Use of cDNA subtraction and RNA interference screens in combination reveals genes required for germ-line development in Caenorhabditis elegans

Caenorhabditis elegans is an ideal organism for the study of the molecular basis of fundamental biological processes such as germ-line development, especially because of availability of the whole genome sequence and applicability of the RNA interference (RNAi) technique. To identify genes involved in germ-line development, we produced subtracted cDNA pools either enriched for or deprived of the cDNAs from germ-line tissues. We then performed differential hybridization on the high-density cDNA grid, on which about 7,600 nonoverlapping expressed sequence tag (EST) clones were spotted, to identify a set of genes specifically expressed in the germ line. One hundred and sixty-eight clones were then tested with the RNAi technique. Of these, 15 clones showed sterility with a variety of defects in germ-line development. Seven of them led to the production of unfertilized eggs, because of defects in spermatogenesis (4 clones), or defects in the oocytes (3 clones). The other 8 clones led to failure of oogenesis. These failures were caused by germ-line proliferation defect (Glp phenotype), meiotic arrest, and defects in sperm–oocyte switch (Mog phenotype) among others. These results demonstrate the efficacy of the screening strategy using the EST library combined with the RNAi technique in C. elegans.

Mice lacking the gene encoding tissue-type plasminogen activator show a selective interference with late-phase long-term potentiation in both Schaffer collateral and mossy fiber pathways.

The gene encoding tissue-type plasminogen activator (t-PA) is an immediate response gene, downstream from CREB-1 and other constitutively expressed transcription factors, which is induced in the hippocampus during the late phase of long-term potentiation (L-LTP). Mice in which the t-PA gene has been ablated (t-PA-/-) showed no gross anatomical, electrophysiological, sensory, or motor abnormalities but manifest a selective reduction in L-LTP in hippocampal slices in both the Schaffer collateral-CA1 and mossy fiber-CA3 pathways. t-PA-/- mice also exhibit reduced potentiation by cAMP analogs and D1/D5 agonists. By contrast, hippocampal-dependent learning and memory were not affected in these mice, whereas performance was impaired on two-way active avoidance, a striatum-dependent task. These results provide genetic evidence that t-PA is a downstream effector gene important for L-LTP and show that modest impairment of L-LTP in CA1 and CA3 does not result in hippocampus-dependent behavioral phenotypes.

Multimeric complexes of the PML-retinoic acid receptor alpha fusion protein in acute promyelocytic leukemia cells and interference with retinoid and peroxisome-proliferator signaling pathways.

The t(15;17) chromosomal translocation, specific for acute promyelocytic leukemia (APL), fuses the PML gene to the retinoic acid receptor alpha (RAR alpha) gene, resulting in expression of a PML-RAR alpha hybrid protein. In this report, we analyzed the nature of PML-RAR alpha-containing complexes in nuclear protein extracts of t(15;17)-positive cells. We show that endogenous PML-RAR alpha can bind to DNA as a homodimer, in contrast to RAR alpha that requires the retinoid X receptor (RXR) dimerization partner. In addition, these cells contain oligomeric complexes of PML-RAR alpha and endogenous RXR. Treatment with retinoic acid results in a decrease of PML-RAR alpha protein levels and, as a consequence, of DNA binding by the different complexes. Using responsive elements from various hormone signaling pathways, we show that PML-RAR alpha homodimers have altered DNA-binding characteristics when compared to RAR alpha-RXR alpha heterodimers. In transfected Drosophila SL-3 cells that are devoid of endogenous retinoid receptors PML-RAR alpha inhibits transactivation by RAR alpha-RXR alpha heterodimers in a dominant fashion. In addition, we show that both normal retinoid receptors and the PML-RAR alpha hybrid bind and activate the peroxisome proliferator-activated receptor responsive element from the Acyl-CoA oxidase gene, indicating that retinoids and peroxisome proliferator receptors may share common target genes. These properties of PML-RAR alpha may contribute to the transformed phenotype of APL cells.

