Computation by Self-assembly of DNA Graphs

Using three dimensional graph structure and DNA self-assembly we show that theoretically 3-SAT and 3-colorability can be solved in a constant number of laboratory steps. In this assembly, junction molecules and duplex DNA molecules are the basic building blocks. The graphs involved are not necessarily regular, so experimental results of self-assembling non regular graphs using junction molecules as vertices and duplex DNA molecules as edge connections are presented.     

Autoantibodies against CD38 (ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase) that impair glucose-induced insulin secretion in noninsulin- dependent diabetes patients

Cyclic ADP-ribose (cADPR) has been shown to be a mediator for intracellular Ca2+ mobilization for insulin secretion by glucose in pancreatic beta cells, and CD38 shows both ADP-ribosyl cyclase to synthesize cADPR from NAD+ and cADPR hydrolase to hydrolyze cADPR to ADP-ribose. We show here that 13.8% of Japanese non-insulin-dependent diabetes (NIDDM) patients examined have autoantibodies against CD38 and that the sera containing anti-CD38 autoantibodies inhibit the ADP-ribosyl cyclase activity of CD38 (P 相似文献   

Topological network alignment uncovers biological function and phylogeny

Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology and disease. Comparison and alignment of biological networks will probably have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for purely topological alignment has yet been devised. In this paper, we present a novel algorithm based solely on network topology, that can be used to align any two networks. We apply it to biological networks to produce by far the most complete topological alignments of biological networks to date. We demonstrate that both species phylogeny and detailed biological function of individual proteins can be extracted from our alignments. Topology-based alignments have the potential to provide a completely new, independent source of phylogenetic information. Our alignment of the protein–protein interaction networks of two very different species—yeast and human—indicate that even distant species share a surprising amount of network topology, suggesting broad similarities in internal cellular wiring across all life on Earth.     

DNA splicing: computing by observing

Motivated by several techniques for observing molecular processes in real-time we introduce a computing device that stresses the role of the observer in biological computations and that is based on the observed behavior of a splicing system. The basic idea is to introduce a marked DNA strand into a test tube with other DNA strands and restriction enzymes. Under the action of these enzymes the DNA starts to splice. An external observer monitors and registers the evolution of the marked DNA strand. The input marked DNA strand is then accepted if its observed evolution follows a certain expected pattern. We prove that using simple observers (finite automata), applied on finite splicing systems (finite set of rules and finite set of axioms), the class of recursively enumerable languages can be recognized.     

Liquefaction of wood,synthesis and characterization of liquefied wood polyester derivatives

Liquefaction of Central‐European softwoods meal was performed using a mixture of diethylene glycol and glycerol and a minor addition of p‐toluenesulfonic acid as a catalyst. The liquefied wood was used as a replacement of a certain amount of the polyhydroxy alcohol in the polyester synthesis, enabled by the large number of hydroxyl groups that were available in the liquefied wood. Three different polyesters were synthesized by using adipic acid and phthalic acid anhydride as reagents. The products were characterized using FTIR, GPC/SEC, and viscosity measurements. The polyesters have hydroxyl values that were reduced due to esterification, from 1043 mg KOH/g of the liquefied wood to 400–800 mg KOH/g. Polyhydroxyl alcohols (22–23%) in the polyester formulations were replaced by wood derivatives. Such saturated polyesters are suitable for further use in polyurethane foam production. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2010     

Resistive heating and electropermeabilization of skin tissue during in vivo electroporation: A coupled nonlinear finite element model

The use of electric pulses to increase cell membrane permeability – electroporation – has, among other applications also been used on skin for (a) enhanced transdermal molecular delivery or (b) the delivery of drugs or DNA into viable skin cells. Based on finite element numerical method, we theoretically described skin electropermeabilization and the amount of heating in and around an electrically created pore in the stratum corneum (SC). With the model, we address both, electrical as well as thermal effects on skin tissue, specifically for electrode design and pulse protocols we used for gene electrotransfer in vivo (already published results), where plasmid DNA was injected intradermally with a syringe and external plate electrodes were used for pulse delivery. Theoretical results obtained with the model show no significant further thermal expansion of the aqueous pore for our specific pulse protocol (one short high voltage pulse: 400 V, 100 μs + one longer low voltage pulse: 80 V, 400 ms), as well as no thermal damage to the tissue. With some modifications to the protocol, electroporation could be used to (a) create pores in the SC through which to transport the DNA, and then (b) introduce the DNA into viable skin cells.     

A longitudinal study of reading development in dyslexic children.

The development of literacy skills was studied in 20 dyslexic children (7 years 7 months to 12 years 7 months). At Time 1, the dyslexic children performed worse on tests of reading, spelling, and phonological processing than chronological age-matched normal readers, but their performance was qualitatively similar to that of younger reading age-matched controls. The dyslexic children made poor progress over the following 2 years and, in comparison with reading age controls at Time 2, showed specific difficulties in nonword reading and repetition and made more dysphonetic spelling errors. The authors argue that this typical dyslexic profile becomes more defined with development and provides support for the theory that phonological deficits in dyslexia compromise the development of reading skills. (PsycINFO Database Record (c) 2010 APA, all rights reserved)