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Journal articles on the topic 'DNA Based Memory'

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Author: Grafiati

Published: 6 September 2023

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1

Deaton, Russell, and Junghuei Chen. "Conceptual and contextual DNA-based memory." International Journal of Knowledge-based and Intelligent Engineering Systems 10, no. 1 (February 5, 2006): 41–48. http://dx.doi.org/10.3233/kes-2006-10104.

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2

Garzon, Max H., Kiran C. Bobba, Andrew Neel, and Vinhthuy Phan. "DNA-Based Indexing." International Journal of Nanotechnology and Molecular Computation 2, no. 3 (July 2010): 25–45. http://dx.doi.org/10.4018/jnmc.2010070102.

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DNA has been acknowledged as a suitable medium for massively parallel computing and as a “smart” glue for self-assembly. In this paper, a third capability of DNA is described in detail as memory capable of encoding and processing large amounts of data so that information can be retrieved associatively based on content. The technique is based on a novel representation of data on DNA that can shed information on the way DNA-, RNA- and other biomolecules encode information, which may be potentially important in applications to fields like bioinformatics and genetics, and natural language processing. Analyses are also provided of the sensitivity, robustness, and bounds on the theoretical capacity of the memories. Finally, the potential use of the memories are illustrated with two applications, one in genomic analysis for identification and classification, another in information retrieval from text data in abiotic form.

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3

Sheth, Ravi U., and Harris H. Wang. "DNA-based memory devices for recording cellular events." Nature Reviews Genetics 19, no. 11 (September 20, 2018): 718–32. http://dx.doi.org/10.1038/s41576-018-0052-8.

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4

Yu, Xu, Yuwei Hu, Jason S. Kahn, Alessandro Cecconello, and Itamar Willner. "Orthogonal Dual-Triggered Shape-Memory DNA-Based Hydrogels." Chemistry - A European Journal 22, no. 41 (August 19, 2016): 14504–7. http://dx.doi.org/10.1002/chem.201603653.

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5

Takinoue, M., and A. Suyama. "Establishing a molecular memory system based on DNA hairpins." Seibutsu Butsuri 43, supplement (2003): S231. http://dx.doi.org/10.2142/biophys.43.s231_2.

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6

Takinoue, M., Y. Hatano, and Akira Suyama. "2P300 A massively parallel memory based on hairpin DNA." Seibutsu Butsuri 44, supplement (2004): S184. http://dx.doi.org/10.2142/biophys.44.s184_4.

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7

Lakhno, V. D., and A. V. Vinnikov. "Molecular devices based on DNA." Mathematical Biology and Bioinformatics 16, no. 1 (May 19, 2021): 115–35. http://dx.doi.org/10.17537/2021.16.115.

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It is shown that DNA molecule can be used for construction of different electronic devices. The results of investigation of DNA conducting properties are presented. The method of DNA based nanowires is considered. It is shown that the conducting properties of DNA can be used for making electronic nanobiochips, which have advantages in comparison with optical one due to their miniaturization, execution speed, absence of marking and exactness. It is also demonstrated the possibility of memory and logic devices made from DNA.

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8

Yamamoto, Masahito, Satoshi Kashiwamura, Azuma Ohuchi, and Masashi Furukawa. "Large-scale DNA memory based on the nested PCR." Natural Computing 7, no. 3 (March 19, 2008): 335–46. http://dx.doi.org/10.1007/s11047-008-9076-x.

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9

Takinoue, Masahiro, and Akira Suyama. "Molecular reactions for a molecular memory based on hairpin DNA." Chem-Bio Informatics Journal 4, no. 3 (2004): 93–100. http://dx.doi.org/10.1273/cbij.4.93.

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10

Expósito, Roberto R., Jorge González-Domínguez, and Juan Touriño. "SMusket: Spark-based DNA error correction on distributed-memory systems." Future Generation Computer Systems 111 (October 2020): 698–713. http://dx.doi.org/10.1016/j.future.2019.10.038.

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11

Hu, Yuwei, Weiwei Guo, Jason S. Kahn, Miguel Angel Aleman-Garcia, and Itamar Willner. "A Shape-Memory DNA-Based Hydrogel Exhibiting Two Internal Memories." Angewandte Chemie International Edition 55, no. 13 (February 24, 2016): 4210–14. http://dx.doi.org/10.1002/anie.201511201.

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12

Hu, Yuwei, Weiwei Guo, Jason S. Kahn, Miguel Angel Aleman-Garcia, and Itamar Willner. "A Shape-Memory DNA-Based Hydrogel Exhibiting Two Internal Memories." Angewandte Chemie 128, no. 13 (February 24, 2016): 4282–86. http://dx.doi.org/10.1002/ange.201511201.

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13

Bernabé-Orts, Joan Miquel, Alfredo Quijano-Rubio, Marta Vazquez-Vilar, Javier Mancheño-Bonillo, Victor Moles-Casas, Sara Selma, Silvia Gianoglio, Antonio Granell, and Diego Orzaez. "A memory switch for plant synthetic biology based on the phage ϕC31 integration system." Nucleic Acids Research 48, no. 6 (February 21, 2020): 3379–94. http://dx.doi.org/10.1093/nar/gkaa104.

