Biomolecular computers with multiple restriction enzymes.

Abstract:

:The development of conventional, silicon-based computers has several limitations, including some related to the Heisenberg uncertainty principle and the von Neumann "bottleneck". Biomolecular computers based on DNA and proteins are largely free of these disadvantages and, along with quantum computers, are reasonable alternatives to their conventional counterparts in some applications. The idea of a DNA computer proposed by Ehud Shapiro's group at the Weizmann Institute of Science was developed using one restriction enzyme as hardware and DNA fragments (the transition molecules) as software and input/output signals. This computer represented a two-state two-symbol finite automaton that was subsequently extended by using two restriction enzymes. In this paper, we propose the idea of a multistate biomolecular computer with multiple commercially available restriction enzymes as hardware. Additionally, an algorithmic method for the construction of transition molecules in the DNA computer based on the use of multiple restriction enzymes is presented. We use this method to construct multistate, biomolecular, nondeterministic finite automata with four commercially available restriction enzymes as hardware. We also describe an experimental applicaton of this theoretical model to a biomolecular finite automaton made of four endonucleases.

journal_name

Genet Mol Biol

authors

Sakowski S,Krasinski T,Waldmajer J,Sarnik J,Blasiak J,Poplawski T

doi

10.1590/1678-4685-GMB-2016-0132

subject

Has Abstract

pub_date

2017-10-01 00:00:00

pages

860-870

issue

4

eissn

1415-4757

issn

1678-4685

pii

S1415-47572017005026101

journal_volume

40

pub_type

杂志文章
  • In silicio expression analysis of PKS genes isolated from Cannabis sativa L.

    abstract::Cannabinoids, flavonoids, and stilbenoids have been identified in the annual dioecious plant Cannabis sativa L. Of these, the cannabinoids are the best known group of this plant's natural products. Polyketide synthases (PKSs) are responsible for the biosynthesis of diverse secondary metabolites, including flavonoids a...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/S1415-47572010005000088

    authors: Flores-Sanchez IJ,Linthorst HJ,Verpoorte R

    更新日期:2010-10-01 00:00:00

  • Phylogenetic analysis, based on EPIYA repeats in the cagA gene of Indian Helicobacter pylori, and the implications of sequence variation in tyrosine phosphorylation motifs on determining the clinical outcome.

    abstract::The population of India harbors one of the world's most highly diverse gene pools, owing to the influx of successive waves of immigrants over regular periods in time. Several phylogenetic studies involving mitochondrial DNA and Y chromosomal variation have demonstrated Europeans to have been the first settlers in Indi...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/s1415-47572011005000003

    authors: Tiwari SK,Sharma V,Sharma VK,Gopi M,Saikant R,Nandan A,Bardia A,Gunisetty S,Katikala P,Habeeb MA,Khan AA,Habibullah CM

    更新日期:2011-04-01 00:00:00

  • DNA methylation dynamics in the rat EGF gene promoter after partial hepatectomy.

    abstract::Epidermal growth factor (EGF), a multifunctional growth factor, is a regulator in a wide variety of physiological processes. EGF plays an important role in the regulation of liver regeneration. This study was aimed at investigating the methylation level of EGF gene throughout liver regeneration. DNA of liver tissue fr...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/s1415-47572014000300017

    authors: Li D,Fan J,Li Z,Xu C

    更新日期:2014-06-01 00:00:00

  • Clonal diversity and conservation genetics of the medicinal plant Carapichea ipecacuanha (Rubiaceae).

    abstract::The roots of the understorey shrub Carapichea ipecacuanha (ipecac) have medicinal properties, and the uprooting of wild plants has supplied most of the world demand for this species. Although under severe population decline, C. ipecacuanha lacks legal protection. In the wild, the aerial stems of ipecac clump together ...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/S1415-47572009005000096

    authors: de Oliveira LO,Venturini BA,Rossi AA,Hastenreiter SS

    更新日期:2010-01-01 00:00:00

  • Chromosome mapping of repetitive sequences in four Serrasalmidae species (Characiformes).

