Structured RNAs in the ENCODE selected regions of the human genome

Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional RNA structures within the ENCODE regions of the human genome. Since structural RNAs in general lack characteristic signals in primary sequence, comparative approaches evaluating evolutionary conservation of structures are most promising. We have used three recently introduced programs based on either phylogenetic–stochastic context-free grammar (EvoFold) or energy directed folding (RNAz and AlifoldZ), yielding several thousand candidate structures (corresponding to ∼2.7% of the ENCODE regions). EvoFold has its highest sensitivity in highly conserved and relatively AU-rich regions, while RNAz favors slightly GC-rich regions, resulting in a relatively small overlap between methods. Comparison with the GENCODE annotation points to functional RNAs in all genomic contexts, with a slightly increased density in 3′-UTRs. While we estimate a significant false discovery rate of ∼50%–70% many of the predictions can be further substantiated by additional criteria: 248 loci are predicted by both RNAz and EvoFold, and an additional 239 RNAz or EvoFold predictions are supported by the (more stringent) AlifoldZ algorithm. Five hundred seventy RNAz structure predictions fall into regions that show signs of selection pressure also on the sequence level (i.e., conserved elements). More than 700 predictions overlap with noncoding transcripts detected by oligonucleotide tiling arrays. One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%).

Thermal evolution of gene expression profiles in Drosophila subobscura

Background: Despite its pervasiveness, the genetic basis of adaptation resulting in variation directly or indirectly related to temperature (climatic) gradients is poorly understood. By using 3-fold replicated laboratory thermal stocks covering much of the physiologically tolerable temperature range for the temperate (i.e., cold tolerant) species Drosophila subobscura we have assessed whole-genome transcriptional responses after three years of thermal adaptation, when the populations had already diverged for inversion frequencies, pre-adult life history components, and morphological traits. Total mRNA from each population was compared to a reference pool mRNA in a standard, highly replicated two-colour competitive hybridization experiment using cDNA microarrays.Results: A total of 306 (6.6%) cDNA clones were identified as 'differentially expressed' (following a false discovery rate correction) after contrasting the two furthest apart thermal selection regimes (i.e., 13°C vs . 22°C), also including four previously reported candidate genes for thermotolerance in Drosophila (Hsp26, Hsp68, Fst, and Treh). On the other hand, correlated patterns of gene expression were similar in cold- and warm-adapted populations. Analysis of functional categories defined by the Gene Ontology project point to an overrepresentation of genes involved in carbohydrate metabolism, nucleic acids metabolism and regulation of transcription among other categories. Although the location of differently expressed genes was approximately at random with respect to chromosomes, a physical mapping of 88 probes to the polytene chromosomes of D. subobscura has shown that a larger than expected number mapped inside inverted chromosomal segments.Conclusion: Our data suggest that a sizeable number of genes appear to be involved in thermal adaptation in Drosophila, with a substantial fraction implicated in metabolism. This apparently illustrates the formidable challenge to understanding the adaptive evolution of complex trait variation. Furthermore, some clustering of genes within inverted chromosomal sections was detected. Disentangling the effects of inversions will be obviously required in any future approach if we want to identify the relevant candidate genes.

Descobriment de serveis en xarxes ad-hoc: JADE Bluetooth Discovery Middleware

En aquest projecte s'ha dissenyat i implementat un nou Discovery Middleware per a la plataforma d'agents mòbils JADE. Aquest DM col·laborarà amb el Directory Facilitator per tal d'oferir als agents un servei transparent que els permetrà descobrir serveis en plataformes remotes que siguin accessibles mitjançant xarxes ad-hoc basades en la tecnologia Bluetooth.

Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions

This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5' rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5' distal to the annotated 5' terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be "noncoding," ultimately relating to the identification of disease-related sequence alterations.

Strategic behavior and price discovery

The paper analyzes the effects of strategic behavior by an insider in a price discovery process, akin to an information tatonnement, in the presence of a competitive informed sector. Such processes are used in the preopening period of continuous trading systems in several exchanges. It is found that the insider manipulates the market using a contrarian strategy in order to neutralize the effect of the trades of competitive informed agents. Furthermore, consistently with the empirical evidence available, we find that information revelation accelerates close to the opening, that the market price does not converge to the fundamental value no matter how many rounds the tatonnement has, and that the expected trading volume displays a U-shaped pattern. We also find that a market with a larger competitive sector (smaller insider) has an improved informational efficiency and an increased trading volume. The insider provides a public good (a lower informativeness of the price) for the competitive informed sector.

Disease discovery, sistema de predicció de malalties

L'objectiu d'aquest projecte consisteix en crear una eina per servir de referència a metges, per tal d'ajudar-los en els diagnòstics, sobretot de malalties més estranyes que són més difícils de diagnostica, ja que no són tant conegudes. Estem interessats en realitzar una aplicació la qual donats uns símptomes ens doni les malalties mé probables. El personal sanitari doncs podrà disposar d'una eina que l'ajudi a diagnosticar malalties segons els símptomes dels pacients. L'eina que es presenta en aquest treball, Disease Discovery, disposa d'una base de dades omplerta des de fonts molt fiables i amb una quantitat elevada d'informació sobre malalties i símptomes. Aquesta base de dades s'entrena segons diferents classificadors. Les prediccions de les malalties es faran emprant un model generat per mitjà d'un entrenament realitzat amb un classificador sobre la base de dades. A més a més, s'ha realitzat una interfície web per ajudar als usuaris i fer que l'eina sigui més usable alhora que més còmoda de distribuir el programari entre el personal sanitari interessat.

