Comparative analysis of ribonuclease P RNA using gene sequences from natural microbial populations reveals tertiary structural elements.

PCR amplification of template DNAs extracted from mixed, naturally occurring microbial populations, using oligonucleotide primers complementary to highly conserved sequences, was used to obtain a large collection of diverse RNase P RNA-encoding genes. An alignment of these sequences was used in a comparative analysis of RNase P RNA secondary and tertiary structure. The new sequences confirm the secondary structure model based on sequences from cultivated organisms (with minor alterations in helices P12 and P18), providing additional support for nearly every base pair. Analysis of sequence covariation using the entire RNase P RNA data set reveals elements of tertiary structure in the RNA; the third nucleotides (underlined) of the GNRA tetraloops L14 and L18 are seen to interact with adjacent Watson-Crick base pairs in helix P8, forming A:G/C or G:A/U base triples. These experiments demonstrate one way in which the enormous diversity of natural microbial populations can be used to elucidate molecular structure through comparative analysis.

Cloning and comparative analysis of the human pre-T-cell receptor alpha-chain gene.

In immature T cells the T-cell receptor (TCR) beta-chain gene is rearranged and expressed before the TCR alpha-chain gene. At this stage TCR beta chain can form disulfide-linked heterodimers with the pre-T-cell receptor alpha chain (pTalpha). Using the recently isolated murine pTalpha cDNA as a probe, we have isolated the human pTalpha cDNA. The complete nucleotide sequence predicts a mature protein of 282 aa consisting of an extracellular immunoglobulin-like domain, a connecting peptide, a transmembrane region, and a long cytoplasmic tail. Amino acid sequence comparison of human pTalpha with the mouse pTalpha molecule reveals high sequence homology in the extracellular as well as the transmembrane region. In contrast, the cytoplasmic region differs in amino acid composition and in length from the murine homologue. The human pTalpha gene is expressed in immature but not mature T cells and is located at the p21.2-p12 region of the short arm of chromosome 6.

Genetic and comparative analyses reveal an alternative secondary structure in the region of nt 912 of Escherichia coli 16S rRNA.

Mutations at position 912 of Escherichia coli 16S rRNA result in two notable phenotypes. The C-->U transition confers resistance to streptomycin, a translational-error-inducing antibiotic, while a C-->G transversion causes marked retardation of cell growth rate. Starting with the slow-growing G912 mutant, random mutagenesis was used to isolate a second site mutation that restored growth nearly to the wild-type rate. The second site mutation was identified as a G-->C transversion at position 885 in 16S rRNA. Cells containing the G912 mutation had an increased doubling time, abnormal sucrose gradient ribosome/subunit profile, increased sensitivity to spectinomycin, dependence upon streptomycin for growth in the presence of spectinomycin, and slower translation rate, whereas cells with the G912/C885 double mutation were similar to wild type in these assays. Comparative analysis showed there was significant covariation between positions 912 and 885. Thus the second-site suppressor analysis, the functional assays, and the comparative data suggest that the interaction between nt 912 and nt 885 is conserved and necessary for normal ribosome function. Furthermore, the comparative data suggest that the interaction extends to include G885-G886-G887 pairing with C912-U911-C910. An alternative secondary structure element for the central domain of 16S rRNA is proposed.

Sequence-specific inhibition of human immunodeficiency virus (HIV) reverse transcription by antisense oligonucleotides: comparative study in cell-free assays and in HIV-infected cells.

We have investigated two regions of the viral RNA of human immunodeficiency virus type 1 (HIV-1) as potential targets for antisense oligonucleotides. An oligodeoxynucleotide targeted to the U5 region of the viral genome was shown to block the elongation of cDNA synthesized by HIV-1 reverse transcriptase in vitro. This arrest of reverse transcription was independent of the presence of RNase H activity associated with the reverse transcriptase enzyme. A second oligodeoxynucleotide targeted to a site adjacent to the primer binding site inhibited reverse transcription in an RNase H-dependent manner. These two oligonucleotides were covalently linked to a poly(L-lysine) carrier and tested for their ability to inhibit HIV-1 infection in cell cultures. Both oligonucleotides inhibited virus production in a sequence- and dose-dependent manner. PCR analysis showed that they inhibited proviral DNA synthesis in infected cells. In contrast, an antisense oligonucleotide targeted to the tat sequence did not inhibit proviral DNA synthesis but inhibited viral production at a later step of virus development. These experiments show that antisense oligonucleotides targeted to two regions of HIV-1 viral RNA can inhibit the first step of viral infection--i.e., reverse transcription--and prevent the synthesis of proviral DNA in cell cultures.

Comparative expressed-sequence-tag analysis of differential gene expression profiles in PC-12 cells before and after nerve growth factor treatment.