    abstract::The Serrasalmidae family is composed of a number of commercially interesting species, mainly in the Amazon region where most of these fishes occur. In the present study, we investigated the genomic organization of the 18S and 5S rDNA and telomeric sequences in mitotic chromosomes of four species from the basal clade o...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/s1415-47572014000100009

    authors: Ribeiro LB,Matoso DA,Feldberg E

    更新日期:2014-03-01 00:00:00

  • Birth defects in Brazil: Outcomes of a population-based study.

    abstract::Birth defects (BDs) are functional and structural alterations in embryonic or fetal development. With an incidence of approximately 3-5%, BDs are a leading cause of infant mortality and lifelong disability. A population-based prospective case-control study was conducted for one year with 5204 infants, between March 1s...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/1678-4685-GMB-2018-0186

    authors: Oliveira-Brancati CIF,Ferrarese VCC,Costa AR,Fett-Conte AC

    更新日期:2020-02-10 00:00:00

  • ADP-ribosylation: from molecular mechanisms to human disease.

    abstract::Post-translational modification of proteins by ADP-ribosylation, catalysed by poly (ADP-ribose) polymerases (PARPs) using NAD+ as a substrate, plays central roles in DNA damage signalling and repair, modulates a range of cellular signalling cascades and initiates programmed cell death by parthanatos. Here, we present ...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/1678-4685-GMB-2019-0075

    authors: Hoch NC,Polo LM

    更新日期:2019-12-13 00:00:00

  • Diverse coactivator recruitment through differential PPARγ nuclear receptor agonism.

    abstract::The PPARγ nuclear receptor regulates the expression of genes involved in lipid and carbohydrate metabolism, and it has protective effects in some patients with type 2 diabetes. Nevertheless, the therapeutic value of the PPARγ nuclear receptor protein is limited due to the secondary effects of some PPARγ ligands. Becau...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/S1415-47572013005000002

    authors: Lizcano F,Vargas D

    更新日期:2013-03-01 00:00:00

  • Comparative analyses of three swallow species (Aves, Passeriformes, Hirundinidae): Insights on karyotype evolution and genomic organization.

    abstract::Despite the richness of species in the Hirudinidae family, little is known about the genome organization of swallows. The Progne tapera species presents genetic and morphological difference when compared to other members of the same genus. Hence, the aims of this study were to analyze the chromosomal evolution of thre...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/1678-4685-GMB-2019-0232

    authors: Barcellos SA,Kretschmer R,Souza MS,Costa AL,Degrandi TM,Lopes CF,Ferguson-Smith MA,Pereira J,Oliveira EHC,Gunski RJ,Garnero ADV

    更新日期:2020-03-09 00:00:00

  • The challenges of organizing an international course in Latin America.

    abstract::The Latin American School of Human and Medical Genetics (ELAG) is the main course of its kind in the genetics field in Latin America. Here we describe the main challenges regarding the organization of such event, including how we obtain funding and how we proceed with student selection. Thus, we aim to share our exper...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/s1415-47572014000200002

    authors: Vairo F,López ML,Cruz CU,Corrêa PG,Baldo G

    更新日期:2014-03-01 00:00:00

  • Evidence of two lineages of the dengue vector Aedes aegypti in the Brazilian Amazon, based on mitochondrial DNA ND4 gene sequences.

    abstract::Genetic variation was estimated in ten samples populations of Aedes aegypti from the Brazilian Amazon, by using a 380 bp fragment of the mitochocondrial NADH dehydrogenase subunit 4 (ND4) gene. A total of 123 individuals were analyzed, whereby 13 haplotypes were found. Mean genetic diversity was slightly high (h = 0.6...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/S1415-47572009005000036

    authors: Lima RS Jr,Scarpassa VM

    更新日期:2009-04-01 00:00:00

  • Exploitation of mitochondrial nad6 as a complementary marker for studying population variability in Lepidoptera.