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Abstract Synthetic biology has advanced from the setup of basic genetic devices to the design of increasingly complex gene circuits to provide organisms with new functions. While many bacterial, fungal and mammalian unicellular chassis have been extensively engineered, this progress has been delayed in plants due to the lack of reliable DNA parts and devices that enable precise control over these new synthetic functions. In particular, memory switches based on DNA site-specific recombination have been the tool of choice to build long-term and stable synthetic memory in other organisms, because they enable a shift between two alternative states registering the information at the DNA level. Here we report a memory switch for whole plants based on the bacteriophage ϕC31 site-specific integrase. The switch was built as a modular device made of standard DNA parts, designed to control the transcriptional state (on or off) of two genes of interest by alternative inversion of a central DNA regulatory element. The state of the switch can be externally operated by action of the ϕC31 integrase (Int), and its recombination directionality factor (RDF). The kinetics, memory, and reversibility of the switch were extensively characterized in Nicotiana benthamiana plants.

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14

Chen, Junghuei, Russell Deaton, and Yu-Zhen Wang. "A DNA-based memory with in vitro learning and associative recall." Natural Computing 4, no. 2 (June 2005): 83–101. http://dx.doi.org/10.1007/s11047-004-4002-3.

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15

Hatano, Y., M. Takinoue, and A. Suyama. "2P299 Development of a molecular memory based on surface-bound hairpin DNA." Seibutsu Butsuri 44, supplement (2004): S184. http://dx.doi.org/10.2142/biophys.44.s184_3.

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16

Allam, Tahani M. "MOTIFSM: Cloudera Motif DNA Finding Algorithm." International Journal of Information Technology and Computer Science 15, no. 4 (August 8, 2023): 10–18. http://dx.doi.org/10.5815/ijitcs.2023.04.02.

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Many studying systems of gene function work depend on the DNA motif. DNA motifs finding generate a lot of trails which make it complex. Regulation of gene expression is identified according to Transcription Factor Binding Sites (TFBSs). There are different algorithms explained, over the past decades, to get an accurate motif tool. The major problems for these algorithms are on the execution time and the memory size which depend on the probabilistic approaches. Our previous algorithm, called EIMF, is recently proposed to overcome these problems by rearranging data. Because cloud computing involves many resources, the challenge of mapping jobs to infinite computing resources is an NP-hard optimization problem. In this paper, we proposed an Impala framework for solving a motif finding algorithms in single and multi-user based on cloud computing. Also, the comparison between Cloud motif and previous EIMF algorithms is performed in three different motif group. The results obtained the Cloudera motif was a considerable finding algorithms in the experimental group that decreased the execution time and the Memory size, when compared with the previous EIMF algorithms. The proposed MOTIFSM algorithm based on the cloud computing decrease the execution time by 70% approximately in MOTIFSM than EIMF framework. Memory size also is decreased in MOTIFSM about 75% than EIMF.

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17

Abd-Alhalem, Samia M., Naglaa F. Soliman, Salah Eldin, S. E. Abd Elrahman, Nabil A. Ismail, El-Sayed M. El-Rabaie, and Fathi E. Abd El-Samie. "Spectral Features Based on Bidirectional Long Short-Term Memory for DNA Classification." Menoufia Journal of Electronic Engineering Research 28, no. 1 (December 1, 2019): 183–88. http://dx.doi.org/10.21608/mjeer.2019.77008.

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18

Jeng, Huei-Yau, Tzu-Chien Yang, Li Yang, James G. Grote, Hsin-Lung Chen, and Yu-Chueh Hung. "Non-volatile resistive memory devices based on solution-processed natural DNA biomaterial." Organic Electronics 54 (March 2018): 216–21. http://dx.doi.org/10.1016/j.orgel.2017.12.048.

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19

Fernandez-Rodriguez, Jesus, Lei Yang, Thomas E. Gorochowski, D. Benjamin Gordon, and Christopher A. Voigt. "Memory and Combinatorial Logic Based on DNA Inversions: Dynamics and Evolutionary Stability." ACS Synthetic Biology 4, no. 12 (November 24, 2015): 1361–72. http://dx.doi.org/10.1021/acssynbio.5b00170.

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20

Chandrasekaran, Arun Richard, Jibin Abraham Punnoose, Vibhav Valsangkar, Jia Sheng, and Ken Halvorsen. "Integration of a photocleavable element into DNA nanoswitches." Chemical Communications 55, no. 46 (2019): 6587–90. http://dx.doi.org/10.1039/c9cc03069g.

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21

Xu, Chengtao, Chao Zhao, Biao Ma, and Hong Liu. "Uncertainties in synthetic DNA-based data storage." Nucleic Acids Research 49, no. 10 (April 9, 2021): 5451–69. http://dx.doi.org/10.1093/nar/gkab230.

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Abstract Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.

