Journal articles: 'DNA storage systems'

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Kruglik, Stanislav, Gregory Kucherov, Kamilla Nazirkhanova, and Mikhail Filitov. "Information-theoretic problems of DNA-based storage systems." Information and Control Systems, no. 3 (June 29, 2021): 39–52. http://dx.doi.org/10.31799/1684-8853-2021-3-39-52.

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Introduction: Currently, we witness an explosive growth in the amount of information produced by humanity. This raises new fundamental problems of its efficient storage and processing. Commonly used magnetic, optical, and semiconductor information storage devices have several drawbacks related to small information density and limited durability. One of the promising novel approaches to solving these problems is DNA-based data storage. Purpose: An overview of modern DNA-based storage systems and related information-theoretic problems. Results: The current state of the art of DNA-based storage systems is reviewed. Types of errors occurring in them as well as corresponding error-correcting codes are analized. The disadvantages of these codes are shown, and possible pathways for improvement are mentioned. Proposed information-theoretic models of DNA-based storage systems are analyzed, and their limitation highlighted. In conclusion, main obstacles to practical implementation of DNA-based storage systems are formulated, which can be potentially overcome using information-theoretic methods considered in this overview.

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Tomek, Kyle J., Kevin Volkel, Alexander Simpson, Austin G. Hass, Elaine W. Indermaur, James M. Tuck, and Albert J. Keung. "Driving the Scalability of DNA-Based Information Storage Systems." ACS Synthetic Biology 8, no. 6 (May 22, 2019): 1241–48. http://dx.doi.org/10.1021/acssynbio.9b00100.

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Minhas-Khan, Aamir, Morteza Ghafar-Zadeh, Tina Shaffaf, Saghi Forouhi, Anthony Scime, Sebastian Magierowski, and Ebrahim Ghafar-Zadeh. "UV-Vis Spectrophotometric Analysis of DNA Retrieval for DNA Storage Applications." Actuators 10, no. 10 (September 24, 2021): 246. http://dx.doi.org/10.3390/act10100246.

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Informational Deoxyribonucleic Acid (iDNA) has gained the attention of many researchers and pioneer companies for the development of novel storage systems for the long-term and high-density storing of information. This research focuses on the physical storage of iDNA strands to address some of the current challenges by evaluating the accuracy of the process of iDNA retrieval from the surface after the dehydration process. For this aim, a UV-Vis spectrophotometric technique was used to measure the concentration of the DNA samples. Although spectroscopy has been widely employed for the evaluation of DNA concentration and contamination in a solution, it has not been used to investigate dry-state DNA, which is one of the preferred storage formats for the long-term retention of information. These results demonstrate that the UV-Vis spectrophotometric technique can be used to accurately measure dry-state DNA before the retrieval and its residues after the DNA retrieval process. This paper further examines the storage/retrieval process by investigating the relationship between the storage time and the amount of retrieved DNA or the DNA residue left on various surfaces. Based on the experimental results demonstrated and discussed in this paper, UV-Vis spectrophotometry can be used for monitoring dry-state DNA with a high accuracy larger than 98%. Moreover, these results reveal that the hydrophilicity and hydrophobicity of the surface do not significantly affect DNA retrieval over a one-month time period.

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Löchel, Hannah F., Marius Welzel, Georges Hattab, Anne-Christin Hauschild, and Dominik Heider. "Fractal construction of constrained code words for DNA storage systems." Nucleic Acids Research 50, no. 5 (December 15, 2021): e30-e30. http://dx.doi.org/10.1093/nar/gkab1209.

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Abstract The use of complex biological molecules to solve computational problems is an emerging field at the interface between biology and computer science. There are two main categories in which biological molecules, especially DNA, are investigated as alternatives to silicon-based computer technologies. One is to use DNA as a storage medium, and the other is to use DNA for computing. Both strategies come with certain constraints. In the current study, we present a novel approach derived from chaos game representation for DNA to generate DNA code words that fulfill user-defined constraints, namely GC content, homopolymers, and undesired motifs, and thus, can be used to build codes for reliable DNA storage systems.

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Lenz, Andreas, Paul H. Siegel, Antonia Wachter-Zeh, and Eitan Yaakobi. "Coding Over Sets for DNA Storage." IEEE Transactions on Information Theory 66, no. 4 (April 2020): 2331–51. http://dx.doi.org/10.1109/tit.2019.2961265.

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Schouhamer Immink, Kees A., and Kui Cai. "Design of Capacity-Approaching Constrained Codes for DNA-Based Storage Systems." IEEE Communications Letters 22, no. 2 (February 2018): 224–27. http://dx.doi.org/10.1109/lcomm.2017.2775608.

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Shomorony, Ilan, and Reinhard Heckel. "DNA-Based Storage: Models and Fundamental Limits." IEEE Transactions on Information Theory 67, no. 6 (June 2021): 3675–89. http://dx.doi.org/10.1109/tit.2021.3058966.

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Song, Xin, Shalin Shah, and John Reif. "Multidimensional data organization and random access in large-scale DNA storage systems." Theoretical Computer Science 894 (November 2021): 190–202. http://dx.doi.org/10.1016/j.tcs.2021.09.021.

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Kovacevic, Mladen, and Vincent Y. F. Tan. "Asymptotically Optimal Codes Correcting Fixed-Length Duplication Errors in DNA Storage Systems." IEEE Communications Letters 22, no. 11 (November 2018): 2194–97. http://dx.doi.org/10.1109/lcomm.2018.2868666.

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Arokiaraj Jovith, A., S. Rama Sree, Gudikandhula Narasimha Rao, K. Vijaya Kumar, Woong Cho, Gyanendra Prasad Joshi, and Sung Won Kim. "DNA Computing with Water Strider Based Vector Quantization for Data Storage Systems." Computers, Materials & Continua 74, no. 3 (2023): 6429–44. http://dx.doi.org/10.32604/cmc.2023.031817.

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Sais, Manar, Najat Rafalia, and Jaafar Abouchabaka. "DNA technology for big data storage and error detection solutions: Hamming code vs Cyclic Redundancy Check (CRC)." E3S Web of Conferences 412 (2023): 01090. http://dx.doi.org/10.1051/e3sconf/202341201090.