    abstract::The applicability of mitochondrial nad6 sequences to studies of DNA and population variability in Lepidoptera was tested in four species of economically important moths and one of wild butterflies. The genetic information so obtained was compared to that of cox1 sequences for two species of Lepidoptera. nad6 primers a...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/S1415-47572011000400028

    authors: Silva-Brandão KL,Lyra ML,Santos TV,Seraphim N,Albernaz KC,Pavinato VA,Martinelli S,Cônsoli FL,Omoto C

    更新日期:2011-10-01 00:00:00

  • Rabies virus diversification in aerial and terrestrial mammals.

    abstract::Rabies is a fatal zoonotic infection of the central nervous system of mammals and has been known to humans for millennia. The etiological agent, is a neurotropic RNA virus in the order Mononegavirales, family Rhabdoviridae, genus Lyssavirus. There are currently accepted to be two cycles for rabies transmission: the ur...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/1678-4685-GMB-2019-0370

    authors: Oliveira RN,Freire CC,Iamarino A,Zanotto PM,Pessoa R,Sanabani SS,Souza SP,Castilho JG,Batista HBCR,Carnieli P Jr,Macedo CI,Watanabe JT,Brandão PE

    更新日期:2020-07-31 00:00:00

  • Genotoxic potential of the latex from cotton-leaf physicnut (Jatropha gossypiifolia L.).

    abstract::Jatropha gossypiifolia L. (Euphorbiaceae), popularly known as cotton-leaf physicnut, is a milky shrub notable for its medicinal properties. The present study aimed to evaluate the toxic, cytotoxic and genotoxic effects of the latex of J. gossypiifolia, using Allium cepa L. as test system. Seeds of A. cepa were exposed...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/S1415-475738120140162

    authors: de Almeida PM,de Sousa Araújo S,Marin-Morales MA,Benko-Iseppon AM,Brasileiro-Vidal AC

    更新日期:2015-03-01 00:00:00

  • VDR polymorphisms influence immunological response in HIV-1+ individuals undergoing antiretroviral therapy.

    abstract::Vitamin D exerts an immuno-modulatory activity on several immune system cells through the vitamin D receptor (VDR). Herein, we verified that age and a therapeutic regimen containing protease inhibitors are associated with failures in antiretroviral therapies (ARVs). In addition, we assessed whether a VDR SNP (rs115688...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/1678-4685-GMB-2017-0289

    authors: Silva RCD,Alves NMP,Pereira JJS,Coelho AVC,Arraes LC,Brandão LAC,Crovella S,Silva JA

    更新日期:2019-04-01 00:00:00

  • Isolation and multiplex genotyping of polymorphic microsatellite DNA markers in the snakehead murrel, Channa striata.

    abstract::Seven polymorphic microsatellite loci were isolated and characterized for the snakehead murrel, Channa striata (Channidae), a valuable tropical freshwater fish species. Among 25 specimens collected from Kedah state in Malaysia, the number of alleles per locus ranged from 2 to 7. Observed and expected heterozygosities ...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:

    authors: Jamsari AF,Min-Pau T,Siti-Azizah MN

    更新日期:2011-04-01 00:00:00

  • Genetic structure of red-handed howler monkey populations in the fragmented landscape of Eastern Brazilian Amazonia.

    abstract::We genotyped 15 microsatellite loci in order to evaluate the effects of habitat fragmentation, caused by flooding of the Tucuruí reservoir, on the genetic structure of Alouatta belzebul in eastern Amazonia. The analysis included two populations sampled in 1984, representing both margins of the Tocantins river, and thr...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/s1415-47572010000400027

    authors: Bastos HB,Gonçalves EC,Ferrari SF,Silva A,Schneider MP

    更新日期:2010-10-01 00:00:00

  • A patient presenting a 22q13 deletion associated with an apparently balanced translocation t(16;22): An illustrative case in the investigation of patients with low ARSA activity.

