Differential integrity of TALE nuclease genes following adenoviral and lentiviral vector gene transfer into human cells

The array of genome editing strategies based on targeted double-stranded DNA break formation have recently been enriched through the introduction of transcription activator-like type III effector (TALE) nucleases (TALENs). To advance the testing of TALE-based approaches, it will be crucial to deliver these custom-designed proteins not only into transformed cell types but also into more relevant, chromosomally stable, primary cells. Viral vectors are among the most effective gene transfer vehicles. Here, we investigated the capacity of human immunodeficiency virus type 1- and adenovirus-based vectors to package and deliver functional TALEN genes into various human cell types. To this end, we attempted to assemble particles of these two vector classes, each encoding a monomer of a TALEN pair targeted to a bipartite sequence within the AAVS1 'safe harbor' locus. Vector DNA analyses revealed that adenoviral vectors transferred intact TALEN genes, whereas lentiviral vectors failed to do so, as shown by their heterogeneously sized proviruses in target cells. Importantly, adenoviral vector-mediated TALEN gene delivery resulted in site-specific double-stranded DNA break formation at the intended AAVS1 target site at similarly high levels in both transformed and non-transformed cells. In conclusion, we demonstrate that adenoviral, but not lentiviral, vectors constitute a valuable TALEN gene delivery platfor

Rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART): study protocol for a randomized controlled trial

BACKGROUND: Acute respiratory distress syndrome (ARDS) is associated with high in-hospital mortality. Alveolar recruitment followed by ventilation at optimal titrated PEEP may reduce ventilator-induced lung injury and improve oxygenation in patients with ARDS, but the effects on mortality and other clinical outcomes remain unknown. This article reports the rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART). METHODS/DESIGN: ART is a pragmatic, multicenter, randomized (concealed), controlled trial, which aims to determine if maximum stepwise alveolar recruitment associated with PEEP titration is able to increase 28-day survival in patients with ARDS compared to conventional treatment (ARDSNet strategy). We will enroll adult patients with ARDS of less than 72 h duration. The intervention group will receive an alveolar recruitment maneuver, with stepwise increases of PEEP achieving 45 cmH2O and peak pressure of 60 cmH2O, followed by ventilation with optimal PEEP titrated according to the static compliance of the respiratory system. In the control group, mechanical ventilation will follow a conventional protocol (ARDSNet). In both groups, we will use controlled volume mode with low tidal volumes (4 to 6 mL/kg of predicted body weight) and targeting plateau pressure 6430 cmH2O. The primary outcome is 28-day survival, and the secondary outcomes are: length of ICU stay; length of hospital stay; pneumothorax requiring chest tube during first 7 days; barotrauma during first 7 days; mechanical ventilation-free days from days 1 to 28; ICU, in-hospital, and 6-month survival. ART is an event-guided trial planned to last until 520 events (deaths within 28 days) are observed. These events allow detection of a hazard ratio of 0.75, with 90% power and two-tailed type I error of 5%. All analysis will follow the intention-to-treat principle. DISCUSSION: If the ART strategy with maximum recruitment and PEEP titration improves 28-day survival, this will represent a notable advance to the care of ARDS patients. Conversely, if the ART strategy is similar or inferior to the current evidence-based strategy (ARDSNet), this should also change current practice as many institutions routinely employ recruitment maneuvers and set PEEP levels according to some titration metho

Trigger and Aperture of the Surface Detector Array of the Pierre Auger Observatory

The surface detector array of the Pierre Auger Observatory consists of 1600 water-Cherenkov detectors, for the study of extensive air showers (EAS) generated by ultra-high-energy cosmic rays. We describe the trigger hierarchy, from the identification of candidate showers at the level of a single detector, amongst a large background (mainly random single cosmic ray muons), up to the selection of real events and the rejection of random coincidences. Such trigger makes the surface detector array fully efficient for the detection of EAS with energy above $3\times 10^{18}$ eV, for all zenith angles between 0$^\circ$ and 60$^\circ$, independently of the position of the impact point and of the mass of the primary particle. In these range of energies and angles, the exposure of the surface array can be determined purely on the basis of the geometrical acceptance.Comment: 29 pages, 12 figure

Ultrahigh energy neutrinos at the Pierre Auger observatory

The observation of ultrahigh energy neutrinos (UHEνs) has become a priority in experimental astroparticle physics. UHEνs can be detected with a variety of techniques. In particular, neutrinos can interact in the atmosphere (downward-going ν) or in the Earth crust (Earth-skimming ν), producing air showers that can be observed with arrays of detectors at the ground. With the surface detector array of the Pierre Auger Observatory we can detect these types of cascades. The distinguishing signature for neutrino events is the presence of very inclined showers produced close to the ground (i.e., after having traversed a large amount of atmosphere). In this work we review the procedure and criteria established to search for UHEνs in the data collected with the ground array of the Pierre Auger Observatory. This includes Earth-skimming as well as downward-going neutrinos. No neutrino candidates have been found, which allows us to place competitive limits to the diffuse flux of UHEνs in the EeV range and above.P. Abreu ... K. B. Barber ... J. A. Bellido ... R. W. Clay ... M. J. Cooper ... B. R. Dawson ... T. A. Harrison ... A. E. Herve ... V. C. Holmes ... J. Sorokin ... P. Wahrlich ... B. J. Whelan ... et al