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There is an increasing need for high-capacity, highdensity storage media that can retain data for a long time, due to the exponential development in the capacity of information generated. The durability and high information density of synthetic deoxyribonucleic acid (DNA) make it an attractive and promising medium for data storage. DNA data storage technology is expected to revolutionize data storage in the coming years, replacing various Big Data storage technologies. As a medium that addresses the need for high-latency, immutable information storage, DNA has several potential advantages. One of the key advantages of DNA storage is its extraordinary density. Theoretically, a gram of DNA can encode 455 exabytes, or 2 bits per nucleotide. Unlike other digital storage media, synthetic DNA enables large quantities of data to be stored in a biological medium. This reduces the need for traditional storage media such as hard disks, which consume energy and require materials such as plastic or metals, and also often leads to the generation of electronic waste when they become obsolete or damaged. Additionally, although DNA degrades over thousands of years under non-ideal conditions, it is generally readable. Furthermore, as DNA possesses natural reading and writing enzymes as part of its biological functions, it is expected to remain the standard for data retrieval in the foreseeable future. However, the high error rate poses a significant challenge for DNA-based information coding strategies. Currently, it is impossible to execute DNA strand synthesis, amplification, or sequencing errors-free. In order to utilize synthetic DNA as a storage medium for digital data, specialized systems and solutions for direct error detection and correction must be implemented. The goal of this paper is to introduce DNA storage technology, outline the benefits and added value of this approach, and present an experiment comparing the effectiveness of two error detection and correction codes (Hamming and CRC) used in the DNA data storage strategy.

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Wei, Hengjia, and Moshe Schwartz. "Improved Coding Over Sets for DNA-Based Data Storage." IEEE Transactions on Information Theory 68, no. 1 (January 2022): 118–29. http://dx.doi.org/10.1109/tit.2021.3119584.

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Coudy, Delphine, Marthe Colotte, Aurélie Luis, Sophie Tuffet, and Jacques Bonnet. "Long term conservation of DNA at ambient temperature. Implications for DNA data storage." PLOS ONE 16, no. 11 (November 11, 2021): e0259868. http://dx.doi.org/10.1371/journal.pone.0259868.

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DNA conservation is central to many applications. This leads to an ever-increasing number of samples which are more and more difficult and costly to store or transport. A way to alleviate this problem is to develop procedures for storing samples at room temperature while maintaining their stability. A variety of commercial systems have been proposed but they fail to completely protect DNA from deleterious factors, mainly water. On the other side, Imagene company has developed a procedure for long-term conservation of biospecimen at room temperature based on the confinement of the samples under an anhydrous and anoxic atmosphere maintained inside hermetic capsules. The procedure has been validated by us and others for purified RNA, and for DNA in buffy coat or white blood cells lysates, but a precise determination of purified DNA stability is still lacking. We used the Arrhenius law to determine the DNA degradation rate at room temperature. We found that extrapolation to 25°C gave a degradation rate constant equivalent to about 1 cut/century/100 000 nucleotides, a stability several orders of magnitude larger than the current commercialized processes. Such a stability is fundamental for many applications such as the preservation of very large DNA molecules (particularly interesting in the context of genome sequencing) or oligonucleotides for DNA data storage. Capsules are also well suited for this latter application because of their high capacity. One can calculate that the 64 zettabytes of data produced in 2020 could be stored, standalone, for centuries, in about 20 kg of capsules.

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Tavella, Federico, Alberto Giaretta, Mauro Conti, and Sasitharan Balasubramaniam. "A machine learning-based approach to detect threats in bio-cyber DNA storage systems." Computer Communications 187 (April 2022): 59–70. http://dx.doi.org/10.1016/j.comcom.2022.01.023.

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Daggubati, Siva Phanindra, Venkata Rao Kasukurthi, and Prasad Reddy PVGD. "Cryptography and Reference Sequence Based DNA/RNA Sequence Compression Algorithms." Ingénierie des systèmes d information 27, no. 3 (June 30, 2022): 509–14. http://dx.doi.org/10.18280/isi.270319.

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This paper proposes two methods for the compression of biological sequences like DNA/RNA. Although many algorithms both lossy and lossless exist in the literature, they vary by the compression ratio. Moreover, existing algorithms show different compression ratios for different inputs. Our proposed methods exhibit nearly constant compression ratio which helps us to know the amount of storage needed in advance. For the first method, we call it CryptoCompress, we use a blend of Cryptographic hash function and partition theory to achieve this compression. The second method, we call it RefCompress, uses a reference DNA for compression. This paper showcases that the proposed methods have constant compression ratio compared to most of the existing methods.

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Nguyen, Tuan Thanh, Kui Cai, Kees A. Schouhamer Immink, and Han Mao Kiah. "Capacity-Approaching Constrained Codes With Error Correction for DNA-Based Data Storage." IEEE Transactions on Information Theory 67, no. 8 (August 2021): 5602–13. http://dx.doi.org/10.1109/tit.2021.3066430.

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Jain, Siddharth, Farzad Farnoud Hassanzadeh, Moshe Schwartz, and Jehoshua Bruck. "Duplication-Correcting Codes for Data Storage in the DNA of Living Organisms." IEEE Transactions on Information Theory 63, no. 8 (August 2017): 4996–5010. http://dx.doi.org/10.1109/tit.2017.2688361.

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Tabatabaei, S. Kasra, Bach Pham, Chao Pan, Jingqian Liu, Shubham Chandak, Spencer A. Shorkey, Alvaro G. Hernandez, et al. "Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing." Nano Letters 22, no. 5 (February 25, 2022): 1905–14. http://dx.doi.org/10.1021/acs.nanolett.1c04203.

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Srimathi, E., and S. P. Chokkalingam. "Improved Cloud Storage Encryption Using Block Cipher-Based DNA Anti-Codify Model." Computer Systems Science and Engineering 47, no. 1 (2023): 903–18. http://dx.doi.org/10.32604/csse.2023.029790.

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Kondratskaya, V. A., M. S. Pokrovskaya, Yu V. Doludin, A. L. Borisova, A. S. Limonova, А. N. Meshkov, and O. M. Drapkina. "Influence of preanalytical variables on the quality of cell-free DNA. Biobanking of cell-free DNA material." Cardiovascular Therapy and Prevention 20, no. 8 (January 10, 2022): 3114. http://dx.doi.org/10.15829/1728-8800-2021-3114.

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The search for early disease markers and the development of diagnostic systems has recently been expanding within genomics. Genomic deoxyribonucleic acid (DNA), cell-free DNA (cfDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. It has been shown that cfDNA that enters the bloodstream, in particular, as a result of apoptosis, necrosis, active tumor secretion and metastasis, is of great importance for studying molecular mechanisms of the pathological process and application in clinical practice. Circulating nucleic acid analysis can be used to monitor response to treatment, assess drug resistance, and quantify minimal residual disease. The review article reflects the following information about the biomaterial: source of cfDNA, methods of cfDNA isolation, storage and use for the diagnosis of certain diseases. Cell-free DNA can be present in biological fluids such as blood, urine, saliva, synovial and cerebrospinal fluid. In most cases, cfDNA is isolated from blood derivatives (serum and plasma), while it is most correct to use blood plasma for cfDNA isolation. Optimal and economically justifiable is the use of ethylenediaminetetra-acetic acid tubes for taking blood and obtaining plasma with subsequent cfDNA isolation. There is evidence that the optimal shelf life in an ethylenediaminetetra-acetic acid tube from the moment of blood sampling to subsequent isolation is a 2-hour interval. After centrifugation, cfDNA in plasma (or serum) can be stored for a long time at a temperature of -80O C. Storage at -20O C is undesirable, since DNA fragmentation increases.