Neural basis of lexical-semantic processing and integration of symbolic gestures with words

Three studies investigated the relation between symbolic gestures and words, aiming at discover the neural basis and behavioural features of the lexical semantic processing and integration of the two communicative signals. The first study aimed at determining whether elaboration of communicative signals (symbolic gestures and words) is always accompanied by integration with each other and, if present, this integration can be considered in support of the existence of a same control mechanism. Experiment 1 aimed at determining whether and how gesture is integrated with word. Participants were administered with a semantic priming paradigm with a lexical decision task and pronounced a target word, which was preceded by a meaningful or meaningless prime gesture. When meaningful, the gesture could be either congruent or incongruent with word meaning. Duration of prime presentation (100, 250, 400 ms) randomly varied. Voice spectra, lip kinematics, and time to response were recorded and analyzed. Formant 1 of voice spectra, and mean velocity in lip kinematics increased when the prime was meaningful and congruent with the word, as compared to meaningless gesture. In other words, parameters of voice and movement were magnified by congruence, but this occurred only when prime duration was 250 ms. Time to response to meaningful gesture was shorter in the condition of congruence compared to incongruence. Experiment 2 aimed at determining whether the mechanism of integration of a prime word with a target word is similar to that of a prime gesture with a target word. Formant 1 of the target word increased when word prime was meaningful and congruent, as compared to meaningless congruent prime. Increase was, however, present for whatever prime word duration. In the second study, experiment 3 aimed at determining whether symbolic prime gesture comprehension makes use of motor simulation. Transcranial Magnetic Stimulation was delivered to left primary motor cortex 100, 250, 500 ms after prime gesture presentation. Motor Evoked Potential of First Dorsal Interosseus increased when stimulation occurred 100 ms post-stimulus. Thus, gesture was understood within 100ms and integrated with the target word within 250 ms. Experiment 4 excluded any hand motor simulation in order to comprehend prime word. The effect of the prior presentation of a symbolic gesture on congruent target word processing was investigated in study 3. In experiment 5, symbolic gestures were presented as primes, followed by semantically congruent target word or pseudowords. In this case, lexical-semantic decision was accompanied by a motor simulation at 100ms after the onset of the verbal stimuli. Summing up, the same type of integration with a word was present for both prime gesture and word. It was probably subsequent to understanding of the signal, which used motor simulation for gesture and direct access to semantics for words. However, gesture and words could be understood at the same motor level through simulation if words were preceded by an adequate gestural context. Results are discussed in the prospective of a continuum between transitive actions and emblems, in parallelism with language; the grounded/symbolic content of the different signals evidences relation between sensorimotor and linguistic systems, which could interact at different levels.

Local form interference in biological motion perception

Peer reviewed

Enriching the integration of semantic resources based on WordNet

In this paper we present the enrichment of the Integration of Semantic Resources based in WordNet (ISR-WN Enriched). This new proposal improves the previous one where several semantic resources such as SUMO, WordNet Domains and WordNet Affects were related, adding other semantic resources such as Semantic Classes and SentiWordNet. Firstly, the paper describes the architecture of this proposal explaining the particularities of each integrated resource. After that, we analyze some problems related to the mappings of different versions and how we solve them. Moreover, we show the advantages that this kind of tool can provide to different applications of Natural Language Processing. Related to that question, we can demonstrate that the integration of semantic resources allows acquiring a multidimensional vision in the analysis of natural language.

Automatic extraction of syntactic semantic patterns for multilingual resources

In this paper we present an automatic system for the extraction of syntactic semantic patterns applied to the development of multilingual processing tools. In order to achieve optimum methods for the automatic treatment of more than one language, we propose the use of syntactic semantic patterns. These patterns are formed by a verbal head and the main arguments, and they are aligned among languages. In this paper we present an automatic system for the extraction and alignment of syntactic semantic patterns from two manually annotated corpora, and evaluate the main linguistic problems that we must deal with in the alignment process.

