Assessing the impact of future CAP reforms on the demand of production factors

The CAP reform process has been a central issue for agricultural economics research in recent years, and is gaining further attention in view of the post-2013 perspectives. The objective of this paper is to assess ex-ante the effect of different post-2013 CAP and market scenarios on the demand of productions factors. The paper is based on the use of farm household dynamic programming models maximising the net present value with a time horizon until 2030. A representative model has been implemented for 18 different farming systems in 8 EU countries. Changes in marginal values of selected resource constraints (land, labour and capital) are used to assess the potential effect of different scenarios on farm-household demand of production factors. Results highlight that both policy and market conditions change strongly the demand of productive factors

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.National Human Genome Research Institute (U.S.)National Institutes of Health (U.S.

A General Definition and Nomenclature for Alternative Splicing Events

Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is one of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenon contributing to the production of different mature transcripts from the same primary RNA sequence. As a plethora of different transcript forms is available in databases, a first step to uncover the biology that drives AS is to identify the different types of reflected splicing variation. In this work, we present a general definition of the AS event along with a notation system that involves the relative positions of the splice sites. This nomenclature univocally and dynamically assigns a specific “AS code” to every possible pattern of splicing variation. On the basis of this definition and the corresponding codes, we have developed a computational tool (AStalavista) that automatically characterizes the complete landscape of AS events in a given transcript annotation of a genome, thus providing a platform to investigate the transcriptome diversity across genes, chromosomes, and species. Our analysis reveals that a substantial part—in human more than a quarter—of the observed splicing variations are ignored in common classification pipelines. We have used AStalavista to investigate and to compare the AS landscape of different reference annotation sets in human and in other metazoan species and found that proportions of AS events change substantially depending on the annotation protocol, species-specific attributes, and coding constraints acting on the transcripts. The AStalavista system therefore provides a general framework to conduct specific studies investigating the occurrence, impact, and regulation of AS

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas

A user's guide to the Encyclopedia of DNA elements (ENCODE)

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease

Panta rhei (QAlign2): an open graphical environment for sequence analysis

Sammeth M, Griebel T, Tille F, Stoye J. Panta rhei (QAlign2): an open graphical environment for sequence analysis. BIOINFORMATICS. 2006;22(7):889-890.Motivation: The first version of the graphical multiple sequence alignment environment QAlign was published in 2003. Heavy response from the molecular-biological user community clearly demonstrated the need for such a platform. Results: Panta rhei extends QAlign by several features. Major redesigns on the user interface, for instance, allow users to flexibily compose views for multiple projects. The new sequence viewer handles datasets with arbitrarily many and arbitrarily large sequences that may still be edited by guided block moving. More distance-based algorithms are available to interactively reconstruct phylogenetic trees which can now also be zoomed and navigated graphicaly

Farm Investment Behaviour Analysis

Despite the fact that agricultural policy should have a prominent role in determining the propensity to invest, recent studies on teh imapct of the CAP reform process (both the Health Check and decoupling), as well as on farming strucutre in new MEmber States, emphasize the role of non-policy and non-farm variables associated with farm household (e.g. demography, ageing) and the surrounding eocnomic environmental (e.g. shadow wages in farm households, return on capital, quality of life in rural areas) in determining farmers' behaviour. This is particualrly true for investments and decommissioning. However , there is limited prmary research on the impact of the CAP reform process on farmers' investment behaviour. Within the above regulatory and economic framework, the present paper aims to investigate farmers' investment behaviour, and evaluate the impact of differenting CAP scenarios - seen in the international economic context - on selcected group of farming systems, hence contributing to the understaning of the relation between policy objectives and farmers' behaviour. this chapter is translated originally from the project report "Farm Investment Behaviour under the cAP Reform Process" IPTS, 2010

Effetti della crisi, aspettative, investimenti: primi risultati di uno studio europeo

The economic and financial crisis and the price volatility in 2007-2008 have negatively influenced the performance of farming activity. The intention to invest is one important theme linked to the farm household economic difficulties. In this view, the crisis effects interact to the choice determinants of investment, and in particular, to credit access and to farmers’ expectations on future prices and trends. Aim of this work is to identify and classify the relations between the crisis effects, the farmers’ characteristics and expectations and the intentions to invest. The paper is based on a survey conducted in 2009 on a sample of 256 farm household in 8 european countries. Furthermore, a multiple correspondence analysis has been carried out considering a subsample of 3 countries (Italy, Germany and Poland). The preliminary results figure out the presence of four different groups that illustrate different behaviour about the crisis effects, the intentions to invest and credit access. Three of these groups could also represent different typologies linked to the countries. Obiettivo di questo lavoro è identificare e classificare la relazione tra gli effetti/percezione della crisi, le caratteristiche e le aspettative degli operatori e le intenzioni di investimento. Il lavoro si basa su un’indagine svolta nel 2009 su un campione di 250 famiglie agricole di 8 paesi Europei. Inoltre un’analisi delle corrispondenze multiple è stata condotta su un sottocampione che include solo tre paesi (Italia, Germania e Polonia). I primi risultati identificano la presenza di quattro gruppi distinti per le risposte sugli effetti della crisi economica, sulle intenzioni di investire e sull’accesso al credito. Per tre gruppi si evidenzia anche una rilevante caraterizzazione legata anche al paese considerato