Experimental Progress in Computation by Self-Assembly of DNA Tilings

Approaches to DNA-based computing by self-assembly require the use of D. T A nanostructures, called tiles, that have efficient chemistries, expressive computational power: and convenient input and output (I/O) mechanisms. We have designed two new classes of DNA tiles: TAO and TAE, both of which contain three double-helices linked by strand exchange. Structural analysis of a TAO molecule has shown that the molecule assembles efficiently from its four component strands. Here we demonstrate a novel method for I/O whereby multiple tiles assemble around a single-stranded (input) scaffold strand. Computation by tiling theoretically results in the formation of structures that contain single-stranded (output) reported strands, which can then be isolated for subsequent steps of computation if necessary. We illustrate the advantages of TAO and TAE designs by detailing two examples of massively parallel arithmetic: construction of complete XOR and addition tables by linear assemblies of DNA tiles. The three helix structures provide flexibility for topological routing of strands in the computation: allowing the implementation of string tile models

The genome of the protozoan parasite Cystoisospora suis and a reverse vaccinology approach to identify vaccine candidates

Vaccine development targeting protozoan parasites remains challenging, partly due to the complex interactions between these eukaryotes and the host immune system. Reverse vaccinology is a promising approach for direct screening of genome sequence assemblies for new vaccine candidate proteins. Here, we applied this paradigm to Cystoisospora suis, an apicomplexan parasite that causes enteritis and diarrhea in suckling piglets and economic losses in pig production worldwide. Using Next Generation Sequencing we produced an ∼84 Mb sequence assembly for the C. suis genome, making it the first available reference for the genus Cystoisospora. Then, we derived a manually curated annotation of more than 11,000 protein-coding genes and applied the tool Vacceed to identify 1,168 vaccine candidates by screening the predicted C. suis proteome. To refine the set of candidates, we looked at proteins that are highly expressed in merozoites and specific to apicomplexans. The stringent set of candidates included 220 proteins, among which were 152 proteins with unknown function, 17 surface antigens of the SAG and SRS gene families, 12 proteins of the apicomplexan-specific secretory organelles including AMA1, MIC6, MIC13, ROP6, ROP12, ROP27, ROP32 and three proteins related to cell adhesion. Finally, we demonstrated in vitro the immunogenic potential of a C. suis-specific 42 kDa transmembrane protein, which might constitute an attractive candidate for further testing

RNA packaging motor: From structure to quantum mechanical modelling and sequential-stochastic mechanism

The bacteriophages of the Cystoviridae family package their single stranded RNA genomic precursors into empty capsid (procapsids) using a hexameric packaging ATPase motor (P4). This molecular motor shares sequence and structural similarity with RecA-like hexameric helicases. A concerted structural, mutational and kinetic analysis helped to define the mechanical reaction coordinate, i.e. the conformational changes associated with RNA translocation. The results also allowed us to propose a possible scheme of coupling between ATP hydrolysis and translocation which requires the cooperative action of three consecutive subunits. Here, we first test this model by preparing hexamers with defined proportions of wild type and mutant subunits and measuring their activity. Then, we develop a stochastic kinetic model which accounts for the catalytic cooperativity of the P4 hexamer. Finally, we use the available structural information to construct a quantum-chemical model of the chemical reaction coordinate and obtain a detailed description of the electron density changes during ATP hydrolysis. The model explains the results of the mutational analyses and yields new insights into the role of several conserved residues within the ATP binding pocket. These hypotheses will guide future experimental work

Genetic Code Based Coding and Mathematical Formulation for DNA Computation

DNA computation is to use DNA molecules for information storing and processing. Challenges currently faced by DNA computation are (1) lack of theoretical computational models for applications, and (2) high error rate for implementation. This paper attempts to address these problems from genetic coding and mathematical modeling aspects. The proposed genetic coding approach provides a promising alternative to reduce high error rate. The mathematical formulation lays down groundwork for studying theoretical aspects of DNA computation

High-throughput screening with the Eimeria tenella CDC2-related kinase2/cyclin complex EtCRK2/EtCYC3a

The poultry disease coccidiosis, caused by infection with Eimeria spp. apicomplexan parasites, is responsible for enormous economic losses to the global poultry industry. The rapid increase of resistance to therapeutic agents, as well as the expense of vaccination with live attenuated vaccines, requires the development of new effective treatments for coccidiosis. Because of their key regulatory function in the eukaryotic cell cycle, cyclin-dependent kinases (CDKs) are prominent drug targets. The Eimeria tenella CDC2-related kinase 2 (EtCRK2) is a validated drug target that can be activated in vitro by the CDK activator XlRINGO (Xenopus laevis rapid inducer of G2/M progression in oocytes). Bioinformatics analyses revealed four putative E. tenella cyclins (EtCYCs) that are closely related to cyclins found in the human apicomplexan parasite Plasmodium falciparum. EtCYC3a was cloned, expressed in Escherichia coli and purified in a complex with EtCRK2. Using the non-radioactive time-resolved fluorescence energy transfer (TR-FRET) assay, we demonstrated the ability of EtCYC3a to activate EtCRK2 as shown previously for XlRINGO. The EtCRK2/EtCYC3a complex was used for a combined in vitro and in silico high-throughput screening approach, which resulted in three lead structures, a naphthoquinone, an 8-hydroxyquinoline and a 2-pyrimidinyl-aminopiperidine-propane-2-ol. This constitutes a promising starting point for the subsequent lead optimization phase and the development of novel anticoccidial drugs

A Mathematical Formulation of DNA Computation

DNA computation is to use DNA molecules for information storing and processing. The task is accomplished by encoding and interpreting DNA molecules in suspended solutions before and after the complementary binding reactions. DNA computation is attractive, due to its fast parallel information processing, remarkable energy efficiency, and high storing capacity. Challenges currently faced by DNA computation are (1) lack of theoretical computational models for applications, and (2) high error rate for implementation. This paper attempts to address these problems from mathematical modeling and genetic coding aspects. The first part of this paper presents a mathematical formulation of DNA computation. The model may serve as a theoretical framework for DNA computation. In the second part, a genetic code based DNA computation approach is presented to reduce error rate for implementation, which has been a major concern for DNA computation. The method provides a promising alternative to reduce error rate for DNA computation