Transcription activator like effector (TALE)-directed piggyBac transposition in human cells.

Insertional therapies have shown great potential for combating genetic disease and safer methods would undoubtedly broaden the variety of possible illness that can be treated. A major challenge that remains is reducing the risk of insertional mutagenesis due to random insertion by both viral and non-viral vectors. Targetable nucleases are capable of inducing double-stranded breaks to enhance homologous recombination for the introduction of transgenes at specific sequences. However, off-target DNA cleavages at unknown sites can lead to mutations that are difficult to detect. Alternatively, the piggyBac transposase is able perform all of the steps required for integration; therefore, cells confirmed to contain a single copy of a targeted transposon, for which its location is known, are likely to be devoid of aberrant genomic modifications. We aimed to retarget transposon insertions by comparing a series of novel hyperactive piggyBac constructs tethered to a custom transcription activator like effector DNA-binding domain designed to bind the first intron of the human CCR5 gene. Multiple targeting strategies were evaluated using combinations of both plasmid-DNA and transposase-protein relocalization to the target sequence. We demonstrated user-defined directed transposition to the CCR5 genomic safe harbor and isolated single-copy clones harboring targeted integrations

What Lies Beneath? Molecular Evolution During the Radiation of Caecilian Amphibians

Background: Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians. Results: A total of 8540 candidate groups of orthologous genes from transcriptomic data of five species of caecilian amphibians and the genome of the frog Xenopus tropicalis were analysed in order to investigate the genetic machinery behind caecilian diversification. We found a total of 168 protein-coding genes with signatures of positive selection at different evolutionary times during the radiation of caecilians. The majority of these genes were related to functional elements of the cell membrane and extracellular matrix with expression in several different tissues. The first colonization of the tropical soils was connected to the largest number of protein-coding genes under positive selection in our analysis. From the results of our study, we highlighted molecular changes in genes involved in perception, reduction-oxidation processes, and aging that likely were involved in the adaptation to different soil strata. Conclusions: The genes inferred to have been under positive selection provide valuable insights into caecilian evolution, potentially underpin adaptations of caecilians to their extreme environments, and contribute to a better understanding of fossorial adaptations and molecular evolution in vertebrates

Unveiling Pseudo-Crucial Events in Noise-Induced Phase Transitions

Noise-induced phase transitions are common in various complex systems, from physics to biology. In this article, we investigate the emergence of crucial events in noise-induced phase transition processes and their potential significance for understanding complexity in such systems. We utilize the first-passage time technique and coordinate transformations to study the dynamics of the system and identify crucial events. Furthermore, we employ Diffusion Entropy Analysis, a powerful statistical tool, to characterize the complexity of the system and quantify the information content of the identified events. Our results show that the emergence of crucial events is closely related to the complexity of the system and can provide insight into its behavior. This approach may have applications in diverse fields, such as climate modeling, financial markets, and biological systems, where understanding the emergence of crucial events is of great importance

Educational Reforms and Implementation of Student-Centered Active Learning in Science at Secondary and University Levels in Qatar

The Qatari government has made significant changes in the organization and staffing of schools over the past decade in an effort to improve the academic performance of school-aged citizens. Of interest is the need to encourage teachers to move from a didactic teacher-led mode of instruction to one that is more student-centred, but also teacher-guided, which encourages the development of critical thinking, problem solving, inquiry, and investigative skills. In this article, we discuss past and current educational changes and developments in Qatar with an emphasis on an initiative in chemistry that explored the utility and cultural transferability of student inquiry learning approaches to improve student conceptual understanding as well as their attitudes and self-efficacy. Based on the current activities described in this article, we argue that the developments and commitment to educational reform in Qatar can act as a guide for other nations that wish to move from a didactic teaching to a more student-centred approach

Superbeam Studies at CERN

A conventional low energy neutrino beam of great intensity could be produced by the Super Proton Linac at CERN as a first stage of a Neutrino Factory. Water Cerenkov and liquid scintillator detectors are studied as possible candidates for a neutrino oscillation experiment which could improve ourcurrent knowledge of the atmospheric parameters deltam2atm , delta23 and measure or severely constrain 13. It is also shown that a very large water detector could eventually observe leptonic CP violation

Complete IRAC mapping of the CFHTLS-DEEP, MUSYC AND NMBS-II FIELDS

The IRAC mapping of the NMBS-II fields program is an imaging survey at 3.6 and 4.5$\mu$m with the Spitzer Infrared Array Camera (IRAC). The observations cover three Canada-France-Hawaii Telescope Legacy Survey Deep (CFHTLS-D) fields, including one also imaged by AEGIS, and two MUSYC fields. These are then combined with archival data from all previous programs into deep mosaics. The resulting imaging covers a combined area of about 3 $deg^2$, with at least $\sim$2 hr integration time for each field. In this work, we present our data reduction techniques and document the resulting coverage maps at 3.6 and 4.5$\mu$m. All of the images are W-registered to the reference image, which is either the z-band stack image of the 25\% best seeing images from the CFHTLS-D for CFHTLS-D1, CFHTLS-D3, and CFHTLS-D4, or the K-band images obtained at the Blanco 4-m telescope at CTIO for MUSYC1030 and MUSYC1255. We make all images and coverage maps described herein publicly available via the Spitzer Science Center.Comment: Accepted in PASP; released IRAC mosaics available upon publication of the pape