Nerve growth factor-induced differentiation of adrenal chromaffin PC-12 cells to a neuronal phenotype involves alterations in gene expression and represents a model system to study neuronal differentiation. We have used the expressed-sequence-tag approach to identify approximately 600 differentially expressed mRNAs in untreated and nerve growth factor-treated PC-12 cells that encode proteins with diverse structural and biochemical functions. Many of these mRNAs encode proteins belonging to cellular pathways not previously known to be regulated by nerve growth factor. Comparative expressed-sequence-tag analysis provides a basis for surveying global changes in gene-expression patterns in response to biological signals at an unprecedented scale, is a powerful tool for identifying potential interactions between different cellular pathways, and allows the gene-expression profiles of individual genes belonging to a particular pathway to be followed.

Structure of the gene for porcine peptide antibiotic PR-39, a cathelin gene family member: comparative mapping of the locus for the human peptide antibiotic FALL-39.

PR-39 is a porcine 39-aa peptide antibiotic composed of 49% proline and 24% arginine, with an activity against Gram-negative bacteria comparable to that of tetracycline. In Escherichia coli, it inhibits DNA and protein synthesis. PR-39 was originally isolated from pig small intestine, but subsequent cDNA cloning showed that the gene is expressed in the bone marrow. The open reading frame of the clone showed that PR-39 is made as 173-aa precursor whose proregion belongs to the cathelin family. The PR39 gene, which is rather compact and spans only 1784 bp has now been sequenced. The coding information is split into four exons. The first exon contains the signal sequence of 29 residues and the first 37 residues of the cathelin propart. Exons 2 and 3 contain only cathelin information, while exon 4 codes for the four C-terminal cathelin residues and the mature PR-39 peptide extended by three residues. The sequenced upstream region (1183 bp) contains four potential recognition sites for NF-IL6 and three for APRF, transcription factors known to regulate genes for both cytokines and acute phase response factors. Genomic hybridizations revealed a fairly high level of restriction fragment length polymorphism and indicated that there are at least two copies of the PR39 gene in the pig genome. PR39 was mapped to pig chromosome 13 by linkage and in situ hybridization mapping. The gene for the human peptide antibiotic FALL-39 (also a member of the cathelin family) was mapped to human chromosome 3, which is homologous to pig chromosome 13.

The International Human Rights Policies of New Democracies: Brazil and Chile in Comparative Perspective

Since the beginning of the 1990s, the majority of Latin American states have attempted to incorporate in some way or another human rights concern into their respective foreign policies, highlighting a history of human rights abuses and the return of democratic political rule as a trigger for galvanizing a commitment to assist in preventing such violations in other countries. Yet, while human rights have come to play a non-trivial role in the contemporary foreign policy of many Latin American states, there is great diversity in the ways and the extent to which they go about incorporating human rights concerns into their foreign policies. Explaining the diversity of human rights foreign policies of new Latin American democracies is at the heat of this project. The main research questions are the following: Why do new democracies incorporate human rights into their foreign policies? And what explains the different international human rights policies of new democracies? To answer these questions, this research compares the human rights foreign policies of Chile and Brazil for over two decades starting from their respective transitions to democracy. The study argues that states commitment to international human rights is the result of the intersection of domestic and international influences. At the international level, the search for international legitimacy and the desire for recognition and credibility affected the adoption of international human rights in both cases but with different degrees of impact. International values and pressures by themselves, while necessary, are an insufficient condition for human rights initiatives perceived to have not insubstantial political, economic or strategic costs. New democracies will be more or less likely to actively include human rights in their international policies depending on the following four domestic conditions: political leadership legitimizing the inclusion of human rights into a state's policies, civil society groups connected to international human rights advocacy networks with a capacity to influencing the foreign policy decisions of their government, and the Foreign Ministry's attitudes towards international human rights and the degree of influence it exercises over the outcome of the foreign policy process.

Investigating and Understanding Student Learning Outcomes in an Online and Face-to-Face Graduate Level Legal Administration Course: An Embedded Mixed Methods Design