Discovery of a High-Energy Gamma-Ray-Emitting Persistent Microquasar

Microquasars are stellar x-ray binaries that behave as a scaled down version of extragalactic quasars. The star LS 5039 is a new microquasar system with apparent persistent ejection of relativistic plasma at a 3 kiloparsec distance from the sun. It may also be associated with a gamma-ray source discovered by the Energetic Gamma Ray Experiment Telescope (EGRET) on board the COMPTON-Gamma Ray Observatory satellite. Before the discovery of LS 5039, merely a handful of microquasars had been identified in the Galaxy, and none of them was detected in high-energy gamma-rays.

High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454-pyrosequencing for the discovery of antiviral immune genes

Turbot (Scophthalmus maximus L.) is an important aquacultural resource both in Europe and Asia. However, there is little information on gene sequences available in public databases. Currently, one of the main problems affecting the culture of this flatfish is mortality due to several pathogens, especially viral diseases which are not treatable. In order to identify new genes involved in immune defense, we conducted 454-pyrosequencing of the turbot transcriptome after different immune stimulations.

Search and Discovery : OER's Open Loop

Open educational resources (OER) promise increased access, participation, quality, and relevance, in addition to cost reduction. These seemingly fantastic promises are based on the supposition that educators and learners will discover existing resources, improve them, and share the results, resulting in a virtuous cycle of improvement and re-use. By anecdotal metrics, existing web scale search is not working for OER. This situation impairs the cycle underlying the promise of OER, endangering long term growth and sustainability. While the scope of the problem is vast, targeted improvements in areas of curation, indexing, and data exchange can improve the situation, and create opportunities for further scale. I explore the way the system is currently inadequate, discuss areas for targeted improvement, and describe a prototype system built to test these ideas. I conclude with suggestions for further exploration and development.

Individual Differences in True and False Memory Retrieval Are Related to White Matter Brain Microstructure

We sometimes vividly remember things that did not happen, a phenomenon with general relevance, not only in the courtroom. It is unclear to what extent individual differences in false memories are driven by anatomical differences in memory-relevant brain regions. Here we show in humans that microstructural properties of different white matter tracts as quantified using diffusion tensor imaging are strongly correlated with true and false memory retrieval. To investigate these hypotheses, we tested a large group of participants in a version of the Deese-Roediger-McDermott paradigm (recall and recognition) and subsequently obtained diffusion tensor images. A voxel-based whole-brain level linear regression analysis was performedto relatefractional anisotropyto indices oftrue andfalse memory recall and recognition. True memory was correlated to diffusion anisotropy in the inferior longitudinal fascicle, the major connective pathway of the medial temporal lobe, whereas a greater proneness to retrieve false items was related to the superior longitudinal fascicle connecting frontoparietal structures. Our results show that individual differences in white matter microstructure underlie true and false memory performance.

Computer-aided discovery of biological activity spectra for anti-aging and anti-cancer olive oil oleuropeins

Aging is associated with common conditions, including cancer, diabetes, cardiovascular disease, and Alzheimer"s disease. The type of multi‐targeted pharmacological approach necessary to address a complex multifaceted disease such as aging might take advantage of pleiotropic natural polyphenols affecting a wide variety of biological processes. We have recently postulated that the secoiridoids oleuropein aglycone (OA) and decarboxymethyl oleuropein aglycone (DOA), two complex polyphenols present in health‐promoting extra virgin olive oil (EVOO), might constitute a new family of plant‐produced gerosuppressant agents. This paper describes an analysis of the biological activity spectra (BAS) of OA and DOA using PASS (Prediction of Activity Spectra for Substances) software. PASS can predict thousands of biological activities, as the BAS of a compound is an intrinsic property that is largely dependent on the compound"s structure and reflects pharmacological effects, physiological and biochemical mechanisms of action, and specific toxicities. Using Pharmaexpert, a tool that analyzes the PASS‐predicted BAS of substances based on thousands of"mechanism‐ effect" and"effect‐mechanism" relationships, we illuminate hypothesis‐generating pharmacological effects, mechanisms of action, and targets that might underlie the anti‐aging/anti‐cancer activities of the gerosuppressant EVOO oleuropeins.

Developmental Readiness in the Understanding of Own and Other’s False Beliefs

One of the most important milestones in the development of theory of mind is the understanding of false beliefs. This study compares children’s understanding of representational change and others’ false beliefs and evaluates the effectiveness of an appearance-reality training for improving children’s false belief understanding. A total of 78 children ranging in age from 41 to 47 months were trained in three sessions and evaluated in a pretest and in a posttest. The results show that for children it is easier to understand representational change than false beliefs in others, and that the improvement after training was greater when starting from a higher score in the pretest. The implications of this for training in false belief understanding are discussed