RNA as a Transcriptional Activator

AbstractTwo recent reports demonstrate that in vivo selection can isolate novel RNAs that activate transcription when tethered to a gene promoter. This highlights the structural plasticity that allows RNA to fulfill many functions normally carried out by proteins

Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases

Individual zinc finger (ZF) domains that recognize DNA triplets with high specificity and affinity can be used to create designer transcription factors and nucleases that are specific for nearly any site in the genome. These domains can be treated as modular units and assembled to create a polydactyl protein that recognizes extended DNA sequences. Deter-mination of valid target sites and the subsequent design of ZF proteins (ZFPs) is error-prone and not trivial, however. As a result, the use of ZFPs have been restricted primarily to those labs with the appropriate expertise. To address these limitations, we have created a user-friendly utility called Zinc Finger Tools (ZF Tools) that can be accessed at the URL . User-supplied DNA sequences can be searched for target sites appropriate for either gene regulation or nuclease targeting. Using a database of experimentally characterized zinc finger domains, the amino acid sequence for a ZFP expected to bind to any chosen target site can be generated. A reverse engineering utility is provided to predict the binding site for a ZFP of known sequence

Isotopic prediction calculation methodologies: application to Vandellos-II Reactor cycles 7-11

Determining as accurate as possible spent nuclear fuel isotopic content is gaining importance due to its safety and economic implications. Since nowadays higher burn ups are achievable through increasing initial enrichments, more efficient burn up strategies within the reactor cores and the extension of the irradiation periods, establishing and improving computation methodologies is mandatory in order to carry out reliable criticality and isotopic prediction calculations. Several codes (WIMSD5, SERPENT 1.1.7, SCALE 6.0, MONTEBURNS 2.0 and MCNP-ACAB) and methodologies are tested here and compared to consolidated benchmarks (OECD/NEA pin cell moderated with light water) with the purpose of validating them and reviewing the state of the isotopic prediction capabilities. These preliminary comparisons will suggest what can be generally expected of these codes when applied to real problems. In the present paper, SCALE 6.0 and MONTEBURNS 2.0 are used to model the same reported geometries, material compositions and burn up history of the Spanish Van de llós II reactor cycles 7-11 and to reproduce measured isotopies after irradiation and decay times. We analyze comparisons between measurements and each code results for several grades of geometrical modelization detail, using different libraries and cross-section treatment methodologies. The power and flux normalization method implemented in MONTEBURNS 2.0 is discussed and a new normalization strategy is developed to deal with the selected and similar problems, further options are included to reproduce temperature distributions of the materials within the fuel assemblies and it is introduced a new code to automate series of simulations and manage material information between them. In order to have a realistic confidence level in the prediction of spent fuel isotopic content, we have estimated uncertainties using our MCNP-ACAB system. This depletion code, which combines the neutron transport code MCNP and the inventory code ACAB, propagates the uncertainties in the nuclide inventory assessing the potential impact of uncertainties in the basic nuclear data: cross-section, decay data and fission yield

Directed evolution of recombinase specificity by split gene reassembly

The engineering of new enzymes that efficiently and specifically modify DNA sequences is necessary for the development of enhanced gene therapies and genetic studies. To address this need, we developed a robust strategy for evolving site-specific recombinases with novel substrate specificities. In this system, recombinase variants are selected for activity on new substrates based on enzyme-mediated reassembly of the gene encoding β-lactamase that confers ampicillin resistance to Escherichia coli. This stringent evolution method was used to alter the specificities of catalytic domains in the context of a modular zinc finger-recombinase fusion protein. Gene reassembly was detectable over several orders of magnitude, which allowed for tunable selectivity and exceptional sensitivity. Engineered recombinases were evolved to react with sequences from the human genome with only three rounds of selection. Many of the evolved residues, selected from a randomly-mutated library, were conserved among other members of this family of recombinases. This enhanced evolution system will translate recombinase engineering and genome editing into a practical and expedient endeavor for academic, industrial and clinical applications

Improving Cry8Ka toxin activity towards the cotton boll weevil (Anthonomus grandis)

<p>Abstract</p> <p>Background</p> <p>The cotton boll weevil (<it>Anthonomus grandis</it>) is a serious insect-pest in the Americas, particularly in Brazil. The use of chemical or biological insect control is not effective against the cotton boll weevil because of its endophytic life style. Therefore, the use of biotechnological tools to produce insect-resistant transgenic plants represents an important strategy to reduce the damage to cotton plants caused by the boll weevil. The present study focuses on the identification of novel molecules that show improved toxicity against the cotton boll weevil. <it>In vitro </it>directed molecular evolution through DNA shuffling and phage display screening was applied to enhance the insecticidal activity of variants of the Cry8Ka1 protein of <it>Bacillus thuringiensis</it>.</p> <p>Results</p> <p>Bioassays carried out with <it>A. grandis </it>larvae revealed that the LC₅₀of the screened mutant Cry8Ka5 toxin was 3.15-fold higher than the wild-type Cry8Ka1 toxin. Homology modelling of Cry8Ka1 and the Cry8Ka5 mutant suggested that both proteins retained the typical three-domain Cry family structure. The mutated residues were located mostly in loops and appeared unlikely to interfere with molecular stability.</p> <p>Conclusions</p> <p>The improved toxicity of the Cry8Ka5 mutant obtained in this study will allow the generation of a transgenic cotton event with improved potential to control <it>A. grandis</it>.</p