Online education is a new teaching and learning medium with few current guidelines for faculty, administrators or students. Its rapid growth over the last decade has challenged academic institutions to keep up with the demand, while also providing a quality education. Our understanding of the factors that determine quality and effective online learning experiences that lead to student learning outcomes is still evolving. There is a lack of consensus on the effectiveness of online versus face-to-face education in the current research. The U.S. Department of Education conducted a meta-analysis in 2009 and concluded that student-learning outcomes in online courses were equal to and, often times, better than face-to-face traditional courses. Subsequent research has found contradictory findings, and further inquiry is necessary. The purpose of this embedded mixed methods design research study is to further our understanding of the factors that create quality and successful educational outcomes in an online course. To achieve this, the first phase of this study measured and compared learning outcomes in an online and in class graduate-level legal administration course. The second phase of the study entailed interviews with those students in both the online and face-to-face sections to understand their perspectives on the factors contributing to learning outcomes. Six themes emerged from the qualitative findings: convenience, higher order thinking, discussions, professor engagement, professor and student interaction, and face-to-face interaction. Findings from this study indicate the factors students perceive as contributing to learning outcomes in an online course are consistent among all students and are supported in the existing literature. Higher order thinking, however, emerged as a stronger theme than indicated in the current research, and the face-to-face nature of the traditional classroom may be more an issue of familiarity than a factor contributing to learning outcomes. As education continues to reach new heights and developments in technology advance, the factors found to contribute to student learning outcomes will be refined and enhanced. These developments will continue to transform the ways in which we deliver and receive knowledge in both traditional and online classrooms. While there is a growing body of research on online education, the field’s evolution has unsettled earlier findings and posed new areas to investigate.

A comparative study of open domain and opinion question answering systems for factual and opinionated queries

The development of the Web 2.0 led to the birth of new textual genres such as blogs, reviews or forum entries. The increasing number of such texts and the highly diverse topics they discuss make blogs a rich source for analysis. This paper presents a comparative study on open domain and opinion QA systems. A collection of opinion and mixed fact-opinion questions in English is defined and two Question Answering systems are employed to retrieve the answers to these queries. The first one is generic, while the second is specific for emotions. We comparatively evaluate and analyze the systems’ results, concluding that opinion Question Answering requires the use of specific resources and methods.

Towards automatic tweet generation: A comparative study from the text summarization perspective in the journalism genre

In recent years, Twitter has become one of the most important microblogging services of the Web 2.0. Among the possible uses it allows, it can be employed for communicating and broadcasting information in real time. The goal of this research is to analyze the task of automatic tweet generation from a text summarization perspective in the context of the journalism genre. To achieve this, different state-of-the-art summarizers are selected and employed for producing multi-lingual tweets in two languages (English and Spanish). A wide experimental framework is proposed, comprising the creation of a new corpus, the generation of the automatic tweets, and their assessment through a quantitative and a qualitative evaluation, where informativeness, indicativeness and interest are key criteria that should be ensured in the proposed context. From the results obtained, it was observed that although the original tweets were considered as model tweets with respect to their informativeness, they were not among the most interesting ones from a human viewpoint. Therefore, relying only on these tweets may not be the ideal way to communicate news through Twitter, especially if a more personalized and catchy way of reporting news wants to be performed. In contrast, we showed that recent text summarization techniques may be more appropriate, reflecting a balance between indicativeness and interest, even if their content was different from the tweets delivered by the news providers.

El modelo de apoyo a las personas con capacidades modificadas judicialmente según Naciones Unidas

Este artículo se basa en una investigación social sobre el sistema de protección jurídica de las personas con algún tipo de discapacidad o en situación de dependencia que se encuentran sometidas a las figuras de tutela o curatela, en aplicación de lo previsto y establecido en el Código Civil Español, en sus artículos 199 y 200, así como en la Ley de Enjuiciamiento Civil. La investigación se plantea como un estudio comparado entre diferentes países de la Unión Europea para ver su adecuación a lo establecido en el artículo 12 de la Convención de Naciones Unidas sobre derechos de las Personas con Discapacidad (en adelante, CDPD) en los procedimientos de incapacitación. Los resultados se analizan sobre la base de modelos técnico-sociales de intervención, los análisis jurídicos y la experiencia adquirida por las Fundación Tutelares de Castilla y León. Se proponen y diseñan algunas alternativas y servicios que pueden mejorar la calidad de vida de las personas adultas incapacitadas judicialmente y el tipo de apoyos que se les puede prestar, de acuerdo a lo establecido en la Convención de Naciones Unidas.

Challenges in Lifestyle Migration Research: Reflections and Findings about the Spanish Crisis

The lifestyle migration conceptual framework is based on the motivation for moving reported by the migrants themselves. We discuss the operability of this approach, which is built on the subjective assessments of individuals. It diminishes the actual importance of economic factors and has an underlying ideological element associated with the categorisation of people according to their nationality. A comparative analysis of residential variations by nationalities between 2005 and 2010 in Alicante (Spain) shows that, when faced with the economic crisis, the so-called lifestyle migrants are changing their mobility patterns in a way similar to the rest of the migrants. This calls into question the adequacy of juxtaposing lifestyle and labour migration. Both theory and research show that this duality, instead of clarifying applied research, makes it more difficult. We argue that the lifestyle migration framework is inadequate to study changes in mobility patterns, particularly when using a quantitative approach.