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Marelli, Alessia, Thomas Chiozzi, Nicholas Battistini, Lorenzo Zuolo, Rino Micheloni, and Cristian Zambelli. "Integrating FPGA Acceleration in the DNAssim Framework for Faster DNA-Based Data Storage Simulations." Electronics 12, no. 12 (June 10, 2023): 2621. http://dx.doi.org/10.3390/electronics12122621.

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DNA-based data storage emerged in this decade as a promising solution for long data durability, low power consumption, and high density. However, such technology has not yet reached a good maturity level, requiring many investigations to improve the information encoding and decoding processes. Simulations can be key to overcoming the time and the cost burdens of the many experiments imposed by thorough design space explorations. In response to this, we have developed a DNA storage simulator (DNAssim) that allows simulating the different steps in the DNA storage pipeline using a proprietary software infrastructure written in Python/C language. Among the many operations performed by the tool, the edit distance calculation used during clustering operations has been identified as the most computationally intensive task in software, thus calling for hardware acceleration. In this work, we demonstrate the integration in the DNAssim framework of a dedicated FPGA hardware accelerator based on the Xilinx VC707 evaluation kit to boost edit distance calculations by up to 11 times with respect to a pure software approach. This materializes in a clustering simulation latency reduction of up to 5.5 times and paves the way for future scale-out DNA storage simulation platforms.

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Song, Wentu, Kui Cai, and Kees A. Schouhamer Immink. "Sequence-Subset Distance and Coding for Error Control in DNA-Based Data Storage." IEEE Transactions on Information Theory 66, no. 10 (October 2020): 6048–65. http://dx.doi.org/10.1109/tit.2020.3002611.

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Barthélémy, Philippe, Stephen J. Lee, and Mark Grinstaff. "Supramolecular assemblies with DNA* (Special Topic Article)." Pure and Applied Chemistry 77, no. 12 (January 1, 2005): 2133–48. http://dx.doi.org/10.1351/pac200577122133.

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Information storage in chemical and biological systems involves recognition processes occurring at the molecular and macromolecular level. The implementation of a "code" can consist of multiple noncovalent interactions, which include hydrogen bonds, π-stacking, hydrophobic interactions, and appropriate molecular and supramolecular architectures. With the double-helical DNA structure stabilized by Watson-Crick hydrogen bond base-pairing and aryl π-π stacking interactions, nature provides to scientists an example of one of the most sophisticated supramolecular systems. Molecular organization using these types of processes has become a very powerful strategy for the construction of well-defined nanostructures. Self-assemblies using noncovalent interactions have been designed to build fibers, membranes, two-dimensional monolayers, hydro, organo gels, etc. This paper highlights the research presented at the workshop entitled DNA Supramolecular Assemblies, which was held in Avignon, France on 5-6 May 2004. In this article, we first focus on the recent progress achieved in the design of supramolecular self-assemblies that mimic the molecular recognition functionalities found with nucleic acids. Second, we present several synthetic-DNA supramolecular assemblies currently developed to transport nucleic acids into cells. The marriage of supramolecular chemistry with nucleic acids as illustrated through examples in this article will open new avenues for designing artificial molecular devices and expand the current repertoire of supramolecular assemblies available.

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Yoon, Jinho, Taek Lee, and Jeong-Woo Choi. "Development of Bioelectronic Devices Using Bionanohybrid Materials for Biocomputation System." Micromachines 10, no. 5 (May 27, 2019): 347. http://dx.doi.org/10.3390/mi10050347.

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Bioelectronic devices have been researched widely because of their potential applications, such as information storage devices, biosensors, diagnosis systems, organism-mimicking processing system cell chips, and neural-mimicking systems. Introducing biomolecules including proteins, DNA, and RNA on silicon-based substrates has shown the powerful potential for granting various functional properties to chips, including specific functional electronic properties. Until now, to extend and improve their properties and performance, organic and inorganic materials such as graphene and gold nanoparticles have been combined with biomolecules. In particular, bionanohybrid materials that are composed of biomolecules and other materials have been researched because they can perform core roles of information storage and signal processing in bioelectronic devices using the unique properties derived from biomolecules. This review discusses bioelectronic devices related to computation systems such as biomemory, biologic gates, and bioprocessors based on bionanohybrid materials with a selective overview of recent research. This review contains a new direction for the development of bioelectronic devices to develop biocomputation systems using biomolecules in the future.

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Han, Ying-Jie, Jian-Wei Wang, Chun Huang, and Qing-Lei Zhou. "Computation Tree Logic Formula Model Checking Using DNA Computing." Journal of Nanoelectronics and Optoelectronics 15, no. 5 (May 1, 2020): 620–29. http://dx.doi.org/10.1166/jno.2020.2781.

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Computation tree logic model checking is a formal verification technology that can ensure the correctness of systems. The vast storage density of deoxyribonucleic acid (DNA) molecules and the massive parallelism of DNA computing offer new methods for computation tree logic model checking. In this study, we propose a computation tree logic model checking method based on DNA computing. First, a system to-be-checked and a computation tree logic formula are encoded by single-stranded DNA molecules. Second, these singlestranded DNA molecules are mixed to spontaneously hybridize and form partial or complete double-stranded molecules. Finally, a series of molecular manipulations are applied to detect the double-stranded molecules so that the result whether the system satisfies the computation tree logic formula is obtained. Biological simulations confirm the validity of the new method.

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Mohammed-Saeid, Waleed, Deborah Michel, Anas El-Aneed, Ronald E. Verrall, Nicholas H. Low, and Ildiko Badea. "Development of Lyophilized Gemini Surfactant-Based Gene Delivery Systems: Influence of Lyophilization on the Structure, Activity and Stability of the Lipoplexes." Journal of Pharmacy & Pharmaceutical Sciences 15, no. 4 (October 7, 2012): 548. http://dx.doi.org/10.18433/j3x60d.

