PREFACE

No abstract (available)

Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models

With the sponsorship of ``Fundacio La Caixa'' we met in Barcelona, November 21st and 22nd, to analyze the reasons why, after the completion of the human genome sequence, the identification all protein coding genes and their variants remains a distant goal. Here we report on our discussions and summarize some of the major challenges that need to be overcome in order to complete the human gene catalog.Comment: Report and discussion resulting from the `Fundacio La Caixa' gene finding meeting held November 21 and 22 2003 in Barcelon

PREFACE

No abstract (available)

BRACKISH MARSH BENTHIC MICROFAUNA AND PALEOENVIRONMENTAL CHANGES DURING THE LAST 6000 YEARS AT THE COASTAL PLAIN OF MARATHON (SE GREECE)

The present study, based mainly on the analysis of foraminifers and ostracodes, provides evidence of paleoenvironmental changes on the coastal plain of Marathon (E. Greece) during the last 6.000 yrs. Three sedimentary units -lagoonal formations - were recognized and identified as A, B and C. They range in time between before 5500BP-3500BP, 3500BP-2500BP and 2500BP-recent, respectively. The study of the brackish marsh microfauna of the Marathon plain Holocene sediments reveals the presence, during the last 5500 yrs., of three distinct biofacies in the sedimentary units already established. Alternating mesohaline - oligohaline (MO), oligohaline - fresh water (OFW) and mesohaline - oligohaline to oligohaline - fresh water (MO-OFW) biofacies in the framework of the sedimentary units indicate a general trend landward along the plain suggesting a slowing of sea-level rise probably correlated with a relevant tectonic uplift. One prominent feature of this study is the clarification of the ecological preference of the species Trichohya1us aguayoi (Bermudez, 1935), which is dominant in oligohaline conditions under an influence of fresh water input (salinity less than 15 ‰).&nbsp

The mounting of a skeleton of the fossil species Candiaceruus sp. II from Liko Cave, Crete, Greece

