Inhibition of gene expression in human cells through small molecule-RNA interactions

Small molecules that bind their biological receptors with high affinity and selectivity can be isolated from randomized pools of combinatorial libraries. RNA-protein interactions are important in many cellular functions, including transcription, RNA splicing, and translation. One example of such interactions is the mechanism of trans-activation of HIV-1 gene expression that requires the interaction of Tat protein with the trans-activation responsive region (TAR) RNA, a 59-base stem-loop structure located at the 5′ end of all nascent HIV-1 transcripts. Here we demonstrate the isolation of small TAR RNA-binding molecules from an encoded combinatorial library. We have made an encoded combinatorial tripeptide library of 24,389 possible members from d-and l-alpha amino acids on TentaGel resin. Using on-bead screening we have identified a small family of mostly heterochiral tripeptides capable of structure-specific binding to the bulge loop of TAR RNA. In vitro binding studies reveal stereospecific discrimination when the best tripeptide ligand is compared with diastereomeric peptide sequences. In addition, the most strongly binding tripeptide was shown to suppress transcriptional activation by Tat protein in human cells with an IC50 of ≈50 nM. Our results indicate that tripeptide RNA ligands are cell permeable, nontoxic to cells, and capable of inhibiting expression of specific genes by interfering with RNA-protein interactions.

Hematopoietic potential of stem cells isolated from murine skeletal muscle

We have discovered that cells derived from the skeletal muscle of adult mice contain a remarkable capacity for hematopoietic differentiation. Cells prepared from muscle by enzymatic digestion and 5-day in vitro culture were harvested, and 18 × 103 cells were introduced into each of six lethally irradiated recipients together with 200 × 103 distinguishable whole bone marrow cells. After 6 or 12 weeks, all recipients showed high-level engraftment of muscle-derived cells representing all major adult blood lineages. The mean total contribution of muscle cell progeny to peripheral blood was 56 ± 20% (SD), indicating that the cultured muscle cells generated approximately 10- to 14-fold more hematopoietic activity than whole bone marrow. When bone marrow from one mouse was harvested and transplanted into secondary recipients, all recipients showed high-level multilineage engraftment (mean 40%), establishing the extremely primitive nature of these stem cells. We also show that muscle contains a population of cells with several characteristics of bone marrow-derived hematopoietic stem cells, including high efflux of the fluorescent dye Hoechst 33342 and expression of the stem cell antigens Sca-1 and c-Kit, although the cells lack the hematopoietic marker CD45. We propose that this population accounts for the hematopoietic activity generated by cultured skeletal muscle. These putative stem cells may be identical to muscle satellite cells, some of which lack myogenic regulators and could be expected to respond to hematopoietic signals.

Complex formation between stage-specific oocyte factors and a Xenopus mRNA localization element

It is a long-standing proposal that localization of maternal factors in eggs can provide the basis for pattern formation in the early embryo. The localized information can be stored as RNA, one example being Vg1 RNA, which is localized exclusively to the vegetal hemisphere of Xenopus oocytes and eggs. Localization of Vg1 mRNA is directed by a 340-nt sequence element contained within its 3′ untranslated region. To understand the mechanism of localization, I have tested whether factors from the oocyte interact specifically with the RNA localization sequence. Results presented here show that a set of oocyte proteins form complexes with the localization element both in vitro and in vivo. These proteins are specifically enriched in the stages of oogenesis during which localization occurs and recognize sub-elements of the RNA localization element that are essential for localization in vivo. These data suggest that formation of a localization-specific RNA–protein complex may be the first step in directing Vg1 mRNA to its subcellular destination.

A vaccine for HIV type 1: The antibody perspective

Antibodies that bind well to the envelope spikes of immunodeficiency viruses such as HIV type 1 (HIV-1) and simian immunodeficiency virus (SIV) can offer protection or benefit if present at appropriate concentrations before viral exposure. The challenge in antibody-based HIV-1 vaccine design is to elicit such antibodies to the viruses involved in transmission in humans (primary viruses). At least two major obstacles exist. The first is that very little of the envelope spike surface of primary viruses appears accessible for antibody binding (low antigenicity), probably because of oligomerization of the constituent proteins and a high degree of glycosylation of one of the proteins. The second is that the mature oligomer constituting the spikes appears to stimulate only weak antibody responses (low immunogenicity). Viral variation is another possible obstacle that appears to present fewer problems than anticipated. Vaccine design should focus on presentation of an intact mature oligomer, increasing the immunogenicity of the oligomer and learning from the antibodies available that potently neutralize primary viruses.

Interaction of the histone (H3-H4)2 tetramer of the nucleosome with positively supercoiled DNA minicircles: Potential flipping of the protein from a left- to a right-handed superhelical form.

