other from the U.S. Each data set contains up to four data points for each adult individual. We use multilevel models for growth. Results It can be shown that growth patterns are different in different cohorts in the two countries: there are only small growth differences in the youngest and oldest, but large differences in the middle ages. The individual BMI increase of the middle age Swiss amounts to only half of that in the comparable U.S. individuals. Conclusion Given the much higher BMI level especially in the youngest cohort, this points to severe obesity problems in the U.S. middle aged population in the near future. A positive correlation between individual BMI level and growth may aggravate this fact.

Evolutionary dynamics of coding and non-coding transcriptomes.

Gene expression changes may underlie much of phenotypic evolution. The development of high-throughput RNA sequencing protocols has opened the door to unprecedented large-scale and cross-species transcriptome comparisons by allowing accurate and sensitive assessments of transcript sequences and expression levels. Here, we review the initial wave of the new generation of comparative transcriptomic studies in mammals and vertebrate outgroup species in the context of earlier work. Together with various large-scale genomic and epigenomic data, these studies have unveiled commonalities and differences in the dynamics of gene expression evolution for various types of coding and non-coding genes across mammalian lineages, organs, developmental stages, chromosomes and sexes. They have also provided intriguing new clues to the regulatory basis and phenotypic implications of evolutionary gene expression changes.

Determinants of Corporate Disclosure : A Multicountry, Multilevel Model

Abstract The complexity of the current business world is making corporate disclosure more and more important for information users. These users, including investors, financial analysts, and government authorities rely on the disclosed information to make their investment decisions, analyze and recommend shares, and to draft regulation policies. Moreover, the globalization of capital markets has raised difficulties for information users in understanding the differences incorporate disclosure across countries and across firms. Using a sample of 797 firms from 34 countries, this thesis advances the literature on disclosure by illustrating comprehensively the disclosure determinants originating at firm systems and national systems based on the multilevel latent variable approach. Under this approach, the overall variation associated with the firm-specific variables is decomposed into two parts, the within-country and the between-country part. Accordingly, the model estimates the latent association between corporate disclosure and information demand at two levels, the within-country and the between-country level. The results indicate that the variables originating from corporate systems are hierarchically correlated with those from the country environment. The information demand factor indicated by the number of exchanges listed and the number of analyst recommendations can significantly explain the variation of corporate disclosure for both "within" and "between" countries. The exogenous influences of firm fundamentals-firm size and performance-are exerted indirectly through the information demand factor. Specifically, if the between-country variation in firm variables is taken into account, only the variables of legal systems and economic growth keep significance in explaining the disclosure differences across countries. These findings strongly support the hypothesis that disclosure is a response to both corporate systems and national systems, but the influence of the latter on disclosure reflected significantly through that of the former. In addition, the results based on ADR (American Depositary Receipt) firms suggest that the globalization of capital markets is harmonizing the disclosure behavior of cross-boundary listed firms, but it cannot entirely eliminate the national features in disclosure and other firm-specific characteristics.

Tandem repeat sequence variation as causative cis-eQTLs for protein-coding gene expression variation: the case of CSTB.

Association studies have revealed expression quantitative trait loci (eQTLs) for a large number of genes. However, the causative variants that regulate gene expression levels are generally unknown. We hypothesized that copy-number variation of sequence repeats contribute to the expression variation of some genes. Our laboratory has previously identified that the rare expansion of a repeat c.-174CGGGGCGGGGCG in the promoter region of the CSTB gene causes a silencing of the gene, resulting in progressive myoclonus epilepsy. Here, we genotyped the repeat length and quantified CSTB expression by quantitative real-time polymerase chain reaction in 173 lymphoblastoid cell lines (LCLs) and fibroblast samples from the GenCord collection. The majority of alleles contain either two or three copies of this repeat. Independent analysis revealed that the c.-174CGGGGCGGGGCG repeat length is strongly associated with CSTB expression (P = 3.14 × 10(-11)) in LCLs only. Examination of both genotyped and imputed single-nucleotide polymorphisms (SNPs) within 2 Mb of CSTB revealed that the dodecamer repeat represents the strongest cis-eQTL for CSTB in LCLs. We conclude that the common two or three copy variation is likely the causative cis-eQTL for CSTB expression variation. More broadly, we propose that polymorphic tandem repeats may represent the causative variation of a fraction of cis-eQTLs in the genome.