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Purpose. Cationic gemini surfactants have been studied as non-viral vectors for gene therapy. Clinical applications of cationic lipid/DNA lipoplexes are restricted by their instability in aqueous formulations. In this work, we investigated the influence of lyophilization on the essential physiochemical properties and in vitro transfection of gemini surfactant-lipoplexes. Additionally, we evaluated the feasibility of lyophilization as a technique for preparing lipoplexes with long term stability. Methods. A gemini surfactant [12-7NH-12] and plasmid DNA encoding for interferon-γ were used to prepare gemini surfactant/pDNA [P/G] lipoplexes. Helper lipid DOPE [L] was incorporated in all formulation producing a [P/G/L] system. Sucrose and trehalose were utilized as stabilizing agents. To evaluate the ability of lyophilization to improve the stability of gemini surfactant-based lipoplexes, four lyophilized formulations were stored at 25˚C for three months. The formulations were analyzed at different time-points for physiochemical properties and in vitro transfection. Results. The results showed that both sucrose and trehalose provided anticipated stabilizing effect. The transfection efficiency of the lipoplexes increased 2-3 fold compared to fresh formulations upon lyophilization. This effect can be attributed to the improvement of DNA compaction and changes in the lipoplex morphology due to the lyophilization/rehydration cycles. The physiochemical properties of the lyophilized formulations were maintained throughout the stability study. All lyophilized formulations showed a significant loss of gene transfection activity after three months of storage. Nevertheless, no significant losses of transfection efficiency were observed for three formulations after two months storage at 25 ˚C. Conclusion. Lyophilization significantly improved the physical stability of gemini surfactant-based lipoplexes compared to liquid formulations. As well, lyophilization improved the transfection efficiency of the lipoplexes. The loss of transfection activity upon storage is most probably due to the conformational changes in the supramolecular structure of the lipoplexes as a function of time and temperature rather than to DNA degradation. This article is open to POST-PUBLICATION REVIEW. Registered readers (see “For Readers”) may comment by clicking on ABSTRACT on the issue’s contents page.

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Carozzi, Francesca Maria, and Cristina Sani. "Fecal Collection and Stabilization Methods for Improved Fecal DNA Test for Colorectal Cancer in a Screening Setting." Journal of Cancer Research 2013 (November 24, 2013): 1–8. http://dx.doi.org/10.1155/2013/818675.

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Early detection of CRC and adenomas reduces CRC-related mortality. The optimal screening test for CRC is still a subject of debate, and molecular stool sample analysis could provide a valid alternative to conventional methods in terms of compliance and practicability. Seven fecal DNA storage systems were evaluated in two successive phases. In the first phase of the study was selected the preservative buffer able to ensure the best human DNA recovery. In the second phase was evaluated human DNA stability, amplificability and integrity in DNA extracted from selected buffer. Results showed that the best performance was obtained in samples stored in 100 mM EDTA buffer and Genefec buffer. Likewise buffer addition yielded a significant increase in DNA stability and integrity without PCR inhibition, compared to the matched aliquots with no buffer added. Our study shows that samples collected in stabilization solution stabilize DNA so that intact nucleic acids, are more effectively detectable in the molecular assay. DNA buffer preservation and storage conditions could be useful to guarantee the most consistent yield in human DNA. Stabilization buffer addition to stool samples prior to transport presents an easily implemented solution that appears to be highly effective. Overall DNA extracted from faeces preserved in preservative buffer can feasibility been used for molecular analysis leading to an increase of assay sensitivity.

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Soniat, Taylor J., Hendra F. Sihaloho, Richard D. Stevens, Todd D. Little, Caleb D. Phillips, and Robert D. Bradley. "Temporal-dependent effects of DNA degradation on frozen tissues archived at −80°C." Journal of Mammalogy 102, no. 2 (April 1, 2021): 375–83. http://dx.doi.org/10.1093/jmammal/gyab009.

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Abstract Frozen tissues, associated with natural history and biological collections, historically have been archived at temperatures between −20°C and −80°C. More recently, the availability of liquid nitrogen systems has enabled the storage of tissue samples (biobanking) at temperatures as low as −196°C. Currently, it is not known how the degree of coldness (e.g., −80°C or −196°C) or longevity (time in storage) impacts preservation of tissue samples. To examine the effects of long-term storage (−80°C and −196°C) on DNA degradation, tissue samples (muscle and liver) archived for 30, 20, 10, or 1 years were obtained from the Natural Science Research Laboratory at Texas Tech University. The integrity of DNA (measured as molecular weight and fragment length) extracted from samples was determined using automated DNA isolation methods followed by microfluidic distribution measurement. DNA distributions were compared using measures of central tendency, a regression-based molecular mass profile, and as a latent variable in a structural equation model. Muscle samples consistently outperformed liver samples in terms of quality of DNA yield. Also, muscle samples exhibited a significant linear relationship with time in which older samples were more degraded than were recent samples. The signal for a temporal effect on DNA was strongest when considering a latent variable of DNA quality based on mode and kurtosis; 37% of the variation in the latent variable was explained by variation in units of time. More recent time points tended to be more similar, but the temporal effect on the latent variable remained strong even when the oldest samples were removed from the analysis. In contrast, integrity of DNA from liver samples did not have a significant linear relationship with time; however, in some years they exhibited non-normally distributed DNA quality metrics that may have reflected sensitivity of liver tissue to degradation during specimen preparation, DNA extraction, or archive parameters. Results indicated that tissue type and temporal effects influenced rates of DNA degradation, with the latter emphasizing the long-term value of biobanking at the coldest temperatures possible (liquid nitrogen storage) to mitigate degradation of biological samples of ever-increasing scientific value.

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McKILLIP, JOHN L., LEE-ANN JAYKUS, and MARYANNE DRAKE. "Influence of Growth in a Food Medium on the Detection of Escherichia coli O157:H7 by Polymerase Chain Reaction." Journal of Food Protection 65, no. 11 (November 1, 2002): 1775–79. http://dx.doi.org/10.4315/0362-028x-65.11.1775.

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The effects of storage time and growth in broth culture and in a food medium on the efficiency of Escherichia coli O157: H7 DNA extraction and on the sensitivity of polymerase chain reaction (PCR) detection of E. coli O157:H7 were investigated. Detection limits were evaluated with dilution series PCR targeting the slt-II gene. The relationship between cell density and DNA yield was generally log-linear for pure cultures of E. coli O157:H7. When the bacteria were suspended in skim milk at a density of 106 CFU/ml, held at 4°C, and sampled at 24-h intervals, cell density, total DNA yield, and PCR detection limits remained stable throughout the 96-h storage period. However, when E. coli O157:H7 was grown in skim milk to a final cell density of 106 CFU/ml, PCR amplification efficiency was drastically reduced, although overall DNA yields from these samples were consistent with those for the samples in which E. coli O157:H7 growth was static over 96 h of storage at 4°C. This result is most likely due to poor DNA purity, which was consistently observed when DNA was extracted from food matrices in which the pathogen was grown rather than stored. The results of this investigation underscore the likelihood that multiple components may drastically affect DNA extraction and PCR amplification efficiency in the detection of pathogens in the food matrix. It is clear that before nucleic acid amplification technologies are widely applied to food systems, it would be prudent to test their efficacy in multiple food matrices and under conditions in which the bacterial population is both static and actively growing.

