Tomáš Martínek

An evolvable image filter: experimental evaluation of a complete hardware implementation in FPGA

This paper describes an evolvable image filter which is completely implemented in a field programmable gate array. The proposed system is able to evolve an image filter in a few seconds if corrupted and original images are supplied by user. The architecture is generic and can easily be modified to realize other evolvable systems. COMBO6 card with Xilinx Virtex xc2v3000 FPGA is used as a target platform.

A dynamic programming algorithm for identification of triplex-forming sequences

MOTIVATION Current methods for identification of potential triplex-forming sequences in genomes and similar sequence sets rely primarily on detecting homopurine and homopyrimidine tracts. Procedures capable of detecting sequences supporting imperfect, but structurally feasible intramolecular triplex structures are needed for better sequence analysis. RESULTS We modified an algorithm for detection of approximate palindromes, so as to account for the special nature of triplex DNA structures. From available literature, we conclude that approximate triplexes tolerate two classes of errors. One, analogical to mismatches in duplex DNA, involves nucleotides in triplets that do not readily form Hoogsteen bonds. The other class involves geometrically incompatible neighboring triplets hindering proper alignment of strands for optimal hydrogen bonding and stacking. We tested the statistical properties of the algorithm, as well as its correctness when confronted with known triplex sequences. The proposed algorithm satisfactorily detects sequences with intramolecular triplex-forming potential. Its complexity is directly comparable to palindrome searching. AVAILABILITY Our implementation of the algorithm is available at http://www.fi.muni.cz/lexa/triplex as source code and a web-based search tool. The source code compiles into a library providing searching capability to other programs, as well as into a stand-alone command-line application based on this library. CONTACT lexa@fi.muni.cz SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Extrinsic and Intrinsic Evolution of Multifunctional Combinational Modules

Multifunctional digital circuits are circuits composed of polymorphic (multifunctional) gates. In addition to its standard logic function (such as NAND), a polymorphic gate exhibits another logic function (such as NOR) which is activated under a specific condition, for example, when Vdd, temperature or illumination reaches a certain level. This paper describes the evolutionary design of multifunctional combinational circuits at the gate level using a circuit simulator and in a field programmable gate array (FPGA). The FPGA-based implementation exhibits a significant speedup against a highly optimized software simulator.

Guanine quadruplexes are formed by specific regions of human transposable elements

BackgroundTransposable elements form a significant proportion of eukaryotic genomes. Recently, Lexa et al. (Nucleic Acids Res 42:968-978, 2014) reported that plant long terminal repeat (LTR) retrotransposons often contain potential quadruplex sequences (PQSs) in their LTRs and experimentally confirmed their ability to adopt four-stranded DNA conformations.ResultsHere, we searched for PQSs in human retrotransposons and found that PQSs are specifically localized in the 3’-UTR of LINE-1 elements, in LTRs of HERV elements and are strongly accumulated in specific regions of SVA elements. Circular dichroism spectroscopy confirmed that most PQSs had adopted monomolecular or bimolecular guanine quadruplex structures. Evolutionarily young SVA elements contained more PQSs than older elements and their propensity to form quadruplex DNA was higher. Full-length L1 elements contained more PQSs than truncated elements; the highest proportion of PQSs was found inside transpositionally active L1 elements (PA2 and HS families).ConclusionsConservation of quadruplexes at specific positions of transposable elements implies their importance in their life cycle. The increasing quadruplex presence in evolutionarily young LINE-1 and SVA families makes these elements important contributors toward present genome-wide quadruplex distribution.

Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes.

Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic, and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons. FISH mapping revealed X chromosome-accumulated, Y chromosome-specific or both sex chromosomes-accumulated satellites but most satellites were found on autosomes. Transposable elements were located mostly in the subtelomeres of all chromosomes. The 5S rDNA and 45S rDNA were localized on one autosomal locus each. Although we demonstrated the small size of the Y chromosome of the seabuckthorn and accumulated satellite DNA there, we were unable to estimate the age and extent of the Y chromosome degeneration. Analysis of dioecious relatives such as Shepherdia would shed more light on the evolution of these sex chromosomes.

GICS: Generic interconnection system

The division of an application between a conventional processor and an acceleration card with FPGA chips has been proved as a suitable way for an acceleration of computationally intensive tasks. In such applications, the designer usually has to implement an interconnection between components placed in FPGA and the host system bus. This task is often complicated by different requirements of user components for throughput, latency of reading operations, need for DMA transfers etc. The objective of this work is to show a new approach for implementation of interconnection systems and to enable the designer to focus on the development of the target application. The proposed interconnection system is based on tree topology. The system eliminates the sensitivity of wide buses to the distance, supports the connection of components with different requirements for throughput, supports split transaction model and many other features. The proposed system is implemented and evaluated on chips with Virtex 5 technology.