    abstract::A 10-year-old speechless, mentally deficient male, with low arylsulfatase A (ARSA) activity, and presumably, methachromatic leukodystrophy, underwent genetic evaluation. As the clinical picture was not compatible with this diagnosisan ARSA gene and chromosome analysis were performed, showing the presence of a pseudode...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/S1415-47572012000300007

    authors: Artigalás O,Paskulin G,Riegel M,Burin M,Saraiva-Pereira ML,Maluf S,Kiss A,Schwartz IV

    更新日期:2012-04-01 00:00:00

  • Mannose-Binding Lectin 2 (MBL2) combined genotypes deficiency is associated with susceptibility for Oral Lichen Planus.

    abstract::Oral Lichen Planus (OLP) is an oral inflammatory condition, mediated by host immune system reaction, presenting basal membrane damages with inflammatory lesions in the mouth and/or skin. In this study, the role of functional polymorphisms in the MBL2 gene, encoding for Mannose-Binding Protein C (MBP-C), a member of th...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/1678-4685-GMB-2018-0015

    authors: Polesello V,Segat L,Biasotto M,Ottaviani G,Gobbo M,Di Lenarda R,Crovella S,Zupin L

    更新日期:2019-01-01 00:00:00

  • Reciprocal regulation between alternative splicing and the DNA damage response.

    abstract::Splicing, the process that catalyzes intron removal and flanking exon ligation, can occur in different ways (alternative splicing) in immature RNAs transcribed from a single gene. In order to adapt to a particular context, cells modulate not only the quantity but also the quality (alternative isoforms) of their transc...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/1678-4685-GMB-2019-0111

    authors: Botto AEC,Muñoz JC,Giono LE,Nieto-Moreno N,Cuenca C,Kornblihtt AR,Muñoz MJ

    更新日期:2020-03-27 00:00:00

  • Identification and detection of a novel human endogenous retrovirus-related gene, and structural characterization of its related elements.

    abstract::Up-regulation of human endogenous retroviruses (HERVs) is associated with many diseases, including cancer. In this study, an H family HERV (HERV-H)-related gene was identified and characterized. Its spliced transcript lacks protein-coding capacity and may belong to the emerging class of noncoding RNAs (ncRNAs). The 1....

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/S1415-47572009005000082

    authors: Liang Q,Ding J,Zheng S

    更新日期:2009-10-01 00:00:00

  • Survey for positively selected coding regions in the genome of the hematophagous tsetse fly Glossina morsitans identifies candidate genes associated with feeding habits and embryonic development.

    abstract::Tsetse flies are responsible for the transmission of Trypanossoma sp. to vertebrate animals in Africa causing huge health issues and economic loss. The availability of the genome sequence of Glossina morsitans enabled the discovery of several genes related to medically important phenotypes and novel physiological feat...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/1678-4685-GMB-2018-0311

    authors: Freitas L,Mesquita RD,Schrago CG

    更新日期:2020-06-10 00:00:00

  • Association between interleukin 6 -174 G/C promoter gene polymorphism and runners' responses to the dietary ingestion of antioxidant supplementation based on pequi (Caryocar brasiliense Camb.) oil: a before-after study.

    abstract::Exercise is a double-edged sword: when practiced in moderation, it increases the expression of antioxidant enzymes, but when practiced strenuously it causes oxidative stress and cell damage. In this context, polymorphisms in the interleukin (IL)-6 gene should be investigated better because they can influence performan...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/1678-4685-GMB-2015-0299

    authors: Miranda-Vilela AL,Ribeiro IF,Grisolia CK

    更新日期:2016-10-01 00:00:00

  • Xylella fastidiosa gene expression analysis by DNA microarrays.