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Nie, Peng, Yanfen Bai, and Hui Mei. "Synthetic Life with Alternative Nucleic Acids as Genetic Materials." Molecules 25, no. 15 (July 31, 2020): 3483. http://dx.doi.org/10.3390/molecules25153483.

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DNA, the fundamental genetic polymer of all living organisms on Earth, can be chemically modified to embrace novel functions that do not exist in nature. The key chemical and structural parameters for genetic information storage, heredity, and evolution have been elucidated, and many xenobiotic nucleic acids (XNAs) with non-canonical structures are developed as alternative genetic materials in vitro. However, it is still particularly challenging to replace DNAs with XNAs in living cells. This review outlines some recent studies in which the storage and propagation of genetic information are achieved in vivo by expanding genetic systems with XNAs.

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Karakose, Mehmet, and Ugur Cigdem. "QPSO-Based Adaptive DNA Computing Algorithm." Scientific World Journal 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/160687.

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DNA (deoxyribonucleic acid) computing that is a new computation model based on DNA molecules for information storage has been increasingly used for optimization and data analysis in recent years. However, DNA computing algorithm has some limitations in terms of convergence speed, adaptability, and effectiveness. In this paper, a new approach for improvement of DNA computing is proposed. This new approach aims to perform DNA computing algorithm with adaptive parameters towards the desired goal using quantum-behaved particle swarm optimization (QPSO). Some contributions provided by the proposed QPSO based on adaptive DNA computing algorithm are as follows: (1) parameters of population size, crossover rate, maximum number of operations, enzyme and virus mutation rate, and fitness function of DNA computing algorithm are simultaneously tuned for adaptive process, (2) adaptive algorithm is performed using QPSO algorithm for goal-driven progress, faster operation, and flexibility in data, and (3) numerical realization of DNA computing algorithm with proposed approach is implemented in system identification. Two experiments with different systems were carried out to evaluate the performance of the proposed approach with comparative results. Experimental results obtained with Matlab and FPGA demonstrate ability to provide effective optimization, considerable convergence speed, and high accuracy according to DNA computing algorithm.

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Salladini, Edoardo, Maria L. M. Jørgensen, Frederik F. Theisen, and Karen Skriver. "Intrinsic Disorder in Plant Transcription Factor Systems: Functional Implications." International Journal of Molecular Sciences 21, no. 24 (December 21, 2020): 9755. http://dx.doi.org/10.3390/ijms21249755.

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Eukaryotic cells are complex biological systems that depend on highly connected molecular interaction networks with intrinsically disordered proteins as essential components. Through specific examples, we relate the conformational ensemble nature of intrinsic disorder (ID) in transcription factors to functions in plants. Transcription factors contain large regulatory ID-regions with numerous orphan sequence motifs, representing potential important interaction sites. ID-regions may affect DNA-binding through electrostatic interactions or allosterically as for the bZIP transcription factors, in which the DNA-binding domains also populate ensembles of dynamic transient structures. The flexibility of ID is well-suited for interaction networks requiring efficient molecular adjustments. For example, Radical Induced Cell Death1 depends on ID in transcription factors for its numerous, structurally heterogeneous interactions, and the JAZ:MYC:MED15 regulatory unit depends on protein dynamics, including binding-associated unfolding, for regulation of jasmonate-signaling. Flexibility makes ID-regions excellent targets of posttranslational modifications. For example, the extent of phosphorylation of the NAC transcription factor SOG1 regulates target gene expression and the DNA-damage response, and phosphorylation of the AP2/ERF transcription factor DREB2A acts as a switch enabling heat-regulated degradation. ID-related phase separation is emerging as being important to transcriptional regulation with condensates functioning in storage and inactivation of transcription factors. The applicative potential of ID-regions is apparent, as removal of an ID-region of the AP2/ERF transcription factor WRI1 affects its stability and consequently oil biosynthesis. The highlighted examples show that ID plays essential functional roles in plant biology and has a promising potential in engineering.

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Jaekel, Stegemann, and Saccà. "Manipulating Enzymes Properties with DNA Nanostructures." Molecules 24, no. 20 (October 14, 2019): 3694. http://dx.doi.org/10.3390/molecules24203694.

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Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their adaptability to the environment make them ideal functional materials. One of the major goals of DNA nanotechnology—and indeed its initial motivation—is to bridge these two worlds in a rational fashion. Combining the predictable base-pairing rule of DNA with chemical conjugation strategies and modern protein engineering methods has enabled the realization of complex DNA-protein architectures with programmable structural features and intriguing functionalities. In this review, we will focus on a special class of biohybrid structures, characterized by one or many enzyme molecules linked to a DNA scaffold with nanometer-scale precision. After an initial survey of the most important methods for coupling DNA oligomers to proteins, we will report the strategies adopted until now for organizing these conjugates in a predictable spatial arrangement. The major focus of this review will be on the consequences of such manipulations on the binding and kinetic properties of single enzymes and enzyme complexes: an interesting aspect of artificial DNA-enzyme hybrids, often reported in the literature, however, not yet entirely understood and whose full comprehension may open the way to new opportunities in protein science.

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Schuler, A. J., M. Onuki, H. Satoh, and T. Mino. "Density separation and molecular methods to characterize enhanced biological phosphorus removal system populations." Water Science and Technology 46, no. 1-2 (July 1, 2002): 195–98. http://dx.doi.org/10.2166/wst.2002.0477.

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A novel approach to the identification of microorganisms that accumulate high density microbial storage products based on density separation, denaturing gradient gel electrophoresis (DGGE), and DNA sequencing was developed and applied to bench and pilot scale enhanced biological phosphorus removal (EBPR) systems. Polyphosphate (PP), glycogen, and polyhydroxyalkanoates (PHAs), are all of higher density than a typical bacterial cell. PP-accumulating organisms (PAOs), the organisms responsible for EBPR, accumulate all three of these storage products. Density separation in a homogenous solution of Percoll produced a high-density biomass fraction with a relatively high concentration of PAOs, as determined by Neisser staining. DNA was extracted from these fractions, amplified, and separated by DGGE. DGGE profiles demonstrated some bacterial strains were present at a greater concentration in the high density fractions than in low density fractions. These strains were considered PAO candidates. 5 of 12 PAO candidates from high density fractions were γ Proteobacteria and only 1 was a β Proteobacterium. 2 PAO candidates were most similar to recently identified γ Proteobacteria sequences obtained by DGGE analysis of a deteriorated benchtop EBPR system.