A general proposal to multilingual information access based on syntactic-semantic patterns

In the last few years, there has been a wide development in the research on textual information systems. The goal is to improve these systems in order to allow an easy localization, treatment and access to the information stored in digital format (Digital Databases, Documental Databases, and so on). There are lots of applications focused on information access (for example, Web-search systems like Google or Altavista). However, these applications have problems when they must access to cross-language information, or when they need to show information in a language different from the one of the query. This paper explores the use of syntactic-sematic patterns as a method to access to multilingual information, and revise, in the case of Information Retrieval, where it is possible and useful to employ patterns when it comes to the multilingual and interactive aspects. On the one hand, the multilingual aspects that are going to be studied are the ones related to the access to documents in different languages from the one of the query, as well as the automatic translation of the document, i.e. a machine translation system based on patterns. On the other hand, this paper is going to go deep into the interactive aspects related to the reformulation of a query based on the syntactic-semantic pattern of the request.

Using WordNet relations and semantic classes in information retrieval tasks

In this paper we explore the use of semantic classes in an existing information retrieval system in order to improve its results. Thus, we use two different ontologies of semantic classes (WordNet domain and Basic Level Concepts) in order to re-rank the retrieved documents and obtain better recall and precision. Finally, we implement a new method for weighting the expanded terms taking into account the weights of the original query terms and their relations in WordNet with respect to the new ones (which have demonstrated to improve the results). The evaluation of these approaches was carried out in the CLEF Robust-WSD Task, obtaining an improvement of 1.8% in GMAP for the semantic classes approach and 10% in MAP employing the WordNet term weighting approach.

Quantum interference in atomic-sized point contacts

The conductance of atomic-sized metallic point contacts is shown to be strongly voltage dependent due to quantum interference with impurities even in samples with low impurity concentrations. Transmission through these small contacts depends not only on the local atomic structure at the contact but also on the distribution of impurities or defects within a coherence length of the contact. In contrast with other mesoscopic systems we show that transport through atomic contacts is coherent even at room temperature. The use of a scanning tunneling microscope (STM) makes it possible to fabricate one atom contacts of gold whose transmission can be controlled by manipulation of the contact allowing inelastic spectroscopy in such small contacts.

Developing Semantic Rich Internet Applications with the Sm4RIA Extension for OIDE

This paper introduces the Sm4RIA Extension for OIDE, which implements the Sm4RIA approach in OIDE (OOH4RIA Integrated Development Environment). The application, based on the Eclipse framework, supports the design of the Sm4RIA models as well as the model-to-model and model-to-text transformation processes that facilitate the generation of Semantic Rich Internet Applications, i.e., RIA applications capable of sharing data as Linked data and consuming external data from other sources in the same manner. Moreover, the application implements mechanisms for the creation of RIA interfaces from ontologies and the automatic generation of administration interfaces for a previously design application.

The role of statistical and semantic features in single-document extractive summarization

This paper reports on the further results of the ongoing research analyzing the impact of a range of commonly used statistical and semantic features in the context of extractive text summarization. The features experimented with include word frequency, inverse sentence and term frequencies, stopwords filtering, word senses, resolved anaphora and textual entailment. The obtained results demonstrate the relative importance of each feature and the limitations of the tools available. It has been shown that the inverse sentence frequency combined with the term frequency yields almost the same results as the latter combined with stopwords filtering that in its turn proved to be a highly competitive baseline. To improve the suboptimal results of anaphora resolution, the system was extended with the second anaphora resolution module. The present paper also describes the first attempts of the internal document data representation.

Power line interference filtering on surface electromyography based on the stationary wavelet packet transform

Power line interference is one of the main problems in surface electromyogram signals (EMG) analysis. In this work, a new method based on the stationary wavelet packet transform is proposed to estimate and remove this kind of noise from EMG data records. The performance has been quantitatively evaluated with synthetic noisy signals, obtaining good results independently from the signal to noise ratio (SNR). For the analyzed cases, the obtained results show that the correlation coefficient is around 0.99, the energy respecting to the pure EMG signal is 98–104%, the SNR is between 16.64 and 20.40 dB and the mean absolute error (MAE) is in the range of −69.02 and −65.31 dB. It has been also applied on 18 real EMG signals, evaluating the percentage of energy respecting to the noisy signals. The proposed method adjusts the reduction level to the amplitude of each harmonic present in the analyzed noisy signals (synthetic and real), reducing the harmonics with no alteration of the desired signal.