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22

Hung, Yu-Chueh, Wei-Ting Hsu, Ting-Yu Lin, and Ljiljana Fruk. "Photoinduced write-once read-many-times memory device based on DNA biopolymer nanocomposite." Applied Physics Letters 99, no. 25 (December 19, 2011): 253301. http://dx.doi.org/10.1063/1.3671153.

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23

Kugonza, D. R., G. H. Kiwuwa, D. Mpairwe, H. Jianlin, M. Nabasirye, A. M. Okeyo, and O. Hanotte. "Accuracy of pastoralists’ memory-based kinship assignment of Ankole cattle: a microsatellite DNA analysis." Journal of Animal Breeding and Genetics 129, no. 1 (August 1, 2011): 30–40. http://dx.doi.org/10.1111/j.1439-0388.2011.00937.x.

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24

Jiang, Liming, Wanzhi Qiu, Feras Al-Dirini, Faruque M. Hossain, Robin Evans, and Efstratios Skafidas. "Feasibility study of molecular memory device based on DNA using methylation to store information." Journal of Applied Physics 120, no. 2 (July 14, 2016): 025501. http://dx.doi.org/10.1063/1.4954219.

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25

Liang, Lijuan, Yasushi Mitsumura, Kazuki Nakamura, Sei Uemura, Toshihide Kamata, and Norihisa Kobayashi. "Temperature dependence of transfer characteristics of OTFT memory based on DNA-CTMA gate dielectric." Organic Electronics 28 (January 2016): 294–98. http://dx.doi.org/10.1016/j.orgel.2015.11.003.

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26

Hirabayashi, Miki, Hirotada Ohashi, and Tai Kubo. "2P571 Kinetic Analysis of Regulatory Mechanism of Transcription-based DNA Memory Probe(53. Bioengineering,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S438. http://dx.doi.org/10.2142/biophys.46.s438_3.

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27

Liang, Li Juan, Yukimoto Tomoyashi, and Xian Fu Wei. "The Effect of Post-Annealing Temperature on the Performance of OTFT Memory." Applied Mechanics and Materials 748 (April 2015): 141–45. http://dx.doi.org/10.4028/www.scientific.net/amm.748.141.

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A nonvolatile memory based on an organic thin-film transistor (OTFT) with biopolymer of DNA-OTMA as the gate dielectric is fabricated. The device prepared by DNA-OTMA show a very large and metastable hysteresis in the transfer characteristics. In order to obtain the organic thin film transistor memory device with high electronic performance, one of the most widely used method such as post annealing have been applied to improve the quality of gate dielectric layer. In conclusion, the post-annealing at elevated temperatures plays a very important role in the performance of the OTFT memory device.

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28

Farzadfard, Fahim, and Timothy K. Lu. "Emerging applications for DNA writers and molecular recorders." Science 361, no. 6405 (August 30, 2018): 870–75. http://dx.doi.org/10.1126/science.aat9249.

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Natural life is encoded by evolvable, DNA-based memory. Recent advances in dynamic genome-engineering technologies, which we collectively refer to as in vivo DNA writing, have opened new avenues for investigating and engineering biology. This Review surveys these technological advances, outlines their prospects and emerging applications, and discusses the features and current limitations of these technologies for building various genetic circuits for processing and recording information in living cells.

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29

Wang, Chen, Michael Fadeev, Junji Zhang, Margarita Vázquez-González, Gilad Davidson-Rozenfeld, He Tian, and Itamar Willner. "Shape-memory and self-healing functions of DNA-based carboxymethyl cellulose hydrogels driven by chemical or light triggers." Chemical Science 9, no. 35 (2018): 7145–52. http://dx.doi.org/10.1039/c8sc02411a.

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Photoresponsive hydrogels crosslinked by trans-azobenzene/β-cyclodextrin and duplex DNA or K⁺-G-quadruplex are described. The hydrogels reveal shape-memory functions and self-healing properties.

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30

Torres García, Ana Victoria, María Concepción Vega-Hernández, Concha Antón Rubio, and Miguel Pérez-Fernández. "Mental Health in Women Victims of Gender Violence: Descriptive and Multivariate Analysis of Neuropsychological Functions and Depressive Symptomatology." International Journal of Environmental Research and Public Health 19, no. 1 (December 29, 2021): 346. http://dx.doi.org/10.3390/ijerph19010346.

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Female victims of abuse, as well as suffering from psychopathological disorders such as depression, can have neuropsychological sequelae affecting memory and attention, with serious consequences, both physical and psychological, in their daily lives. Therefore, the objective of this study is to analyse these sequelae that affect attention and memory, as well as the possible association of these sequelae to depression. A total of 68 women, victims of gender-based violence, between the ages of 15 and 62 participated in this study. The Luria DNA Battery (Neuropsychological Diagnosis of Adults) by Manga and Ramos (2000); and the Beck Depression Inventory (2011) were applied. It is shown that female victims of gender-based violence present poor short-term memory, attentional control, and score low on the Luria-DNA battery. Of these women, 60% suffer from some relevant type of depression. Through HJ-Biplot analysis, a direct relationship was found between memory and attentional control with the total score of the Luria battery. However, an inverse relationship was found between short-term memory and depression. In addition, three well-differentiated clusters of female victims of gender-based violence were identified. It is concluded that a lower rate of depression is observed in female victims of abuse when they have a more intact short-term memory.