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Lathwal, Sushil, Saigopalakrishna S. Yerneni, Susanne Boye, Upenyu L. Muza, Shuntaro Takahashi, Naoki Sugimoto, Albena Lederer, Subha R. Das, Phil G. Campbell, and Krzysztof Matyjaszewski. "Engineering exosome polymer hybrids by atom transfer radical polymerization." Proceedings of the National Academy of Sciences 118, no. 2 (December 31, 2020): e2020241118. http://dx.doi.org/10.1073/pnas.2020241118.

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Exosomes are emerging as ideal drug delivery vehicles due to their biological origin and ability to transfer cargo between cells. However, rapid clearance of exogenous exosomes from the circulation as well as aggregation of exosomes and shedding of surface proteins during storage limit their clinical translation. Here, we demonstrate highly controlled and reversible functionalization of exosome surfaces with well-defined polymers that modulate the exosome’s physiochemical and pharmacokinetic properties. Using cholesterol-modified DNA tethers and complementary DNA block copolymers, exosome surfaces were engineered with different biocompatible polymers. Additionally, polymers were directly grafted from the exosome surface using biocompatible photo-mediated atom transfer radical polymerization (ATRP). These exosome polymer hybrids (EPHs) exhibited enhanced stability under various storage conditions and in the presence of proteolytic enzymes. Tuning of the polymer length and surface loading allowed precise control over exosome surface interactions, cellular uptake, and preserved bioactivity. EPHs show fourfold higher blood circulation time without altering tissue distribution profiles. Our results highlight the potential of precise nanoengineering of exosomes toward developing advanced drug and therapeutic delivery systems using modern ATRP methods.

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Ibrahim, Dina, Kareem Ahmed, Mohamed Abdallah, and AbdElmgeid A. Ali. "A New Chaotic-Based RGB Image Encryption Technique Using a Nonlinear Rotational 16 × 16 DNA Playfair Matrix." Cryptography 6, no. 2 (June 8, 2022): 28. http://dx.doi.org/10.3390/cryptography6020028.

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Due to great interest in the secure storage and transmission of color images, the necessity for an efficient and robust RGB image encryption technique has grown. RGB image encryption ensures the confidentiality of color images during storage and transmission. In the literature, a large number of chaotic-based image encryption techniques have been proposed, but there is still a need for a robust, efficient and secure technique against different kinds of attacks. In this paper, a novel RGB image encryption technique is proposed for encrypting individual pixels of RGB images using chaotic systems and 16 rounds of DNA encoding, transpositions and substitutions. First, round keys are generated randomly using a logistic chaotic function. Then, these keys are used across different rounds to alter individual pixels using a nonlinear randomly generated 16×16 DNA Playfair matrix. Experimental results show the robustness of the proposed technique against most attacks while reducing the consumed time for encryption and decryption. The quantitative metrics show the ability of the proposed technique to maintain reference evaluation values while resisting statistical and differential attacks. The obtained horizontal, vertical and diagonal correlation is less than 0.01, and the NPCR and UACI are larger than 0.99 and 0.33, respectively. Finally, NIST analysis is presented to evaluate the randomness of the proposed technique.

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Wolski, Pawel, Krzysztof Nieszporek, and Tomasz Panczyk. "Cytosine-Rich DNA Fragments Covalently Bound to Carbon Nanotube as Factors Triggering Doxorubicin Release at Acidic pH. A Molecular Dynamics Study." International Journal of Molecular Sciences 22, no. 16 (August 6, 2021): 8466. http://dx.doi.org/10.3390/ijms22168466.

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This works deals with analysis of properties of a carbon nanotube, the tips of which were functionalized by short cytosine-rich fragments of ssDNA. That object is aimed to work as a platform for storage and controlled release of doxorubicin in response to pH changes. We found that at neutral pH, doxorubicin molecules can be intercalated between the ssDNA fragments, and formation of such knots can effectively block other doxorubicin molecules, encapsulated in the nanotube interior, against release to the bulk. Because at the neutral pH, the ssDNA fragments are in form of random coils, the intercalation of doxorubicin is strong. At acidic pH, the ssDNA fragments undergo folding into i-motifs, and this leads to significant reduction of the interaction strength between doxorubicin and other components of the system. Thus, the drug molecules can be released to the bulk at acidic pH. The above conclusions concerning the storage/release mechanism of doxorubicin were drawn from the observation of molecular dynamics trajectories of the systems as well as from analysis of various components of pair interaction energies.

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N K, Sushma. "Distributed Computing of DNA Cryptography and Randomly Generated Mealy Machine." International Journal for Research in Applied Science and Engineering Technology 10, no. 6 (June 30, 2022): 2516–23. http://dx.doi.org/10.22214/ijraset.2022.44050.

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Abstract: The volumes of information created and saved in operating systems are growing at an alarming rate these days. Between all of these devices, massive volumes of essential and sensitive files are transmitted. As a result, ensuring the protection of all of these irreplaceable data is critical. Cryptography is a well-known method for ensuring data security. Cryptography's main goal is to transmitthe information from the source to the destination in the most secure method possible, preventing an adversary from extracting the actual datainformation. This research suggests a novel cryptographic algorithm depending on DNA encryption and the notion of restricted automata. The system consists of three components: cryptographic keys, a generator, a transmitter, and a transceiver. Based on the features of the receiver, the transmitter generates a 256-bit DNA-based secret key, which is used to encrypt information. The DNA sequence is then coded using a procedurally generated Mealy machine, that provides the ciphertext more safe. The suggested approach can defend the system from a variety of security attacks. This technique has provenits capacity to provide an individual user with better safe storage by dividing the user's vital information into bits.

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Ma, Rong, Anna V. Kellner, Victor Pui-Yan Ma, Hanquan Su, Brendan R. Deal, Joshua M. Brockman, and Khalid Salaita. "DNA probes that store mechanical information reveal transient piconewton forces applied by T cells." Proceedings of the National Academy of Sciences 116, no. 34 (August 7, 2019): 16949–54. http://dx.doi.org/10.1073/pnas.1904034116.

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The advent of molecular tension probes for real-time mapping of piconewton forces in living systems has had a major impact on mechanobiology. For example, DNA-based tension probes have revealed roles for mechanics in platelet, B cell, T cell, and fibroblast function. Nonetheless, imaging short-lived forces transmitted by low-abundance receptors remains a challenge. This is a particular problem for mechanoimmunology where ligand–receptor bindings are short lived, and a few antigens are sufficient for cell triggering. Herein, we present a mechanoselection strategy that uses locking oligonucleotides to preferentially and irreversibly bind DNA probes that are mechanically strained over probes at rest. Thus, infrequent and short-lived mechanical events are tagged. This strategy allows for integration and storage of mechanical information into a map of molecular tension history. Upon addition of unlocking oligonucleotides that drive toehold-mediated strand displacement, the probes reset to the real-time state, thereby erasing stored mechanical information. As a proof of concept, we applied this strategy to study OT-1 T cells, revealing that the T cell receptor (TCR) mechanically samples antigens carrying single amino acid mutations. Such events are not detectable using conventional tension probes. Each mutant peptide ligand displayed a different level of mechanical sampling and spatial scanning by the TCR that strongly correlated with its functional potency. Finally, we show evidence that T cells transmit pN forces through the programmed cell death receptor-1 (PD1), a major target in cancer immunotherapy. We anticipate that mechanical information storage will be broadly useful in studying the mechanobiology of the immune system.