Improved Chondrogenic Differentiation of rAAV SOX9-Modified Human MSCs Seeded in Fibrin-Polyurethane Scaffolds in a Hydrodynamic Environment

The repair of focal articular cartilage defects remains a problem. Combining gene therapy with tissue engineering approaches using bone marrow-derived mesenchymal stem cells (MSCs) may allow the development of improved options for cartilage repair. Here, we examined whether a three-dimensional fibrin-polyurethane scaffold provides a favorable environment for the effective chondrogenic differentiation of human MSCs (hMSCs) overexpressing the cartilage-specific SOX9 transcription factor via recombinant adeno-associated virus (rAAV) -mediated gene transfer cultured in a hydrodynamic environment in vitro. Sustained SOX9 expression was noted in the constructs for at least 21 days, the longest time point evaluated. Such spatially defined SOX9 overexpression enhanced proliferative, metabolic, and chondrogenic activities compared with control (reporter lacZ gene transfer) treatment. Of further note, administration of the SOX9 vector was also capable of delaying premature hypertrophic and osteogenic differentiation in the constructs. This enhancement of chondrogenesis by spatially defined overexpression of human SOX9 demonstrate the potential benefits of using rAAV-modified hMSCs seeded in fibrin-polyurethane scaffolds as a promising approach for implantation in focal cartilage lesions to improve cartilage repair

Clumpy Galaxies in CANDELS. I. The Definition of UV Clumps and the Fraction of Clumpy Galaxies at 0.5<z<3

Although giant clumps of stars are crucial to galaxy formation and evolution, the most basic demographics of clumps are still uncertain, mainly because the definition of clumps has not been thoroughly discussed. In this paper, we study the basic demographics of clumps in star-forming galaxies (SFGs) at 0.5<z<3, using our proposed physical definition that UV-bright clumps are discrete star-forming regions that individually contribute more than 8% of the rest-frame UV light of their galaxies. Clumps defined this way are significantly brighter than the HII regions of nearby large spiral galaxies, either individually or blended, when physical spatial resolution and cosmological dimming are considered. Under this definition, we measure the fraction of SFGs that contain at least one off-center clump (Fclumpy) and the contributions of clumps to the rest-frame UV light and star formation rate of SFGs in the CANDELS/GOODS-S and UDS fields, where our mass-complete sample consists of 3239 galaxies with axial ratio q>0.5. The redshift evolution of Fclumpy changes with the stellar mass (M*) of the galaxies. Low-mass (log(M*/Msun)<9.8) galaxies keep an almost constant Fclumpy of about 60% from z~3.0 to z~0.5. Intermediate-mass and massive galaxies drop their Fclumpy from 55% at z~3.0 to 40% and 15%, respectively, at z~0.5. We find that (1) the trend of disk stabilization predicted by violent disk instability matches the Fclumpy trend of massive galaxies; (2) minor mergers are a viable explanation of the Fclumpy trend of intermediate-mass galaxies at z<1.5, given a realistic observability timescale; and (3) major mergers are unlikely responsible for the Fclumpy trend in all masses at z<1.5. The clump contribution to the rest-frame UV light of SFGs shows a broad peak around galaxies with log(M*/Msun)~10.5 at all redshifts, possibly linked to the molecular gas fraction of the galaxies. (Abridged)Comment: 22 pages, 15 figures. Appeared in ApJ (2015, 800, 39). A few typos correcte

Smooth(er) Stellar Mass Maps in CANDELS: Constraints on the Longevity of Clumps in High-redshift Star-forming Galaxies

We perform a detailed analysis of the resolved colors and stellar populations of a complete sample of 323 star-forming galaxies at 0.5 < z < 1.5, and 326 star-forming galaxies at 1.5 < z < 2.5 in the ERS and CANDELS-Deep region of GOODS-South. Galaxies were selected to be more massive than 10^10 Msun and have specific star formation rates above 1/t_H. We model the 7-band optical ACS + near-IR WFC3 spectral energy distributions of individual bins of pixels, accounting simultaneously for the galaxy-integrated photometric constraints available over a longer wavelength range. We analyze variations in rest-frame color, stellar surface mass density, age, and extinction as a function of galactocentric radius and local surface brightness/density, and measure structural parameters on luminosity and stellar mass maps. We find evidence for redder colors, older stellar ages, and increased dust extinction in the nuclei of galaxies. Big star-forming clumps seen in star formation tracers are less prominent or even invisible on the inferred stellar mass distributions. Off-center clumps contribute up to ~20% to the integrated SFR, but only 7% or less to the integrated mass of all massive star-forming galaxies at z ~ 1 and z ~ 2, with the fractional contributions being a decreasing function of wavelength used to select the clumps. The stellar mass profiles tend to have smaller sizes and M20 coefficients, and higher concentration and Gini coefficients than the light distribution. Our results are consistent with an inside-out disk growth scenario with brief (100 - 200 Myr) episodic local enhancements in star formation superposed on the underlying disk. Alternatively, the young ages of off-center clumps may signal inward clump migration, provided this happens efficiently on the order of an orbital timescale.Comment: Accepted by The Astrophysical Journal, 27 pages, 1 table, 16 figure