We have studied the ability of the histone (H3-H4)2 tetramer, the central part of the nucleosome of eukaryotic chromatin, to form particles on DNA minicircles of negative and positive superhelicities, and the effect of relaxing these particles with topoisomerase I. The results show that even modest positive torsional stress from the DNA, and in particular that generated by DNA thermal fluctuations, can trigger a major, reversible change in the conformation of the particle. Neither a large excess of naked DNA, nor a crosslink between the two H3s prevented the transition from one form to the other. This suggested that during the transition, the histones neither dissociated from the DNA nor were even significantly reshuffled. Moreover, the particles reconstituted on negatively and positively supercoiled minicircles look similar under electron microscopy. These data agree best with a transition involving a switch of the wrapped DNA from a left- to a right-handed superhelix. It is further proposed, based on the left-handed overall superhelical conformation of the tetramer within the octamer [Arents, G., Burlingame, R. W., Wang, B. C., Love, W. E. & Moudrianakis, E. N. (1991) Proc. Natl.Acad. Sci. USA 88, 10148-10152] that this change in DNA topology is mediated by a similar change in the topology of the tetramer itself, which may occur through a rotation (or a localized deformation) of the two H3-H4 dimers about their H3-H3 interface. Potential implications of this model for nucleosome dynamics in vivo are discussed.

High affinity type I interleukin 1 receptor antagonists discovered by screening recombinant peptide libraries.

Two families of peptides that specifically bind the extracellular domain of the human type I interleukin I (IL-1) receptor were identified from recombinant peptide display libraries. Peptides from one of these families blocked binding of IL-lalpha to the type I IL-1 receptor with IC50 values of 45-140 microM. Affinity-selective screening of variants of these peptides produced ligands of much higher affinity (IC50 approximately 2 nM). These peptides block IL-1-driven responses in human and monkey cells; they do not bind the human type II IL-1 receptor or the murine type I IL-1 receptor. This is the first example (that we know of) of a high affinity peptide that binds to a cytokine receptor and acts as a cytokine antagonist.

7-Chloro-3-methyl-3,4-dihydro-2H-1,2,4-benzothiadiazine S,S-dioxide (IDRA 21), a congener of aniracetam, potently abates pharmacologically induced cognitive impairments in patas monkeys.

We report here on the ability of IDRA 21 and aniracetam, two negative allosteric modulators of glutamate-induced DL-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor desensitization, to attenuate alprazolam-induced learning deficit in patas monkeys working in a complex behavioral task. In one component of a multiple schedule (repeated acquisition or "learning"), patas monkeys acquired a different four-response chain each session by responding sequentially on three keys in the presence of four discriminative stimuli (geometric forms or numerals). In the other component (performance) the four-response chain was the same each session. The response chain in each component was maintained by food presentation under a fixed-ratio schedule. When alprazolam (0.1 or 0.32 mg/kg p.o.) was administered alone, this full allosteric modulator of gamma-aminobutyric acid type A (GABAA) receptors produced large decreases in the response rate and accuracy in the learning component of the task. IDRA 21 (3 or 5.6 mg/kg p.o.) and aniracetam (30 mg/kg p.o.) administered 60 min before alprazolam, having no effect when given alone, antagonized the large disruptive effects of alprazolam on learning. From dose-response studies, it can be estimated that IDRA 21 is approximately 10-fold more potent than aniracetam in antagonizing alprazolam-induced learning deficit. We conclude that IDRA 21, a chemically unrelated pharmacological congener of aniracetam, improves learning deficit induced in patas monkeys by the increase of GABAergic tone elicited by alprazolam. Very likely IDRA 21 exerts its behavioral effects by antagonizing AMPA receptor desensitization.

Anti-melanoma antibodies from melanoma patients immunized with genetically modified autologous tumor cells: selection of specific antibodies from single-chain Fv fusion phage libraries.