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Ghosh, Debasis, Lakshmi P. Datta, and Thimmaiah Govindaraju. "Molecular architectonics of DNA for functional nanoarchitectures." Beilstein Journal of Nanotechnology 11 (January 9, 2020): 124–40. http://dx.doi.org/10.3762/bjnano.11.11.

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DNA is the key biomolecule central to almost all processes in living organisms. The eccentric idea of utilizing DNA as a material building block in molecular and structural engineering led to the creation of numerous molecular-assembly systems and materials at the nanoscale. The molecular structure of DNA is believed to have evolved over billions of years, with structure and stability optimizations that allow life forms to sustain through the storage and transmission of genetic information with fidelity. The nanoscale structural characteristics of DNA (2 nm thickness and ca. 40–50 nm persistence length) have inspired the creation of numerous functional patterns and architectures through noncovalent conventional and unconventional base pairings as well as through mutual templating-interactions with small organic molecules and metal ions. The recent advancements in structural DNA nanotechnology allowed researchers to design new DNA-based functional materials with chemical and biological properties distinct from their parent components. The modulation of structural and functional properties of hybrid DNA ensembles of small functional molecules (SFMs) and short oligonucleotides by adapting the principles of molecular architectonics enabled the creation of novel DNA nanoarchitectures with potential applications, which has been termed as templated DNA nanotechnology or functional DNA nanoarchitectonics. This review highlights the molecular architectonics-guided design principles and applications of the derived DNA nanoarchitectures. The advantages and ability of functional DNA nanoarchitectonics to overcome the trivial drawbacks of classical DNA nanotechnology to fulfill realistic and practical applications are highlighted, and an outlook on future developments is presented.

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Galbraith, David A., Brad N. White, Ronald J. Brooks, and Peter T. Boag. "Multiple paternity in clutches of snapping turtles (Chelydra serpentina) detected using DNA fingerprints." Canadian Journal of Zoology 71, no. 2 (February 1, 1993): 318–24. http://dx.doi.org/10.1139/z93-044.

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Female common snapping turtles (Chelydra serpentina) are capable of storing viable sperm for at least several months and are likely to be inseminated by more than one male. Consequently, we tested the hypothesis that multiple paternity occurred within individual clutches of three common snapping turtles from Algonquin Provincial Park, Ontario, Canada, by examining DNA fingerprints. Positive evidence of multiple paternity was detected among samples of offspring from two of the three clutches. In these clutches, the distributions of both paternal DNA fingerprint bands and band-sharing coefficients deviated from those expected under the assumption of a single father, suggesting that paternity was distributed between two or more males in each clutch. Multiple paternity and the ability of females to store sperm make turtles good animals in which to study sperm competition. The mating systems and life-history features of turtles should be studied with the consequences of sperm storage and multiple paternity in mind.

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Chapouthier, Georges. "From the Search for a Molecular Code of Memory to the Role of Neurotransmitters: A Historical Perspective." Neural Plasticity 11, no. 3-4 (2004): 151–58. http://dx.doi.org/10.1155/np.2004.151.

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The history of the neurochemistry of mnesic processes can be divided into two main periods: the first (1946-1978) was inspired by the results of molecular genetics, providing evidence for storage of hereditary information in the DNA of genes. Therefore, the chemical bases for memory were investigated in the macromolecules of the brain. Such attempts were relatively unsuccessful, which led to a second period (starting in 1978) with the research emphasizing, in a less ambitious way, the role of the molecular correlates of mnesic processes, in particular in the main transmitter systems of the brain.

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Gao, Qi, Yang Zhang, Congcong Gao, Huimin Li, Yudou Cheng, Xun Qian, Lishu Zhang, Jinyu Liu, Solabomi Olaitan Ogunyemi, and Junfeng Guan. "The Microbial Diversity in Relation to Postharvest Quality and Decay: Organic vs. Conventional Pear Fruit." Foods 12, no. 10 (May 12, 2023): 1980. http://dx.doi.org/10.3390/foods12101980.

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(1) Background: Organic food produced in environmentally friendly farming systems has become increasingly popular. (2) Methods: We used a DNA metabarcoding approach to investigate the differences in the microbial community between organic and conventional ‘Huangguan’ pear fruit; and (3) Results: Compared to a conventional orchard, the fruit firmness in the organic orchard had significantly lowered after 30 days of shelf-life storage at 25 °C, and the soluble solids content (SSC), titratable acid (TA), and decay index were higher. There were differences in the microbial diversity between organic and conventional orchards pears. After 30 days of storage, Fusarium and Starmerella became the main epiphytic fungi in organic fruits, while Meyerozyma was dominant in conventional fruits. Gluconobacter, Acetobacter, and Komagataeibacter were dominant epiphytic bacteria on pears from both organic and conventional orchards after a 30-day storage period. Bacteroides, Muribaculaceae, and Nesterenkonia were the main endophytic bacteria throughout storage. There was a negative correlation between fruit firmness and decay index. Moreover, the abundance of Acetobacter and Starmerella were positively correlated with fruit firmness, while Muribaculaceae was negatively correlated, implying that these three microorganisms may be associated with the postharvest decay of organic fruit; (4) Conclusions: The difference in postharvest quality and decay in organic and conventional fruits could potentially be attributed to the variation in the microbial community during storage.

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Coster, Stephanie S., Megan N. Dillon, William Moore, and George T. Merovich. "The update and optimization of an eDNA assay to detect the invasive rusty crayfish (Faxonius rusticus)." PLOS ONE 16, no. 10 (October 29, 2021): e0259084. http://dx.doi.org/10.1371/journal.pone.0259084.

