The influence of the 5 '-terminal nucleotide on AgoshRNA activity and biogenesis: importance of the polymerase III transcription initiation site

Recent evidence indicates that shRNAs with a relatively short basepaired stem do not require Dicer processing, but instead are processed by the Argonaute 2 protein (Ago2). We named these molecules AgoshRNAs as both their processing and silencing function are mediated by Ago2. This alternative processing yields only a single RNA guide strand, which can avoid off-target effects induced by the passenger strand of regular shRNAs. It is important to understand this alternative processing route in mechanistic detail such that one can design improved RNA reagents. We verified that AgoshRNAs trigger site-specific cleavage of a complementary mRNA. Second, we document the importance of the identity of the 5΄-terminal nucleotide and its basepairing status for AgoshRNA activity. AgoshRNA activity is significantly reduced or even abrogated with C or U at the 5΄-terminal and is enhanced by introduction of a bottom mismatch and 5΄-terminal nucleotide A or G. The 5΄-terminal RNA nucleotide also represents the +1 position of the transcriptional promoter in the DNA, thus further complicating the analysis. Indeed, we report that +1 modification affects the transcriptional efficiency and accuracy of start site selection, with A or G as optimal nucleotide. These combined results allow us to propose general rules for the design and expression of potent AgoshRNA molecule

ESTÁGIO SUPERVISIONADO EM CIÊNCIAS CONTÁBEIS: EMPRESA DE PRODUÇÃO DE MOLDES DE GARRAFAS PET

O Presente trabalho foi apresentado para a conclusão do componente curricular do Estágio Supervisionado no curso de Ciências Contábeis. Para tanto, constitui-se uma empresa de responsabilidade limitada, com atividade industrial e forma de tributação do Lucro Real, com razão social R&H Moldes Ltda., voltada ao ramo de fabricação de moldes para Indústria de plásticos, peças e acessórios, especializada na produção de moldes para garrafa PET. O Objetivo do trabalho foi aliar todo o conhecimento adquirido em sala de aula com a parte prática da contabilidade. Na primeira etapa da fase do estágio, por meio de pesquisa e visitas a empresas do ramo, foi possível a elaboração da ficha técnica dos produtos e processo produtivo, da estrutura de produção e de pessoal. Também buscou-se compreender a legislação específica para o produto e para a forma de tributação da própria empresa. Ainda, foi necessário identificar os custos com o pessoal, com matéria-prima, gastos gerais e despesas, cálculo da margem de contribuição, do preço de venda e do ponto de equilíbrio. Na segunda etapa do trabalho, foi efetuada toda a escrituração contábil do trabalho planejado, afim de apresentar os resultados através de demonstrativos contábeis no período de um trimestre. Desta forma, foi possível desenvolver habilidades e competências inerentes ao profissional contábil e determinar os resultados de uma empresa que industrializa moldes pelos métodos de sopro com base na realidade pesquisada

Two rapid assays for screening of patulin biodegradation

Artículo sobre distintos ensayos para comprobar la biodegradación de la patulinaThe mycotoxin patulin is produced by the blue mould pathogen Penicillium expansum in rotting apples during postharvest storage. Patulin is toxic to a wide range of organisms, including humans, animals, fungi and bacteria. Wash water from apple packing and processing houses often harbours patulin and fungal spores, which can contaminate the environment. Ubiquitous epiphytic yeasts, such as Rhodosporidium kratochvilovae strain LS11 which is a biocontrol agent of P. expansum in apples, have the capacity to resist the toxicity of patulin and to biodegrade it. Two non-toxic products are formed. One is desoxypatulinic acid. The aim of the work was to develop rapid, high-throughput bioassays for monitoring patulin degradation in multiple samples. Escherichia coli was highly sensitive to patulin, but insensitive to desoxypatulinic acid. This was utilized to develop a detection test for patulin, replacing time-consuming thin layer chromatography or high-performance liquid chromatography. Two assays for patulin degradation were developed, one in liquid medium and the other in semi-solid medium. Both assays allow the contemporary screening of a large number of samples. The liquid medium assay utilizes 96-well microtiter plates and was optimized for using a minimum of patulin. The semisolid medium assay has the added advantage of slowing down the biodegradation, which allows the study and isolation of transient degradation products. The two assays are complementary and have several areas of utilization, from screening a bank of microorganisms for biodegradation ability to the study of biodegradation pathways

Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA

The TAR hairpin of the human immunodeficiency virus type 1 (HIV-1) RNA genome is essential for virus replication. TAR forms the binding site for the transcriptional trans-activator protein Tat and multiple additional TAR functions have been proposed. We previously constructed an HIV-1 variant in which the TAR-Tat transcription control mechanism is replaced by the components of the Tet-ON regulatory system. In this context, the surprising finding was that TAR can be truncated or even deleted, but partial TAR deletions that destabilize the stem structure cause a severe replication defect. In this study, we demonstrate that the HIV-1 RNA genome requires a stable hairpin at its 5′-end because unpaired TAR sequences affect the proper folding of the untranslated leader RNA. Consequently, multiple leader-encoded functions are affected by partial TAR deletions. Upon evolution of such mutant viruses, the replication capacity was repaired through the acquisition of additional TAR mutations that restore the local RNA folding, thus preventing the detrimental effect on the leader conformation

Conversion of the Mycotoxin Patulin to the Less Toxic Desoxypatulinic Acid by the Biocontrol Yeast Rhodosporidium kratochvilovae Strain LS11

Se describe en este artículo el descubrimiento de la degradación de la micotoxina patulina por una levaduraThe infection of stored apples by the fungus Penicillium expansum causes the contamination of fruits and fruit-derived products with the mycotoxin patulin, which is a major issue in food safety. Fungal attack can be prevented by beneficial microorganisms, so-called biocontrol agents. Previous time-course thin layer chromatography analyses showed that the aerobic incubation of patulin with the biocontrol yeast Rhodosporidium kratochvilovae strain LS11 leads to the disappearance of the mycotoxin spot and the parallel emergence of two new spots, one of which disappears over time. In this work, we analyzed the biodegradation of patulin effected by LS11 through HPLC. The more stable of the two compounds was purified and characterized by nuclear magnetic resonance as desoxypatulinic acid, whose formation was also quantitated in patulin degradation experiments. After R. kratochvilovae LS11 had been incubated in the presence of 13C-labeled patulin, label was traced to desoxypatulinic acid, thus proving that this compound derives from the metabolization of patulin by the yeast. Desoxypatulinic acid was much less toxic than patulin to human lymphocytes and, in contrast to patulin, did not react in vitro with the thiol-bearing tripeptide glutathione. The lower toxicity of desoxypatulinic acid is proposed to be a consequence of the hydrolysis of the lactone ring and the loss of functional groups that react with thiol groups. The formation of desoxypatulinic acid from patulin represents a novel biodegradation pathway that is also a detoxification process

Isolation of human β-defensin-4 in lung tissue and its increase in lower respiratory tract infection

BACKGROUND: Human β-defensin-4 (hBD-4), a new member of the β-defensin family, was discovered by an analysis of the genomic sequence. The objective of this study was to clarify hBD-4 expression in human lung tissue, along with the inducible expression in response to infectious stimuli, localization, and antimicrobial activities of hBD-4 peptides. We also investigated the participation of hBD-4 in chronic lower respiratory tract infections (LRTI) by measuring the concentrations of hBD-4 peptides in human bronchial epithelial lining fluid (ELF). METHODS: The antimicrobial activity of synthetic hBD-4 peptides against E. coli and P. aeruginosa was measured by radial diffusion and colony count assays. We identified hBD-4 in homogenated human lung tissue by reverse-phase high-performance liquid chromatography coupled with a radioimmunoassay (RIA). Localization of hBD-4 was studied through immunohistochemical analysis (IHC). We investigated the effects of lipopolysaccharide (LPS) on hBD-4 expression and its release from small airway epithelial cells (SAEC). We collected ELF from patients with chronic LRTI using bronchoscopic microsampling to measure hBD-4 concentrations by RIA. RESULTS: hBD-4 exhibited salt-sensitive antimicrobial activity against P. aeruginosa. We detected the presence of hBD-4 peptides in human lung tissue. IHC demonstrated the localization of hBD-4-producing cells in bronchial and bronchiolar epithelium. The levels of hBD-4 peptides released from LPS-treated SAECs were higher than those of untreated control cells. ELF hBD-4 was detectable in 4 of 6 patients with chronic LRTI, while the amounts in controls were all below the detectable level. CONCLUSION: This study suggested that hBD-4 plays a significant role in the innate immunity of the lower respiratory tract