Fusion phage libraries expressing single-chain Fv antibodies were constructed from the peripheral blood lymphocytes of two melanoma patients who had been immunized with autologous melanoma cells transduced the gamma-interferon gene to enhance immunogenicity, in a trial conducted at another institution. Anti-melanoma antibodies were selected from each library by panning the phage against live cultures of the autologous tumor. After two or three rounds of panning, clones of the phage were tested by ELISA for binding to the autologous tumor cells; > 90% of the clones tested showed a strong ELISA reaction, demonstrating the effectiveness of the panning procedure for selecting antimelanoma antibodies. The panned phage population was extensively absorbed against normal melanocytes to enrich for antibodies that react with melanoma cells but not with melanocytes. The unabsorbed phage were cloned, and the specificities of the expressed antibodies were individually tested by ELISA with a panel of cultured human cells. The first tests were done with normal endothelial and fibroblast cells to identify antibodies that do not react, or react weakly, with two normal cell types, indicating some degree of specificity for melanoma cells. The proportion of phage clones expressing such antibodies was approximately 1%. Those phage were further tested by ELISA with melanocytes, several melanoma lines, and eight other tumor lines, including a glioma line derived from glial cells that share a common lineage with melanocytes. The ELISA tests identified three classes of anti-melanoma antibodies, as follows: (i) a melanoma-specific class that reacts almost exclusively with the melanoma lines; (ii) a tumor-specific class that reacts with melanoma and other tumor lines but does not react with the normal melanocyte, endothelial and fibroblast cells; and (iii) a lineage-specific class that reacts with the melanoma lines, melanocytes, and the glioma line but does not react with the other lines. These are rare classes from the immunized patients' repertoires of anti-melanoma antibodies, most of which are relatively nonspecific anti-self antibodies. The melanoma-specific class was isolated from one patient, and the lineage-specific class was isolated from the other patient, indicating that different patients can have markedly different responses to the same immunization protocol. The procedures described here can be used to screen the antibody repertoire of any person with cancer, providing access to an enormous untapped pool of human monoclonal anti-tumor antibodies with clinical and research potential.

A simple test of the vicarious trial-and-error hypothesis of hippocampal function.

Vicarious trial-and-error (VTE) is a term that Muenzinger and Tolman used to describe the rat's conflict-like behavior before responding to choice. Recently, VTE was proposed as a mechanism alternative to the concept of "cognitive map" in accounts of hippocampal function. That is, many phenomena of impaired learning and memory related to hippocampal interventions may be explained by behavioral first principles: reduced conflicting, incipient, pre-choice tendencies to approach and avoid. The nonspatial black-white discrimination learning and VTE behavior of the rat were investigated. Hippocampal-lesioned and sham-lesioned animals were trained for 25 days (20 trials per day) starting at 60 days of age. Each movement of the head from one discriminative stimulus to the other was counted as a VTE instance. Lesioned rats had fewer VTEs than sham controls, and the former learned much more slowly or never learned. After learning, VTE frequency declined. Male and female rats showed no significant differences in VTE behavior or discrimination learning.

Early termination of R&D projects

Early project termination is one of the most difficult decisions to be made by Research and Development managers. While there is the risk of terminating good projects, there is also the opposite risk of not terminating bad projects and overspend resources in unproductive research. Criteria used for identifying these projects are common subject of research in Business Administration. In addition, companies might take important lessons from its interrupted projects that could improve their overall portfolio technical and commercial success. Finally, the set and weight of criteria, as well as the procedures companies use for achieve learning from cancelled projects may vary depending on the project type. This research intends to contribute to the understanding of policies applied to projects that were once considered attractive, but by some reason is not appreciated anymore. The research addressed the question: How companies deal with projects that become unattractive? More specifically, this research tried to answer the following questions: (1) Are projects killed or (otherwise) they die naturally by lack of resources? (2) What criteria are used to terminate projects during development? (3) How companies learn from the terminated projects to improve the overall portfolio performance? (4) Are the criteria and learning procedures different for different types of projects? In order to answer these questions, we performed a multiple case study with four companies that are reference in business administration and innovation: (1) Oxiteno, considered the base case, (2) Natura, the literal replication, (3) Mahle and (4) AES, the theoretical replications. The case studies were performed using a semi-structured protocol for interviews, which were recorded and analyzed for comparison. We found that the criteria companies use for selecting projects for termination are very similar to those anticipated by the literature, except for a criteria related to compliance. We have evidences to confirm that the set of criteria is not altered when dealing with different project types, however the weight they are applied indeed varies. We also found that learning with cancelled projects is yet very incipient, with very few structured formal procedures being described for capturing learning with early-terminated projects. However, we could observe that these procedures are more common when dealing with projects labeled as innovative, risky, big and costly, while those smaller and cheaper derivative projects aren\'t subject of a complete investigation on the learning they brought to the company. For these, the most common learning route is the informal, where the project team learns and passes the knowledge though interpersonal information exchange. We explain that as a matter of cost versus benefit of spending time to deeply investigate projects with little potential to bring new knowledge to the project team and the organization

Evaluating knowledge-based approaches to the multilingual extension of a temporal expression normalizer

The extension to new languages is a well known bottleneck for rule-based systems. Considerable human effort, which typically consists in re-writing from scratch huge amounts of rules, is in fact required to transfer the knowledge available to the system from one language to a new one. Provided sufficient annotated data, machine learning algorithms allow to minimize the costs of such knowledge transfer but, up to date, proved to be ineffective for some specific tasks. Among these, the recognition and normalization of temporal expressions still remains out of their reach. Focusing on this task, and still adhering to the rule-based framework, this paper presents a bunch of experiments on the automatic porting to Italian of a system originally developed for Spanish. Different automatic rule translation strategies are evaluated and discussed, providing a comprehensive overview of the challenge.