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31

Choi, Yeongjae, Hyung Jong Bae, Amos C. Lee, Hansol Choi, Daewon Lee, Taehoon Ryu, Jinwoo Hyun, et al. "DNA Micro‐Disks for the Management of DNA‐Based Data Storage with Index and Write‐Once–Read‐Many (WORM) Memory Features." Advanced Materials 32, no. 37 (July 29, 2020): 2001249. http://dx.doi.org/10.1002/adma.202001249.

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32

Heller, Richard, Cathryn Lundberg, Chelsea Edelblute, Sezgi Arpag-Mcintosh, and Guilan Shi. "Immunotherapy for melanoma using nonviral plasmid DNA based approach." Journal of Immunology 200, no. 1_Supplement (May 1, 2018): 122.4. http://dx.doi.org/10.4049/jimmunol.200.supp.122.4.

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Abstract Malignant melanoma is the deadliest form of skin cancer. New immunotherapy approaches including anti-CTLA4, anti-PD-1 and anti-PD1-L1 have improved this prognosis for several patients. While the results obtained with these therapies are encouraging, there is still a need to establish improved therapies. IL-12 is a potent cytokine mediating antitumor activity. However, it has only achieved modest antitumor effects in clinical trials, often accompanied by unacceptable adverse events. We evaluated if intratumoral delivery of a plasmid encoding IL-12 using gene electrotransfer (GET) could be used to induce an anti-tumor response. Effective protocols delivering plasmids with GET directly into tumors induced not only local immune response, but a systemic one as well. We have been evaluating the specific response following pIL-12 delivery as well as the potential to combine with checkpoint inhibitors to determine if the response could be further augmented. Using a B16F10 mouse melanoma model, we show that melanoma exhibited unique immune cell composition within the tumor microenvironment after intratumoral injection of pIL12 with GET. The total number of memory immune cells was markedly increased in pIL12 GET melanoma groups compared with control group. pIL12 GET displayed significant regulation of multiple immune cell types, including CD8+ cells, regulatory T cells and myeloid cells, which were induced to mount a CD8+ immune response. It was also observed that there was an increase in PD-1 expression following pIl-12 delivery. Taken together, these findings suggest a sequence of immune activity following pIL12 GET. Further, these results suggest that pretreatment or simultaneous treatment with IL-12 may augment anti-PD1 therapy.

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33

Weber Boutros, Sydney, Vivek K. Unni, and Jacob Raber. "An Adaptive Role for DNA Double-Strand Breaks in Hippocampus-Dependent Learning and Memory." International Journal of Molecular Sciences 23, no. 15 (July 28, 2022): 8352. http://dx.doi.org/10.3390/ijms23158352.

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DNA double-strand breaks (DSBs), classified as the most harmful type of DNA damage based on the complexity of repair, lead to apoptosis or tumorigenesis. In aging, DNA damage increases and DNA repair decreases. This is exacerbated in disease, as post-mortem tissue from patients diagnosed with mild cognitive impairment (MCI) or Alzheimer’s disease (AD) show increased DSBs. A novel role for DSBs in immediate early gene (IEG) expression, learning, and memory has been suggested. Inducing neuronal activity leads to increases in DSBs and upregulation of IEGs, while increasing DSBs and inhibiting DSB repair impairs long-term memory and alters IEG expression. Consistent with this pattern, mice carrying dominant AD mutations have increased baseline DSBs, and impaired DSB repair is observed. These data suggest an adaptive role for DSBs in the central nervous system and dysregulation of DSBs and/or repair might drive age-related cognitive decline (ACD), MCI, and AD. In this review, we discuss the adaptive role of DSBs in hippocampus-dependent learning, memory, and IEG expression. We summarize IEGs, the history of DSBs, and DSBs in synaptic plasticity, aging, and AD. DSBs likely have adaptive functions in the brain, and even subtle alterations in their formation and repair could alter IEGs, learning, and memory.

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34

Bronner, Christian, Guy Fuhrmann, Frédéric L. Chédin, Marcella Macaluso, and Sirano Dhe-Paganon. "UHRF1 Links the Histone Code and DNA Methylation to Ensure Faithful Epigenetic Memory Inheritance." Genetics & Epigenetics 2 (January 2009): GEG.S3992. http://dx.doi.org/10.4137/geg.s3992.

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Epigenetics is the study of the transmission of cell memory through mitosis or meiosis that is not based on the DNA sequence. At the molecular level the epigenetic memory of a cell is embedded in DNA methylation, histone post-translational modifications, RNA interference and histone isoform variation. There is a tight link between histone post-translational modifications (the histone code) and DNA methylation, as modifications of histones contribute to the establishment of DNA methylation patterns and vice versa. Interestingly, proteins have recently been identified that can simultaneously read both methylated DNA and the histone code. UHRF1 fulfills these requirements by having unique structural domains that allow concurrent recognition of histone modifications and methylated DNA. Herein, we review our current knowledge of UHRF1 and discuss how this protein ensures the link between histone marks and DNA methylation. Understanding the molecular functions of this protein may reveal the physiological relevance of the linkage between these layers of epigenetic marks.

