Precise targeted integration by a chimaeric transposase zinc-finger fusion protein

Transposons of the Tc1/mariner family have been used to integrate foreign DNA stably into the genome of a large variety of different cell types and organisms. Integration is at TA dinucleotides located essentially at random throughout the genome, potentially leading to insertional mutagenesis, inappropriate activation of nearby genes, or poor expression of the transgene. Here, we show that fusion of the zinc-finger DNA-binding domain of Zif268 to the C-terminus of ISY100 transposase leads to highly specific integration into TA dinucleotides positioned 6-17 bp to one side of a Zif268 binding site. We show that the specificity of targeting can be changed using Zif268 variants that bind to sequences from the HIV-1 promoter, and demonstrate a bacterial genetic screen that can be used to select for increased levels of targeted transposition. A TA dinucleotide flanked by two Zif268 binding sites was efficiently targeted by our transposase-Zif268 fusion, suggesting the possibility of designer ‘Z-transposases’ that could deliver transgenic cargoes to chosen genomic locations

Induced subarrays of Latin squares without repeated symbols

We show that for any Latin square L of order 2m, we can partition the rows and columns of L into pairs so that at most (m+3)/2 of the 2x2 subarrays induced contain a repeated symbol. We conjecture that any Latin square of order 2m (where m ≥ 2, with exactly five transposition class exceptions of order 6) has such a partition so that every 2x2 subarray induced contains no repeated symbol. We verify this conjecture by computer when m ≤ 4

FFT for the APE Parallel Computer

We present a parallel FFT algorithm for SIMD systems following the `Transpose Algorithm' approach. The method is based on the assignment of the data field onto a 1-dimensional ring of systolic cells. The systolic array can be universally mapped onto any parallel system. In particular for systems with next-neighbour connectivity our method has the potential to improve the efficiency of matrix transposition by use of hyper-systolic communication. We have realized a scalable parallel FFT on the APE100/Quadrics massively parallel computer, where our implementation is part of a 2-dimensional hydrodynamics code for turbulence studies. A possible generalization to 4-dimensional FFT is presented, having in mind QCD applications.Comment: 17 pages, 13 figures, figures include

High-throughput chromatin accessibility profiling at single-cell resolution.

Here we develop a high-throughput single-cell ATAC-seq (assay for transposition of accessible chromatin) method to measure physical access to DNA in whole cells. Our approach integrates fluorescence imaging and addressable reagent deposition across a massively parallel (5184) nano-well array, yielding a nearly 20-fold improvement in throughput (up to ~1800 cells/chip, 4-5 h on-chip processing time) and library preparation cost (~81¢ per cell) compared to prior microfluidic implementations. We apply this method to measure regulatory variation in peripheral blood mononuclear cells (PBMCs) and show robust, de novo clustering of single cells by hematopoietic cell type

Algoritma Paralel Odd Even Transposition Pada Model Jaringan Non-linier

Odd-even-transposition adalah suatu algoritma paralel yang merupakan pengembangan dari algoritma sekuensial “bubble sortâ€. Algoritma odd-even-transposition ini didesain khusus untuk model jaringan array linier (homogen). Untuk n elemen data, kompleksitas waktu dari algoritma bubble sort adalah O(n2), sedangkan pada odd-even-transposition yang bekerja di atas n prosesor adalah ï‘(n). Ada peningkatan kecepatan waktu pada kinerja algoritma paralel ini sebesar n kali dibanding algoritma sekuensialnya. Hypercube dimensi k adalah model jaringan non-linier (non-homogen) terdiri dari n = 2k prosesor, di mana setiap prosesor berderajat k. Model jaringan Fibonacci cube dan extended Lucas cube masing-masing merupakan model subjaringan hypercube dengan jumlah prosesor < 2k prosesor dan maksimum derajat prosesornya adalah k. Pada paper ini, diperlihatkan bagaimana algoritma odd-even-transposition dapat dijalankan juga pada model jaringan komputer cluster non-linier hypercube, Fibonacci cube, dan extended Lucas cube dengan kompleksitas waktu O(n). Odd-even-transposition is a parallel algorithm which is the development of sequential algorithm “bubble sortâ€. Odd-even transposition algorithm is specially designed for linear array network model (homogeneous). For n data elements, the time complexity of bubble sort algorithm is O(n2), while the odd-even-transposition that works with n processor is ï‘(n). There in an increase in the speed of time on the performance of this parallel algorithms for n times than its sequential algorithm. K-dimensional hypercube is a non-linear network model (non-homogeneous) consists of n = 2k processors, where each processor has k degree . Network model of Fibonacci cube and extended Lucas cube are the hypercube sub-network model with the number of processor

A Concept for Exploring Western Music Tonality in Physical Space

Musical theory about the structure and morphology of Western tonality is quite difficult to teach to young children, due to the relatively complex mathematical concepts behind tonality. Children usually grasp the concepts of musical harmony intuitively through listening to music examples. Placing the 12 notes of the well-tempered scale into a spatial arrangement, in which the proximity of these notes represents their mutual harmonic relationship, would allow to link physical motion through a spatial area with the exploration of music tonality. Music theorists have postulated the Circle of Fifth, the “Spiral Array”, and the “Tonnetz” as paradigms for spatial arrangements of music notes which allow mapping the distance between notes onto their “mutual consonance”. These approaches mostly have been of qualitative nature, leaving the actual numeric parameters of the spatial description undetermined. In this paper, these parameters have been determined, leading to a concrete numerical description of the planar Tonnetz. This allows the design of a physical space in which the music notes are distributed in space according to their musical consonance. Set up in an outdoor area, handheld devices (e.g. PDA) with integrated Global Positioning System can be used to play these notes at their actual physical location. This makes it possible for children to explore this musical space by moving through the real spatial area and experience the relationships of the notes through their proximity. Defining a range for each note as a circular area around each note location, consonant chords can be produced in those areas where those circles overlap. Using this concept, games can be developed in which the listeners have to perform certain tasks related to this musical space. This appears to be a promising approach for the music education of young children who can intuitively learn about music morphology without being explicitly taught about the complex theoretical mathematical background