Teaching-learning process of historical heritage: a Journey as a beginning, path and end

The implantation of new university degrees within the European Higher Education Area implies the need of innovative methodologies in teaching and learning to improve the skills and competencies of students and to answer the growing needs that society continuously demands to heritage management experts. The present work shows an application of the teaching methodology proposed during the international workshop entitled “I International Planning Preservation Workshop. Learning from Al Andalus”, which included the participation of the University of Alicante and Granada, Università Politecnico di Milano and Hunter College City University of New York; where we tried to dissolve traditional boundaries derived of interuniversity cooperation programs. The main objective of the workshop was to discuss and debate the role of urban Historical Centers within the Global Heritage by the integrated work through multidisciplinary teams and the creation of a permanent international working group between these universities to both teach and research. The methodology of this workshop was very participatory and considered the idea of a new learning process generated by "a journey experience." A trip from global to local (from the big city to the small village) but also a trip from the local (historical) part of a big city to the global dimension of contemporary historical villages identified by the students through a system of exhibition panels in affinity groups, specific projects proposed by lecturers and teachers or the generation of publications in various areas (texts, photographs, videos, etc.). So, the participation of the students in this multidisciplinary meeting has enhanced their capacity for self-criticism in several disciplines and has promoted their ability to perform learning and research strategies in an autonomous way. As a result, it has been established a permanent international work structure for the development of projects of the Historical City. This relationship has generated the publication of several books whose contents have reflected the conclusions developed in the workshop and several teaching proposals shared between those institutions. All these aspects have generated a new way of understanding the teaching process through a journey, in order to study the representative role of university in the historical heritage and to make students (from planning, heritage management, architecture, geography, sociology, history or engineering areas) be compromised on searching strategies for sustainable development in the Contemporary City.

Inhibitory Control is a Rate-Limiting Factor to Preschoolers' Use of Irregular Inflection

We investigated whether children’s inhibitory control is associated with their ability to produce irregular verb forms as well as learn from corrective feedback following their use of an over-regularized form. Forty-eight 3.5 to 4.5 year old children were tested on the irregular past tense and provided with adult corrective input via models of correct use or recasts of errors following ungrammatical responses. Inhibitory control was assessed with a three-item battery of tasks that required suppressing a prepotent response in favor of a non-canonical one. Results showed that inhibitory control was predictive of children’s initial production of irregular forms and not associated with their post-feedback production of irregulars. These findings show that children’s executive functioning skills may be a rate-limiting factor on their ability to produce correct forms, but might not interact with their ability to learn from input in this domain. Findings are discussed in terms of current theories of past-tense acquisition and learning from input more broadly.

Constitution for a new Hungary - the domestic and regional implications. OSW Commentary No. 60, 2011-07-29

The new constitution will come into force in Hungary on 1 January 20121. Its adoption is part of the state reform which the Fidesz party led by Prime Minister Viktor Orbán has been implementing since it won the election in April 2010. Fidesz, along with the Christian Democrats which support it, has a qualified majority of two-thirds of the votes in parliament and may introduce solutions to facilitate its rule without support from other groupings and it is taking advantage of this opportunity. One example of this has been the amendment of the constitution ten times followed by a speedy adoption of a new constitution. The next step will be passing dozens of constitutional laws which regulate essential areas of the functioning of the state over the next few months. Both the way and the scope in which the changes have been made have raised controversies both at home and abroad. The regulations reinforce the position of the ruling camp on the Hungarian political scene, assisting it in passing the test of the next elections. Slovakia, which has criticised the practice of granting Hungarian citizenship to ethnic Hungarians living in other countries, is opposing the promise of also granting them electoral rights. The constitutional reinforcement of the state’s ‘responsibility’ for the diaspora linked with the collective concept of national minority rights fostered by Hungary has already led to tensions in the region.

Economics of Policy Errors and Learning in the European Union. Bruges European Economic Policy (BEEP) Briefing 31/2013

Policy errors occur regularly in EU Member States. Learning from these errors can be beneficial. This paper explains how the European Union can facilitate this learning. At present, much attention is given to “best practices”. But learning from mistakes is also valuable. The paper develops the concept of “avoidable error” and examines evidence from infringement proceedings and special reports of the European Court of Auditors which indicate that Member States do indeed commit avoidable errors. The paper considers how Member States may take measures not to repeat avoidable or predictable errors and makes appropriate proposals.