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35

Salimi, M., S. Fathizadeh, and S. Behnia. "Molecular spin switch triggered by voltage and magnetic field: towards DNA-based molecular devices." Physica Scripta 97, no. 5 (April 4, 2022): 055005. http://dx.doi.org/10.1088/1402-4896/ac5af1.

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Abstract Spin state switching of the DNA sequences due to external stimuli is investigated theoretically. A molecular-based memory or logic device such as a spin switch could be directly realized within an electronic circuit. The DNA system is subjected to an electrical potential difference through the metal leads for controlling the spin transport. The spectral analysis of spin states demonstrates that voltage operates as a crucial tool to turn the switch on. The width of the functional voltage range changes when the system is subjected to an external magnetic field. The magnetic field reduces the system’s symmetry and drives the system to an extended state. Hence, the voltage and magnetic field can modulate the spin transport properties of DNA. The ability to control the spin localization/delocalization states in DNA chains opens up a new approach for efficient computation and data storage.

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36

Taghipour, Hassan, Mahdi Rezaei, and Heydar Ali Esmaili. "Solving the 0/1 Knapsack Problem by a Biomolecular DNA Computer." Advances in Bioinformatics 2013 (February 18, 2013): 1–6. http://dx.doi.org/10.1155/2013/341419.

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Solving some mathematical problems such as NP-complete problems by conventional silicon-based computers is problematic and takes so long time. DNA computing is an alternative method of computing which uses DNA molecules for computing purposes. DNA computers have massive degrees of parallel processing capability. The massive parallel processing characteristic of DNA computers is of particular interest in solving NP-complete and hard combinatorial problems. NP-complete problems such as knapsack problem and other hard combinatorial problems can be easily solved by DNA computers in a very short period of time comparing to conventional silicon-based computers. Sticker-based DNA computing is one of the methods of DNA computing. In this paper, the sticker based DNA computing was used for solving the 0/1 knapsack problem. At first, a biomolecular solution space was constructed by using appropriate DNA memory complexes. Then, by the application of a sticker-based parallel algorithm using biological operations, knapsack problem was resolved in polynomial time.

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37

González, César, Mariano Pérez, Juan M. Orduña, Javier Chaves, and Ana-Bárbara García. "HPG-HMapper: A DNA hydroxymethylation analysis tool." International Journal of High Performance Computing Applications 34, no. 1 (April 15, 2019): 57–65. http://dx.doi.org/10.1177/1094342019840792.

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DNA methylation (mC) and hydroxymethylation (hmC) can significantly affect the normal human development, as well as health and disease status. hmC studies require not only specific treatment of DNA, but also software tools for their analysis. However, there are no software tools capable of analyzing DNA hmC currently. In this article, we propose HPG-HMapper, a parallel software tool for analyzing the DNA hmC data obtained by ten-eleven translocation–assisted bisulfite sequencing. This tool takes as input data the output files of mC aligner tools, and it yields mC maps and the accounting of methylated and hydroxymethylated bases on each chromosome. The design of this tool includes the consideration of different approaches, one of them based on binary trees and the other one based on bit arrays. The performance evaluation results show that a hybrid implementation is the most efficient option, allowing fast read and update operations while keeping a small memory footprint.

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38

Farkaš, Tomáš, Jozef Sitarčík, Broňa Brejová, and Mária Lucká. "SWSPM: A Novel Alignment-Free DNA Comparison Method Based on Signal Processing Approaches." Evolutionary Bioinformatics 15 (January 2019): 117693431984907. http://dx.doi.org/10.1177/1176934319849071.

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Computing similarity between 2 nucleotide sequences is one of the fundamental problems in bioinformatics. Current methods are based mainly on 2 major approaches: (1) sequence alignment, which is computationally expensive, and (2) faster, but less accurate, alignment-free methods based on various statistical summaries, for example, short word counts. We propose a new distance measure based on mathematical transforms from the domain of signal processing. To tolerate large-scale rearrangements in the sequences, the transform is computed across sliding windows. We compare our method on several data sets with current state-of-art alignment-free methods. Our method compares favorably in terms of accuracy and outperforms other methods in running time and memory requirements. In addition, it is massively scalable up to dozens of processing units without the loss of performance due to communication overhead. Source files and sample data are available at https://bitbucket.org/fiitstubioinfo/swspm/src

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39

Younesian, Samareh, Amir-Mohammad Yousefi, Majid Momeny, Seyed H. Ghaffari, and Davood Bashash. "The DNA Methylation in Neurological Diseases." Cells 11, no. 21 (October 31, 2022): 3439. http://dx.doi.org/10.3390/cells11213439.