    abstract::Xylella fastidiosa genome sequencing has generated valuable data by identifying genes acting either on metabolic pathways or in associated pathogenicity and virulence. Based on available information on these genes, new strategies for studying their expression patterns, such as microarray technology, were employed. A t...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/S1415-47572009005000038

    authors: Travensolo RF,Carareto-Alves LM,Costa MV,Lopes TJ,Carrilho E,Lemos EG

    更新日期:2009-04-01 00:00:00

  • Familial Dysautonomia: Mechanisms and Models.

    abstract::Hereditary Sensory and Autonomic Neuropathies (HSANs) compose a heterogeneous group of genetic disorders characterized by sensory and autonomic dysfunctions. Familial Dysautonomia (FD), also known as HSAN III, is an autosomal recessive disorder that affects 1/3,600 live births in the Ashkenazi Jewish population. The m...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/1678-4685-GMB-2015-0335

    authors: Dietrich P,Dragatsis I

    更新日期:2016-10-01 00:00:00

  • bFGF promotes adipocyte differentiation in human mesenchymal stem cells derived from embryonic stem cells.

    abstract::In this work we describe the establishment of mesenchymal stem cells (MSCs) derived from embryonic stem cells (ESCs) and the role of bFGF in adipocyte differentiation. The totipotency of ESCs and MSCs was assessed by immunofluorescence staining and RT-PCR of totipotency factors. MSCs were successfully used to induce o...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/s1415-47572014000100019

    authors: Song X,Li Y,Chen X,Yin G,Huang Q,Chen Y,Xu G,Wang L

    更新日期:2014-03-01 00:00:00

  • The catalase gene family in cucumber: genome-wide identification and organization.

    abstract::Catalase (CAT) is a common antioxidant enzyme in almost all living organisms. Currently, detailed reports on cucumber (Cucumis sativus L.) CAT (CsCAT) genes and tissue expression profiling are limited. In the present study, four candidate CsCAT genes were identified in cucumber. Phylogenetic analysis indicated that Cs...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/1678-4685-GMB-2015-0192

    authors: Hu L,Yang Y,Jiang L,Liu S

    更新日期:2016-07-01 00:00:00

  • Colombian Creole horse breeds: Same origin but different diversity.

    abstract::In order to understand the genetic ancestry and mitochondrial DNA (mtDNA) diversity of current Colombian horse breeds we sequenced a 364-bp fragment of the mitocondrial DNA D-loop in 116 animals belonging to five Spanish horse breeds and the Colombian Paso Fino and Colombian Creole cattle horse breeds. Among Colombian...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/S1415-47572012005000064

    authors: Jimenez LM,Mendez S,Dunner S,Cañón J,Cortés O

    更新日期:2012-12-01 00:00:00

  • Comparative chromosomal mapping of microsatellite repeats reveals divergent patterns of accumulation in 12 Siluridae (Teleostei: Siluriformes) species.

    abstract::The freshwater family Siluridae occurs in Eurasia and is especially speciose in South and Southeast Asia, representing an important aquaculture and fishery targets. However, despite the restricted cytogenetic data, a high diploid number variation (from 2n=40 to 92) characterizes this fish group. Considering the large ...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/1678-4685-GMB-2020-0091

    authors: Ditcharoen S,Sassi FMC,Bertollo LAC,Molina WF,Liehr T,Saenjundaeng P,Tanomtong A,Supiwong W,Suwannapoom C,Cioffi MB

    更新日期:2020-11-06 00:00:00

  • Successful crosses between fungal-resistant wild species of Arachis (section Arachis) and Arachis hypogaea.

    abstract::Peanut (Arachis hypogaea) is the fifth most produced oil crop worldwide. Besides lack of water, fungal diseases are the most limiting factors for the crop. Several species of Arachis are resistant to certain pests and diseases. This study aimed to successfully cross the A-genome with B-K-A genome wild species previous...

    journal_title:Genetics and molecular biology

    pub_type: 杂志文章

    doi:10.1590/S1415-475738320140376

    authors: Fávero AP,Dos Santos RF,Simpson CE,Valls JF,Vello NA

    更新日期:2015-07-01 00:00:00