S'ha muntat un esquelet del cérvol pleistocènic endèmic de Creta per a la nova exhibició del Museu de Geologia de la Universitat d'Atenes. Aquest cérvol difereix de tots els cérvols continentals vivents i extingits, principalment en les seves proporcions. Les mesures i comparacions confirmen aquesta observació, però això no és prou com per a que el públic general se n'adoni del seu impacte. Per contra, un esquelet muntat deixa clar que aquest cérvol tertia uns membres considerablement escurçats, especialment els metàpodes, mentre que la llargària del cos, a la llargària de la columna vertebral, eren més aviat normals. La impressió global és més propera a la d'un bòvid nan insular, com ara Myotragus, que a la d'un cérvol petit, tal com Axis axis. El primer problema a resoldre fou la selecció de material. Ja que mai s'ha trobat un esquelet articulat complet, se n'ha de fer un de compost. Amb aquest motiu, només es varen seleccionar ossos de la classe de talla II (de Vos, 1979 ; Dermitzakis & de Vos, 1987) provinents d'un nivell d'una cova (cova de Liko, estrat B). D'aquesta manera es garanteix un interval geològic estret. Tot seguit, es varen mesurar tots els espècimens disponibles, i es va calcular el promig per a tots els elements. D'acord amb això, es va triar l'exemplar de cada element que més s'apropava a la mitjana calculada. Les peces dretes i esquerres havien de ser de la mateixa mida i robustesa, i els elements contigus havien de casar anatòmicament. Només en alguns casos s'ha hagut de recórrer a triar algun element que faltava a partir d'un llivell diferent, però mai a partir d'una cova diferent i mai a partir d'una classe de talla diferent. S'ha prioritzat la mida, la robustesa i l'ajustament anatòmic, i després que els ossos fossin complets i el color. Hi havia alguns peus articulats disponibles, encara que de mida i robustesa diferents, que s'han emprat per determinar les proporcions correctes i la posició correcta entre les falanges individuals, i els ossos carpians i tarsians. La mateixa cosa fou vàlida per a la columna vertebral. Per a l'establiment de la postura es van fer servir cérvols vivents com a comparació; per a l'extrapolació dels teixits tous (discos intervertebrals, cartílags de les articulacions) també es va recórrer al model dels cérvols vivents. De cara a amagar els bastiments de suport, es va inserir dins els ossos una armadura metàl-lica interna fent forats i fitxant-la amb goma de poliuretà. S'ha fabricat l'esquelet complet en parts modulars bones d'ajuntar pel seu transport fàcil a la mostra. Parts absents petites (principalment processos vertebrals, parts costals i les ales pèlviques) s'han reconstruït amb apoxy, en base a altres elements disponibles de Candiacervus de la cova de Liko a per interpolació del millor ajustament entre dues parts absents. Les traces de la matriu original han estat estretes, per a una impressió millor del material fòssil. Per completar l'esquelet s'ha fet una rèplica del crani de l'espècimen tipus de la classe de talla II de de Vos (1979) i una rèplica de l'espècimen tipus del banyam tipus I de de Vos (1984).For the new exhibition in the Museum of Palaeontology and Geology of the University of Athens a skeleton of the endemic Pleistocene Cretan deer was mounted. This deer differs from all known recent and extinct mainland deer, mainly in its proportions. Measurements and comparisons confirm this observation, but are not enough to make the public realize its impact. A mounted skeleton on the contrary makes it at once clear that this deer had considerably shortened limbs, especially the metapodals, whereas the body length and the vertebral column length are rather normal. The overall impression is closer to that of an insular dwarf bovid like Myotragus than to that of a small deer such as the spotted deer (Axis axis). The first problem to be tackled was the selection of the material. Since a complete articulated skeleton has never been found, a composite had to be made. For this purpose, only bones of size class II (de Vas, 1979; Dermitzakis & de Vas, 1987) coming from one layer of one cave (Liko Cave, layer El were selected. In this way a narrow geological range was assured. Subsequently, tile available specimens were measured, and of all elements the average size was calculated. Accordingly, of each element tile specimen that came tile most close to tile calculated average was selected. Left and right had to be of exactly the same size and robustness, and adjoining elements had to fit anatornically. Only in some cases a missing element had to be chosen from a different layer (layers C and Dl. but never from a different cave, and never from a different size class. Priority was first given to size, robustness and anatomical fitting, and next to completeness and colour. Several articulated feet were available, although of tile wrong size or robustness, which were used in determining the right proportions and right stance between individual phalanges, tarsal and carpal bones. The same was valid for tile vertebral column. For postural aspects, living deer were used as comparison; for extrapolation of soft tissue (intervertebral disks, articulation cartilage) also living deer stood model. In order to keep the supporting fabrication as hidden as possible, an internal metal armature was inserted in tile bones through drilled holes and fixed with polyurethane glue. The complete skeleton is fabricated in ready-to-assemble modular parts for easy transportation and reassembly on the spot. Minor missing parts (mainly vertebral processes, costal parts and tile pelvic wings) have been reconst: ructed in epoxy putty, based on other Candiaceruus elements from Liko or by interpolating the best fit between two existing parts. For a better impression of the fossil material, traces of tile original matrix were left on the bones. A cast of the skull of the type specimen of size II of de Vas (1979) and a cast of tile type specimen of antler type 1 of de Vas (1984) were made to complete the skeleton

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

The fraction of experimentally active conserved non-coding sequences within any given cell type is low, so classical assays are unlikely to expose their potential

Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes.