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DNA methylation is critical for the normal development and functioning of the human brain, such as the proliferation and differentiation of neural stem cells, synaptic plasticity, neuronal reparation, learning, and memory. Despite the physical stability of DNA and methylated DNA compared to other epigenetic modifications, some DNA methylation-based biomarkers have translated into clinical practice. Increasing reports indicate a strong association between DNA methylation profiles and various clinical outcomes in neurological diseases, making DNA methylation profiles valuable as novel clinical markers. In this review, we aim to discuss the latest evidence concerning DNA methylation alterations in the development of neurodegenerative, neurodevelopmental, and neuropsychiatric diseases. We also highlighted the relationship of DNA methylation alterations with the disease progression and outcome in many neurological diseases such as Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis, frontotemporal dementia, and autism.

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40

Qaid, Gamil R. S., and Nadhem Sultan Ebrahim. "A Lightweight Cryptographic Algorithm Based on DNA Computing for IoT Devices." Security and Communication Networks 2023 (May 8, 2023): 1–12. http://dx.doi.org/10.1155/2023/9967129.

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Internet of Things (IoT) applications are used in almost every part of our life, so it is important to protect the sensitive data and information that is transmitted over wireless networks such as images and documents. The IoT devices have limited computational resources; they are called limited devices due to their limited processors and memory size. Traditional encryption methods require a lot of computing power; therefore, it is difficult to implement traditional cryptographic algorithm on IoT processor. Finally, a new, lightweight encryption method based on the DNA sequence is proposed to suit the IoT devices in a way to make an easy and secure the communications among the IoT devices. DNA sequences are very random, so we have used it to make a strong secret key that is hard for attackers to break. The proposed method has an advantage in terms of efficiency and strength. Experiments and security tests show that the proposed encryption system not only has a good encryption effect and can withstand known attacks, but it is also fast enough for real-world use. The DNA key is used to encrypt files using two simple and reliable methods such as substitution and transposition procedures that meet IoT computational requirements. In addition, when compared with other encryption algorithms, the experimental results shows that the key size, encryption time, and distortion preparation are all superior.

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Salikhov, Kamil. "Improved Compression of DNA Sequencing Data with Cascading Bloom Filters." International Journal of Foundations of Computer Science 29, no. 08 (December 2018): 1249–55. http://dx.doi.org/10.1142/s0129054118430013.

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Modern DNA sequencing technologies generate prodigious volumes of sequence data consisting of short DNA fragments (reads). Storing and transferring this data is often challenging. With this motivation, several specialized compression methods have been developed. In this paper, we present an improvement of the lossless reference-free compression algorithm, suggested by Rozov et al., based on the technique of cascading Bloom filters. Through computational experiments on real data, we demonstrate that our method results in a significant associated memory reduction in practice.

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Xie, Jiaxiang, Leijie Xie, Huixian Wei, Xiao-Jiang Li, and Li Lin. "Dynamic Regulation of DNA Methylation and Brain Functions." Biology 12, no. 2 (January 18, 2023): 152. http://dx.doi.org/10.3390/biology12020152.

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DNA cytosine methylation is a principal epigenetic mechanism underlying transcription during development and aging. Growing evidence suggests that DNA methylation plays a critical role in brain function, including neurogenesis, neuronal differentiation, synaptogenesis, learning, and memory. However, the mechanisms underlying aberrant DNA methylation in neurodegenerative diseases remain unclear. In this review, we provide an overview of the contribution of 5-methycytosine (5mC) and 5-hydroxylcytosine (5hmC) to brain development and aging, with a focus on the roles of dynamic 5mC and 5hmC changes in the pathogenesis of neurodegenerative diseases, particularly Alzheimer’s disease (AD), Parkinson’s disease (PD), and Huntington’s disease (HD). Identification of aberrant DNA methylation sites could provide potential candidates for epigenetic-based diagnostic and therapeutic strategies for neurodegenerative diseases.

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Lu, Weizhong, Xiaoyi Chen, Yu Zhang, Hongjie Wu, Yijie Ding, Jiawei Shen, Shixuan Guan, and Haiou Li. "Research on DNA-Binding Protein Identification Method Based on LSTM-CNN Feature Fusion." Computational and Mathematical Methods in Medicine 2022 (June 2, 2022): 1–10. http://dx.doi.org/10.1155/2022/9705275.

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Protein is closely related to life activities. As a kind of protein, DNA-binding protein plays an irreplaceable role in life activities. Therefore, it is very important to study DNA-binding protein, which is a subject worthy of study. Although traditional biotechnology has high precision, its cost and efficiency are increasingly unable to meet the needs of modern society. Machine learning methods can make up for the deficiencies of biological experimental techniques to a certain extent, but they are not as simple and fast as deep learning for data processing. In this paper, a deep learning framework based on parallel long and short-term memory(LSTM) and convolutional neural networks(CNN) was proposed to identify DNA-binding protein. This model can not only further extract the information and features of protein sequences, but also the features of evolutionary information. Finally, the two features are combined for training and testing. On the PDB2272 dataset, compared with PDBP_Fusion model, Accuracy(ACC) and Matthew’s Correlation Coefficient (MCC) increased by 3.82% and 7.98% respectively. The experimental results of this model have certain advantages.

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Bradde, Serena, Armita Nourmohammad, Sidhartha Goyal, and Vijay Balasubramanian. "The size of the immune repertoire of bacteria." Proceedings of the National Academy of Sciences 117, no. 10 (February 18, 2020): 5144–51. http://dx.doi.org/10.1073/pnas.1903666117.