Isostructural second-order phase transition of b-Bi2O3 at high pressures: an experimental and theoretical study

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/jp507826jWe report a joint experimental and theoretical study of the structural and vibrational properties of synthetic sphaerobismoite (beta-Bi2O3) at high pressures in which room-temperature angle-dispersive X-ray diffraction (XRD) and Raman scattering measurements have been complemented with ab initio total energy and lattice dynamics calculations. Striking changes in Raman spectra were observed around 2 GPa, whereas X-ray diffraction measurements evidence no change in the tetragonal symmetry of the compound up to 20 GPa; however, a significant change exists in the compressibility when increasing pressure above 2 GPa. These features have been understood by means of theoretical calculations, which show that beta-Bi2O3 undergoes a pressure-induced isostructural phase transition near 2 GPa. In the new isostructural beta' phase, the Bi3+ and O2- environments become more regular than those in the original beta phase because of the strong decrease in the activity of the lone electron pair of Bi above 2 GPa. Raman measurements and theoretical calculations provide evidence of the second-order nature of the pressure-induced isostructural transition. Above 20 GPa, XRD measurements suggest a partial amorphization of the sample despite Raman measurements still show weak peaks, probably related to a new unknown phase which remains up to 27 GPa. On pressure release, XRD patterns and Raman spectra below 2 GPa correspond to elemental Bi-I, thus evidencing a pressure-induced decomposition of the sample during downstroke.Financial support from the Spanish Consolider Ingenio 2010 Program (MALTA Project CSD2007-00045) is acknowledged. This work was also supported by Brazilian Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) under Project 201050/2012-9, Spanish MICINN under Projects MAT2010-21270-004-01/03/04 and MAT2013-46649-C4-2/3/4-P, Spanish MINECO under Project CTQ2012-36253-C03-02, and from Vicerrectorado de Investigacion de la Universitat Politecnica de Valencia under Projects UPV2011-0914 PAID-05-11 and UPV2011-0966 PAID-06-11. Supercomputer time has been provided by the Red Espanola de Supercomputacion (RES) and the MALTA cluster. JAS. acknowledges Juan de la Cierva fellowship program for financial support.Pereira, ALJ.; Sans Tresserras, JÁ.; Vilaplana Cerda, RI.; Gomis, O.; Manjón Herrera, FJ.; Rodriguez-Hernandez, P.; Muñoz, A.... (2014). Isostructural second-order phase transition of b-Bi2O3 at high pressures: an experimental and theoretical study. Journal of Physical Chemistry C. 118(40):23189-23201. https://doi.org/10.1021/jp507826jS23189232011184

Determining the Orientation of Protegrin-1 in DLPC Bilayers Using an Implicit Solvent-Membrane Model

Continuum models that describe the effects of solvent and biological membrane molecules on the structure and behavior of antimicrobial peptides, holds a promise to improve our understanding of the mechanisms of antimicrobial action of these peptides. In such methods, a lipid bilayer model membrane is implicitly represented by multiple layers of relatively low dielectric constant embedded in a high dielectric aqueous solvent, while an antimicrobial peptide is accounted for by a dielectric cavity with fixed partial charge at the center of each one of its atoms. In the present work, we investigate the ability of continuum approaches to predict the most probable orientation of the β-hairpin antimicrobial peptide Protegrin-1 (PG-1) in DLPC lipid bilayers by calculating the difference in the transfer free energy from an aqueous environment to a membrane-water environment for multiple orientations. The transfer free energy is computed as a sum of two terms; polar/electrostatic and non-polar. They both include energetic and entropic contributions to the free energy. We numerically solve the Poisson-Boltzmann equation to calculate the electrostatic contribution to the transfer free energy, while the non-polar contribution to the free energy is approximated using a linear solvent accessible surface area relationships. The most probable orientation of PG-1 is that with the lowest relative transfer free energy. Our simulation results indicate that PG-1 assumes an oblique orientation in DLPC lipid bilayers. The predicted most favorable orientation was with a tilt angle of 19°, which is in qualitative agreement with the experimentally observed orientations derived from solid-state NMR data