A primary motivation for sequencing the mouse genome was to accelerate the discovery of mammalian genes by using sequence conservation between mouse and human to identify coding exons. Achieving this goal proved challenging because of the large proportion of the mouse and human genomes that is apparently conserved but apparently does not code for protein. We developed a two-stage procedure that exploits the mouse and human genome sequences to produce a set of genes with a much higher rate of experimental verification than previously reported prediction methods. RT-PCR amplification and direct sequencing applied to an initial sample of mouse predictions that do not overlap previously known genes verified the regions flanking one intron in 139 predictions, with verification rates reaching 76%. On average, the confirmed predictions show more restricted expression patterns than the mouse orthologs of known human genes, and two-thirds lack homologs in fish genomes, demonstrating the sensitivity of this dual-genome approach to hard-to-find genes. We verified 112 previously unknown homologs of known proteins, including two homeobox proteins relevant to developmental biology, an aquaporin, and a homolog of dystrophin. We estimate that transcription and splicing can be verified for >1,000 gene predictions identified by this method that do not overlap known genes. This is likely to constitute a significant fraction of the previously unknown, multiexon mammalian genes

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR

Background Understanding the influence of genetic variants on DNA methylation is fundamental for the interpretation of epigenomic data in the context of disease. There is a need for systematic approaches not only for determining methylation quantitative trait loci (methQTL), but also for discriminating general from cell type-specific effects. Results Here, we present a two-step computational framework MAGAR (https://bioconductor.org/packages/MAGAR), which fully supports the identification of methQTLs from matched genotyping and DNA methylation data, and additionally allows for illuminating cell type-specific methQTL effects. In a pilot analysis, we apply MAGAR on data in four tissues (ileum, rectum, T cells, B cells) from healthy individuals and demonstrate the discrimination of common from cell type-specific methQTLs. We experimentally validate both types of methQTLs in an independent data set comprising additional cell types and tissues. Finally, we validate selected methQTLs located in the PON1, ZNF155, and NRG2 genes by ultra-deep local sequencing. In line with previous reports, we find cell type-specific methQTLs to be preferentially located in enhancer elements. Conclusions Our analysis demonstrates that a systematic analysis of methQTLs provides important new insights on the influences of genetic variants to cell type-specific epigenomic variation

Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR.

BackgroundUnderstanding the influence of genetic variants on DNA methylation is fundamental for the interpretation of epigenomic data in the context of disease. There is a need for systematic approaches not only for determining methylation quantitative trait loci (methQTL), but also for discriminating general from cell type-specific effects.ResultsHere, we present a two-step computational framework MAGAR ( https://bioconductor.org/packages/MAGAR ), which fully supports the identification of methQTLs from matched genotyping and DNA methylation data, and additionally allows for illuminating cell type-specific methQTL effects. In a pilot analysis, we apply MAGAR on data in four tissues (ileum, rectum, T cells, B cells) from healthy individuals and demonstrate the discrimination of common from cell type-specific methQTLs. We experimentally validate both types of methQTLs in an independent data set comprising additional cell types and tissues. Finally, we validate selected methQTLs located in the PON1, ZNF155, and NRG2 genes by ultra-deep local sequencing. In line with previous reports, we find cell type-specific methQTLs to be preferentially located in enhancer elements.ConclusionsOur analysis demonstrates that a systematic analysis of methQTLs provides important new insights on the influences of genetic variants to cell type-specific epigenomic variation

Epistatic Interactions Alter Dynamics of Multilocus Gene-for-Gene Coevolution

Fitness costs associated with resistance or virulence genes are thought to play a key role in determining the dynamics of gene-for-gene (GFG) host-parasite coevolution. However, the nature of interactions between fitness effects of multiple resistance or virulence genes (epistasis) has received less attention. To examine effects of the functional form of epistasis on the dynamics of GFG host-parasite coevolution we modified a classic multilocus GFG model framework. We show that the type of epistasis between virulence genes largely determines coevolutionary dynamics, and that coevolutionary fluctuations are more likely with acceleratingly costly (negative) than with linear or deceleratingly costly (positive) epistasis. Our results demonstrate that the specific forms of interaction between multiple resistance or virulence genes are a crucial determinant of host-parasite coevolutionary dynamics