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Some bacteria and archaea possess an immune system, based on the CRISPR-Cas mechanism, that confers adaptive immunity against viruses. In such species, individual prokaryotes maintain cassettes of viral DNA elements called spacers as a memory of past infections. Typically, the cassettes contain several dozen expressed spacers. Given that bacteria can have very large genomes and since having more spacers should confer a better memory, it is puzzling that so little genetic space would be devoted by prokaryotes to their adaptive immune systems. Here, assuming that CRISPR functions as a long-term memory-based defense against a diverse landscape of viral species, we identify a fundamental tradeoff between the amount of immune memory and effectiveness of response to a given threat. This tradeoff implies an optimal size for the prokaryotic immune repertoire in the observational range.

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Kim, Eung-Sam, Jung Sook Kim, Nishan Chakrabarty, and Chul-Ho Yun. "Covalent Positioning of Single DNA Molecules for Nanopatterning." Nanomaterials 11, no. 7 (June 30, 2021): 1725. http://dx.doi.org/10.3390/nano11071725.

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Bottom-up micropatterning or nanopatterning can be viewed as the localization of target molecules to the desired area of a surface. A majority of these processes rely on the physical adsorption of ink-like molecules to the paper-like surface, resulting in unstable immobilization of the target molecules owing to their noncovalent linkage to the surface. Herein, successive single nick-sealing facilitated the covalent immobilization of individual DNA molecules at defined positions on a dendron-coated silicon surface using atomic force microscopy. The covalently-patterned ssDNA was visualized when the streptavidin-coated gold nanoparticles bound to the biotinylated DNA. The successive covalent positioning of the target DNA under ambient conditions may facilitate the bottom-up construction of DNA-based durable nanostructures, nanorobots, or memory system.

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Lau, Chun H., Ryan Reeves, and Edward L. Bolt. "Adaptation processes that build CRISPR immunity: creative destruction, updated." Essays in Biochemistry 63, no. 2 (June 11, 2019): 227–35. http://dx.doi.org/10.1042/ebc20180073.

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Abstract Prokaryotes can defend themselves against invading mobile genetic elements (MGEs) by acquiring immune memory against them. The memory is a DNA database located at specific chromosomal sites called CRISPRs (clustered regularly interspaced short palindromic repeats) that store fragments of MGE DNA. These are utilised to target and destroy returning MGEs, preventing re-infection. The effectiveness of CRISPR-based immune defence depends on ‘adaptation’ reactions that capture and integrate MGE DNA fragments into CRISPRs. This provides the means for immunity to be delivered against MGEs in ‘interference’ reactions. Adaptation and interference are catalysed by Cas (CRISPR-associated) proteins, aided by enzymes well known for other roles in cells. We survey the molecular biology of CRISPR adaptation, highlighting entirely new developments that may help us to understand how MGE DNA is captured. We focus on processes in Escherichia coli, punctuated with reference to other prokaryotes that illustrate how common requirements for adaptation, DNA capture and integration, can be achieved in different ways. We also comment on how CRISPR adaptation enzymes, and their antecedents, can be utilised for biotechnology.

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Cartwright, Emily K., David Palesch, Maud Mavigner, Mirko Paiardini, Ann Chahroudi, and Guido Silvestri. "Initiation of Antiretroviral Therapy Restores CD4+T Memory Stem Cell Homeostasis in Simian Immunodeficiency Virus-Infected Macaques." Journal of Virology 90, no. 15 (May 11, 2016): 6699–708. http://dx.doi.org/10.1128/jvi.00492-16.

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ABSTRACTTreatment of human immunodeficiency virus (HIV) infection with antiretroviral therapy (ART) has significantly improved prognosis. Unfortunately, interruption of ART almost invariably results in viral rebound, attributed to a pool of long-lived, latently infected cells. Based on their longevity and proliferative potential, CD4+T memory stem cells (TSCM) have been proposed as an important site of HIV persistence. In a previous study, we found that in simian immunodeficiency virus (SIV)-infected rhesus macaques (RM), CD4+TSCMare preserved in number but show (i) a decrease in the frequency of CCR5+cells, (ii) an expansion of the fraction of proliferating Ki-67+cells, and (iii) high levels of SIV DNA. To understand the impact of ART on both CD4+TSCMhomeostasis and virus persistence, we conducted a longitudinal analysis of these cells in the blood and lymph nodes of 25 SIV-infected RM. We found that ART induced a significant restoration of CD4+CCR5+TSCMboth in blood and in lymph nodes and a reduction in the fraction of proliferating CD4+Ki-67+TSCMin blood (but not lymph nodes). Importantly, we found that the level of SIV DNA in CD4+transitional memory (TTM) and effector memory (TEM) T cells declined ∼100-fold after ART in both blood and lymph nodes, while the level of SIV DNA in CD4+TSCMand central memory T cells (TCM-) did not significantly change. These data suggest that ART is effective at partially restoring CD4+TSCMhomeostasis, and the observed stable level of virus in TSCMsupports the hypothesis that these cells are a critical contributor to SIV persistence.IMPORTANCEUnderstanding the roles of various CD4+T cell memory subsets in immune homeostasis and HIV/SIV persistence during antiretroviral therapy (ART) is critical to effectively treat and cure HIV infection. T memory stem cells (TSCM) are a unique memory T cell subset with enhanced self-renewal capacity and the ability to differentiate into other memory T cell subsets, such as central and transitional memory T cells (TCMand TTM, respectively). CD4+TSCMare disrupted but not depleted during pathogenic SIV infection. We find that ART is partially effective at restoring CD4+TSCMhomeostasis and that SIV DNA harbored within this subset contracts more slowly than virus harbored in shorter-lived subsets, such as TTMand effector memory (TEM). Because of their ability to persist long-term in an individual, understanding the dynamics of virally infected CD4+TSCMduring suppressive ART is important for future therapeutic interventions aimed at modulating immune activation and purging the HIV reservoir.

