Search results for "Shuffling"
showing 10 items of 11 documents
A Robust and All-Inclusive Pipeline for Shuffling of Adeno-Associated Viruses.
2018
Adeno-associated viruses (AAV) are attractive templates for engineering of synthetic gene delivery vectors. A particularly powerful technology for breeding of novel vectors with improved properties is DNA family shuffling, i.e., generation of chimeric capsids by homology-driven DNA recombination. Here, to make AAV DNA shuffling available to a wider community, we present a robust experimental and bioinformatical pipeline comprising: (i) standardized and partially codon-optimized plasmids carrying 12 different AAV capsid genes; (ii) a scalable protocol including troubleshooting guide for viral library production; and (iii) the freely available software SALANTO for comprehensive analysis of ch…
Transition from Protozoa to Metazoa: An Experimental Approach
1998
Until recently, stromatolites were thought to be the oldest fossils on earth that were very abundant 2000 to 3000 Ma (million years) ago (Walter 1994). Recently, the biological origin of these fossils has been questioned (Walter 1996). The universal phylogenetic tree exhibits a tripartite division of the living world into Bacteria (“eubacterial”), Archaea (“archebacterial”), and Eucarya [“eukaryotic” (Woese 1987; Woese et al. 1991)]. Based on comparisons of amino acid (aa) sequence data from enzymes, it has been proposed that the common ancestor of prokaryotes and eukaryotes lived about 2000 Ma ago (Doolittle et al. 1996). Phylogenetic analysis of the 70kDa heat-shock proteins suggested tha…
GEOBACTER METALLIREDUCENS MUTANTS FOR CHROMIUM BIOREMEDIATION
2011
Geobacter metallireducens is known to use oxidized metals such as Fe(III) and Mn(IV) as terminal extracellular electron acceptors. G. metallireducens can reduce the highly soluble and toxic Cr(VI) to its insoluble form Cr(III), thus enabling chromium removal from contaminated water and soil. This process is limited by the low toxicity resistance of G. metallireducens to Cr(VI). Genome shuffling can generate mutants with improved phenotype. In our work we are carrying out G. metallireducens genome shuffling, in order to increase its resistance to Cr(VI). In Geobacter species, metal toxicity resistance is correlated to the respiration rate, hence to the reduction rate of the metallic electron…
Gene structure and function of tyrosine kinases in the marine sponge Geodia cydonium: Autapomorphic characters of Metazoa
1999
Abstract Porifera (sponges) represent the most ancient, extant metazoan phylum. They existed already prior to the ‘Cambrian Explosion’. Based on the analysis of aa sequences of informative proteins, it is highly likely that all metazoan phyla evolved from only one common ancestor (monophyletic origin). As ‘autapomorphic’ proteins which are restricted to Metazoa only, integrin receptors, receptors with scavenger receptor cysteine-rich repeats, neuronal-like receptors and protein–tyrosine kinases (PTKs) have been identified in Porifera. From the marine sponge Geodia cydonium , a receptor tyrosine kinase (RTK) has been cloned that comprises the characteristic structural topology known from oth…
The human complement C9 gene: structural analysis of the 5′ gene region and genetic polymorphism studies
2001
Summary C9 is the last of the human complement components creating the membrane attack complex. The single chain serum protein is encoded by a gene located on chromosome 5p13 that is composed of 11 exons. With the aid of inverse PCR, the hitherto unknown regions flanking exon 1 and the 3′ part of exon 11 (3′UTR) have been sequenced. A computer-based analysis of the 300-bp region located just upstream of the AUG start codon showed homologies to known DNA modules which affect the transcriptional regulation of certain genes. The most striking of these is a sequence that may substitute the missing TATA box in initiating C9 transcription. In the 3′UTR, three successive polyadenylation signals we…
Molecular dissection of human Argonaute proteins by DNA shuffling.
2013
A paramount task in RNA interference research is to decipher the complex biology of cellular effectors, exemplified in humans by four pleiotropic Argonaute proteins (Ago1-Ago4). Here, we exploited DNA family shuffling, a molecular evolution technology, to generate chimeric Ago protein libraries for dissection of intricate phenotypes independently of prior structural knowledge. Through shuffling of human Ago2 and Ago3, we discovered two N-terminal motifs that govern RNA cleavage in concert with the PIWI domain. Structural modeling predicts an impact on protein rigidity and/or RNA-PIWI alignment, suggesting new mechanistic explanations for Ago3's slicing deficiency. Characterization of hybrid…
Sponges (Porifera) Molecular Model Systems to Study Cellular Differentiation in Metazoa
1998
Evolution is a gradual process whereby primarily new genes are formed either by gene duplication (Ohno 1970) or exon shuffling (Gilbert 1978). New proteins can also be produced by overlapping genes, alternative splicing or gene sharing (Li and Graur 1991). These facts imply that (1) proteins found in a given phylum contain elements or modules which are present already in ancestral protein(s) of members of phylogenetically older phyla and (2) that new combinations of such modules create proteins that possess new functions.
The non-random walk of stock prices: The long-term correlation between signs and sizes
2007
We investigate the random walk of prices by developing a simple model relating the properties of the signs and absolute values of individual price changes to the diffusion rate (volatility) of prices at longer time scales. We show that this benchmark model is unable to reproduce the diffusion properties of real prices. Specifically, we find that for one hour intervals this model consistently over-predicts the volatility of real price series by about 70%, and that this effect becomes stronger as the length of the intervals increases. By selectively shuffling some components of the data while preserving others we are able to show that this discrepancy is caused by a subtle but long-range non-…
Parallelization of the Wolff single-cluster algorithm.
2010
A parallel [open multiprocessing (OpenMP)] implementation of the Wolff single-cluster algorithm has been developed and tested for the three-dimensional (3D) Ising model. The developed procedure is generalizable to other lattice spin models and its effectiveness depends on the specific application at hand. The applicability of the developed methodology is discussed in the context of the applications, where a sophisticated shuffling scheme is used to generate pseudorandom numbers of high quality, and an iterative method is applied to find the critical temperature of the 3D Ising model with a great accuracy. For the lattice with linear size L=1024, we have reached the speedup about 1.79 times …
Evolutionary implications of intron-exon distribution and the properties and sequences of the RPL10A gene in eukaryotes.
2013
The RPL10A gene encodes the RPL10 protein, required for joining 40S and 60S subunits into a functional 80S ribosome. This highly conserved gene, ubiquitous across all eukaryotic super-groups, is characterized by a variable number of spliceosomal introns, present in most organisms. These properties facilitate the recognition of orthologs among distant taxa and thus comparative studies of sequences as well as the distribution and properties of introns in taxonomically distant groups of eukaryotes. The present study examined the multiple ways in which RPL10A conservation vs. sequence changes in the gene over the course of evolution, including in exons, introns, and the encoded proteins, can be…