Efeitos da temperatura e do alimento no desenvolvimento de Dysdercus maurus Distant (Hemiptera, Pyrrhocoridae)

Dysdercus maurus Distant, 1901 (Hemiptera, Pyrrhocoridae) é uma importante praga de Gossypium spp. (algodoeiro), Citrus Sinensis Osbeck (Rutaceae) (laranjeira) e Citrus reticulata (Rutaceae) (tangerineira), além de sementes de Chorisia speciosa St. Hil. (paineira). Este trabalho objetivou avaliar os efeitos da temperatura e do alimento no desenvolvimento de D. maurus. Foram realizados oito tratamentos, seis em que os percevejos foram alimentados com sementes de paineira e mantidos a 15, 18, 20, 25 e 30 ± 1ºC, UR 80 ± 3% e fotofase de 12 h ou em condições ambientais de laboratório (23,5 ± 2,6ºC, UR 73,3 ± 9,9 %), e dois em que foram alimentados com sementes de algodão variedade IAC-22 e mantidos a 25 e 30ºC. Em todos os tratamentos foram observados cinco estágios imaturos. O aumento da temperatura proporcionou diminuição do tempo de desenvolvimento. A temperatura de 15ºC foi letal para ovos e ninfas de D. maurus. A menor mortalidade de ninfas ocorreu quando os percevejos foram alimentados com sementes de algodão a 25ºC (24,07%). A menor temperatura base (Tb) foi obtida para o 1º ínstar (11,54ºC) e a maior para o 2º ínstar (15,33ºC). As fêmeas de D. maurus necessitam de maior quantidade de graus-dias (329,93 graus-dias) que os machos (300,49 graus-dias) para atingir o estádio adulto

A comparative analysis of biotic indices that use macroinvertebrates to assess water quality in a coastal river of Paran\ue1 state, southern Brazil

Biotic indices to monitor water quality are helpful tools for evaluating the health of rivers and lakes. In Brazil water samples are mainly analyzed using physical and chemical attributes, because most biotic indices were developed in other countries and their effective application to Brazilian ecosystems requires significant research. This study compared four biotic indices commonly used to evaluate water quality via benthic macroinvertebrates in order to determine which index best reflects ecosystem health in a coastal river in Brazil's Paraná state. We also analyzed functional feeding groups. The indices studied were: 1) EPT (percent of Ephemeroptera, Plecoptera and Trichoptera); 2) BMWP' (Biological Monitoring Work Party System); 3) BMWP'-ASPT (Average Score per Taxon); and 4) HFBI (Hilsenhoff Family Biotic Index). All indices were calculated from five samples collected from April 2005 to April 2006 at two stations on the coastal do Pinto River. The river's headwaters are inside a protected area but impacts increase downriver (e.g., towns, cattle grazing, tourism). The HFBI index did the poorest job of reflecting water quality. No one index performed better than the others, and all indices yielded water quality scores that did not accurately reflect macroinvertebrate community structure because all of them had differences between ordination scores and the structure of assemblage. The functional feeding groups protocol classified the lower stretch of the river as disturbed due to human impacts, suggesting that this method is a good one to evaluate health in environments

Levantamento de Orchidaceae em quatro fragmentos de Campos de Altitude em Campos do Jord\ue3o, SP, Brasil

Orchidaceae é uma das maiores famílias das Angiospermas, sendo também uma das mais ricas e com mais alto grau de endemismo na Mata Atlântica, bioma que inclui a Floresta Ombrófila Mista e os Campos de Altitude, típicos da região de Campos do Jordão. Este trabalho teve como objetivo fazer um levantamento das espécies de Orchidaceae ocorrentes em quatro campos de altitude em uma Área de Proteção Ambiental pertencente ao Instituto Presbiteriano Mackenzie em Campos do Jordão, Estado de São Paulo, no bairro de Umuarama. Foram realizadas expedições mensais de 16 de fevereiro de 2013 até 15 de fevereiro de 2014. Foram coletadas, ao todo, 12 espécies pertencentes a nove gêneros, sendo que desses, os mais representativos foram Coppensia (três espécies) e Habenaria (duas espécies), os demais representados por apenas uma espécie. Foram observados muitos fatores que colocam em risco a integridade desses ambientes já tão pouco valorizados e estudados