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Kowalski, Tomasz M., and Szymon Grabowski. "PgRC: pseudogenome-based read compressor." Bioinformatics 36, no. 7 (December 9, 2019): 2082–89. http://dx.doi.org/10.1093/bioinformatics/btz919.

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Abstract Motivation The amount of sequencing data from high-throughput sequencing technologies grows at a pace exceeding the one predicted by Moore’s law. One of the basic requirements is to efficiently store and transmit such huge collections of data. Despite significant interest in designing FASTQ compressors, they are still imperfect in terms of compression ratio or decompression resources. Results We present Pseudogenome-based Read Compressor (PgRC), an in-memory algorithm for compressing the DNA stream, based on the idea of building an approximation of the shortest common superstring over high-quality reads. Experiments show that PgRC wins in compression ratio over its main competitors, SPRING and Minicom, by up to 15 and 20% on average, respectively, while being comparably fast in decompression. Availability and implementation PgRC can be downloaded from https://github.com/kowallus/PgRC. Supplementary information Supplementary data are available at Bioinformatics online.

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Sohsah, Gihad N., Ali Reza Ibrahimzada, Huzeyfe Ayaz, and Ali Cakmak. "Scalable classification of organisms into a taxonomy using hierarchical supervised learners." Journal of Bioinformatics and Computational Biology 18, no. 05 (October 2020): 2050026. http://dx.doi.org/10.1142/s0219720020500262.

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Accurately identifying organisms based on their partially available genetic material is an important task to explore the phylogenetic diversity in an environment. Specific fragments in the DNA sequence of a living organism have been defined as DNA barcodes and can be used as markers to identify species efficiently and effectively. The existing DNA barcode-based classification approaches suffer from three major issues: (i) most of them assume that the classification is done within a given taxonomic class and/or input sequences are pre-aligned, (ii) highly performing classifiers, such as SVM, cannot scale to large taxonomies due to high memory requirements, (iii) mutations and noise in input DNA sequences greatly reduce the taxonomic classification score. In order to address these issues, we propose a multi-level hierarchical classifier framework to automatically assign taxonomy labels to DNA sequences. We utilize an alignment-free approach called spectrum kernel method for feature extraction. We build a proof-of-concept hierarchical classifier with two levels, and evaluated it on real DNA sequence data from barcode of life data systems. We demonstrate that the proposed framework provides higher f1-score than regular classifiers. Besides, hierarchical framework scales better to large datasets enabling researchers to employ classifiers with high classification performance and high memory requirement on large datasets. Furthermore, we show that the proposed framework is more robust to mutations and noise in sequence data than the non-hierarchical classifiers.

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Cheng, Xin, Jun Wang, Qianyue Li, and Taigang Liu. "BiLSTM-5mC: A Bidirectional Long Short-Term Memory-Based Approach for Predicting 5-Methylcytosine Sites in Genome-Wide DNA Promoters." Molecules 26, no. 24 (December 7, 2021): 7414. http://dx.doi.org/10.3390/molecules26247414.

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An important reason of cancer proliferation is the change in DNA methylation patterns, characterized by the localized hypermethylation of the promoters of tumor-suppressor genes together with an overall decrease in the level of 5-methylcytosine (5mC). Therefore, identifying the 5mC sites in the promoters is a critical step towards further understanding the diverse functions of DNA methylation in genetic diseases such as cancers and aging. However, most wet-lab experimental techniques are often time consuming and laborious for detecting 5mC sites. In this study, we proposed a deep learning-based approach, called BiLSTM-5mC, for accurately identifying 5mC sites in genome-wide DNA promoters. First, we randomly divided the negative samples into 11 subsets of equal size, one of which can form the balance subset by combining with the positive samples in the same amount. Then, two types of feature vectors encoded by the one-hot method, and the nucleotide property and frequency (NPF) methods were fed into a bidirectional long short-term memory (BiLSTM) network and a full connection layer to train the 22 submodels. Finally, the outputs of these models were integrated to predict 5mC sites by using the majority vote strategy. Our experimental results demonstrated that BiLSTM-5mC outperformed existing methods based on the same independent dataset.

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