FireProt: web server for automated design of thermostable proteins

Abstract There is a continuous interest in increasing proteins stability to enhance their usability in numerous biomedical and biotechnological applications. A number of in silico tools for the prediction of the effect of mutations on protein stability have been developed recently. However, only single-point mutations with a small effect on protein stability are typically predicted with the existing tools and have to be followed by laborious protein expression, purification, and characterization. Here, we present FireProt, a web server for the automated design of multiple-point thermostable mutant proteins that combines structural and evolutionary information in its calculation core. FireProt utilizes sixteen tools and three protein engineering strategies for making reliable protein designs. The server is complemented with interactive, easy-to-use interface that allows users to directly analyze and optionally modify designed thermostable mutants. FireProt is freely available at http://loschmidt.chemi.muni.cz/fireprot.

pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R

Motivation G‐quadruplexes (G4s) are one of the non‐B DNA structures easily observed in vitro and assumed to form in vivo. The latest experiments with G4‐specific antibodies and G4‐unwinding helicase mutants confirm this conjecture. These four‐stranded structures have also been shown to influence a range of molecular processes in cells. As G4s are intensively studied, it is often desirable to screen DNA sequences and pinpoint the precise locations where they might form. Results We describe and have tested a newly developed Bioconductor package for identifying potential quadruplex‐forming sequences (PQS). The package is easy‐to‐use, flexible and customizable. It allows for sequence searches that accommodate possible divergences from the optimal G4 base composition. A novel aspect of our research was the creation and training (parametrization) of an advanced scoring model which resulted in increased precision compared to similar tools. We demonstrate that the algorithm behind the searches has a 96% accuracy on 392 currently known and experimentally observed G4 structures. We also carried out searches against the recent G4‐seq data to verify how well we can identify the structures detected by that technology. The correlation with pqsfinder predictions was 0.622, higher than the correlation 0.491 obtained with the second best G4Hunter. Availability and implementation http://bioconductor.org/packages/pqsfinder/ This paper is based on pqsfinder‐1.4.1. Contact lexa@fi.muni.cz Supplementary information Supplementary data are available at Bioinformatics online.

P53 specifically binds triplex DNA in vitro and in cells

Triplex DNA is implicated in a wide range of biological activities, including regulation of gene expression and genomic instability leading to cancer. The tumor suppressor p53 is a central regulator of cell fate in response to different type of insults. Sequence and structure specific modes of DNA recognition are core attributes of the p53 protein. The focus of this work is the structure-specific binding of p53 to DNA containing triplex-forming sequences in vitro and in cells and the effect on p53-driven transcription. This is the first DNA binding study of full-length p53 and its deletion variants to both intermolecular and intramolecular T.A.T triplexes. We demonstrate that the interaction of p53 with intermolecular T.A.T triplex is comparable to the recognition of CTG-hairpin non-B DNA structure. Using deletion mutants we determined the C-terminal DNA binding domain of p53 to be crucial for triplex recognition. Furthermore, strong p53 recognition of intramolecular T.A.T triplexes (H-DNA), stabilized by negative superhelicity in plasmid DNA, was detected by competition and immunoprecipitation experiments, and visualized by AFM. Moreover, chromatin immunoprecipitation revealed p53 binding T.A.T forming sequence in vivo. Enhanced reporter transactivation by p53 on insertion of triplex forming sequence into plasmid with p53 consensus sequence was observed by luciferase reporter assays. In-silico scan of human regulatory regions for the simultaneous presence of both consensus sequence and T.A.T motifs identified a set of candidate p53 target genes and p53-dependent activation of several of them (ABCG5, ENOX1, INSR, MCC, NFAT5) was confirmed by RT-qPCR. Our results show that T.A.T triplex comprises a new class of p53 binding sites targeted by p53 in a DNA structure-dependent mode in vitro and in cells. The contribution of p53 DNA structure-dependent binding to the regulation of transcription is discussed.

Hardware Acceleration of Approximate Tandem Repeat Detection

Understanding the structure and function of DNA sequences represents an important area of research in modern biology. Unfortunately, analysis of such data is often complicated by the presence of mutations introduced by evolutionary processes. At the lowest scale, these usually occur in biological sequences as character substitutions, insertions or deletions (indel). They increase the time-complexity of algorithms for sequence analysis by introducing an element of uncertainty, complicating their practical usage. One class of such algorithms has been designed to search for tandem repeats with possible errors - approximate tandem repeats. This paper investigates the possibilities for hardware acceleration of approximate tandem repeat searching and describes a parametrized architecture suitable for chips with FPGA technology. The proposed architecture is able to detect tandems with both types of errors (mismatches and indels) and does not limit the length of detected tandem. A prototype of the circuit was implemented in VHDL language and synthesized for Virtex5 technology. Application on test sequences shows that the circuit is able to speed up tandem searching in orders of thousands in comparison with the best-known software method relying on suffix arrays.