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Environmental DNA (eDNA) is nuclear or mitochondrial DNA shed into the environment, and amplifying this DNA can serve as a reliable, noninvasive way to monitor aquatic systems for the presence of an invasive species. Assays based on the collection of eDNA are becoming increasingly popular, and, when optimized, can aid in effectively and efficiently tracking invasion fronts. We set out to update an eDNA assay to detect the invasive rusty crayfish, Faxonius rusticus. We tested for species specificity compared to other stream crayfish and field tested the assay at sites with known presence (N = 3) and absence (N = 4) in the Juniata River watershed in central Pennsylvania, USA. To maximize sensitivity, we field tested different storage buffers (Longmire’s buffer and ethanol), DNA extraction methods (Qiagen’s DNEasy and PowerWater kits), and quantitative polymerase chain reaction (qPCR) chemistries (TaqMan and SYBR green). Our assay confirmed the presence data and performed optimally when filter samples were stored in Longmire’s buffer, DNA was extracted with DNeasy Blood and Tissue Kit, and TaqMan qPCR chemistry was utilized. With proper sample processing, our assay allows for accurate, noninvasive detection of F. rusticus in streams.

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JAAKOLA, ANU, MARK NELSON, ALBERT ALLEN, MARKUS KORHONEN, MARKO KOLARI, and JAAKO EKMAN. "Using novel DNA methods to achieve higher process efficiency and performance." January 2023 22, no. 1 (January 24, 2023): 7–16. http://dx.doi.org/10.32964/tj22.1.7.

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Uncontrolled microbiological activity is a challenge for recycled fiber (RCF) mills as it can have negative effects on production and end-product quality. The microbes that exist in these systems have been largely unknown, and the strategies employed to control microbiology have been non-specific. Understanding the specific microbial groups present in RCF mills, their properties, and where they exist, as well as having the ability to accurately measure the true troublemakers, are key to targeted control of the bad actors. In this study, we present the results of a global survey of over 40 RCF paper machines. The same RCF-specific problem-causing bacterial groups were found on different continents, including large densities of newly identified bacteria in paper processes. Those can degrade cellulose and starch, produce acids and odorous substances, and have a significant impact on fiber strength and additive consumption. We also demonstrate how modern DNA tools can quantify the impact of biocidal countermeasures against the actual troublemakers, including bacteria found to degrade cellulose during RCF pulp storage, which may be linked to a negative impact on end-product strength. These novel DNA tools give producers updated biocide program key performance indicators (KPIs) and actionable information to more effectively design and adjust microbiological control to achieve higher process efficiency and performance.

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Kadam, Santosh T., and Ashalata D. Pawar. "CONSERVATION OF MEDICINAL PLANTS: A REVIEW." International Ayurvedic Medical Journal 8, no. 7 (July 18, 2020): 3890–95. http://dx.doi.org/10.46607/iamj0807112020.

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Ayurveda [traditional medicine of India as per WHO], the holistic science of medicine, as practised and utilized by Indians at large since centuries is now being globally accepted which has increased the demand for medicinal plants. Majority of population in the developing countries like India depends on the tradi-tional systems of medicine like Ayurveda for their primary healthcare needs. Increasing demand of medic-inal plants leads to irrational cutting deforestation leading to depletion of the wild resources. Moreover, the natural and manmade calamities lead to further depletion of medicinal plant diversity. Conservation aims at supporting sustainable development by wing the biological resources in ways that don’t deplete the world’s variety of species or destroy their ecosystems. It involves measures such as collection, propagation, evalua-tion, disease identification and elimination, storage and distribution. Conservation of medicinal plants and their genetic resources can be undertaken by in-situ and ex-situ conservation. Ex-situ conservation involves conservation of medium plants outside their natural habitat used to safeguard them from destruction, re-placement or deterioration. Ex-situ conservation includes procedure like seed storage, DNA storage, field gene banks and botanical gardens etc

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Souza, Lorena da Silva, Estefanía Bonnail, Luis Felipe de Almeida Duarte, Augusto Cesar, Inmaculada Riba, and Camilo Dias Seabra Pereira. "Integrated Assessment of CO2-Induced Acidification Lethal and Sub-Lethal Effects on Tropical Mussels Perna perna." Applied Sciences 13, no. 12 (June 16, 2023): 7199. http://dx.doi.org/10.3390/app13127199.

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Leakages of CO2 capture and storage systems from the seabed are able to cause significant adverse biological effects in marine species. Adult mussels were exposed to different CO2 enrichment scenarios (pH from 8.3 to 6.0) for 96 h, and endpoints (lysosomal membrane deterioration, lipid peroxidation and primary damages in DNA) were assessed. Mortality and reduced health status can occur after short exposure of the tropical mussel Perna perna to pH levels lower than 7.5. Results pointed out cytogenotoxic effects in the hemolymph and gills after 48 and 96 h of exposure, respectively. These findings should be considered when environmental monitoring approaches are performed in tropical marine areas employing CCS strategies.

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Mächler, Elvira, Anham Salyani, Jean-Claude Walser, Annegret Larsen, Bettina Schaefli, Florian Altermatt, and Natalie Ceperley. "Environmental DNA simultaneously informs hydrological and biodiversity characterization of an Alpine catchment." Hydrology and Earth System Sciences 25, no. 2 (February 18, 2021): 735–53. http://dx.doi.org/10.5194/hess-25-735-2021.

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Abstract. Alpine streams are particularly valuable for downstream water resources and of high ecological relevance; however, a detailed understanding of water storage and release in such heterogeneous environments is often still lacking. Observations of naturally occurring tracers, such as stable isotopes of water or electrical conductivity, are frequently used to track and explain hydrologic patterns and processes. Importantly, some of these hydrologic processes also create microhabitat variations in Alpine aquatic systems, each inhabited by characteristic organismal communities. The inclusion of such ecological diversity in a hydrologic assessment of an Alpine system may improve our understanding of hydrologic flows while also delivering biological information. Recently, the application of environmental DNA (eDNA) to assess biological diversity in water and connected habitats has gained popularity in the field of aquatic ecology. A few of these studies have started to link aquatic diversity with hydrologic processes but hitherto never in an Alpine system. Here, we collected water from an Alpine catchment in Switzerland and compared the genetic information of eukaryotic organisms conveyed by eDNA with the hydrologic information conveyed by naturally occurring hydrologic tracers. Between March and September 2017, we sampled water at multiple time points at 10 sites distributed over the 13.4 km2 Vallon de Nant catchment (Switzerland). The sites corresponded to three different water types and habitats, namely low-flow or ephemeral tributaries, groundwater-fed springs, and the main channel receiving water from both previous mentioned water types. Accompanying observations of typical physicochemical hydrologic characteristics with eDNA revealed that in the main channel and in the tributaries, the biological richness increases according to the change in streamflow, dq/dt, whereas, in contrast, the richness in springs increased in correlation with electrical conductivity. At the catchment scale, our results suggest that transport of additional, and probably terrestrial, DNA into water storage or flow compartments occurs with increasing streamflow. Such processes include overbank flow, stream network expansion, and hyporheic exchange. In general, our results highlight the importance of considering the at-site sampling habitat in combination with upstream connected habitats to understand how streams integrate eDNA over a catchment and to interpret spatially distributed eDNA samples, both for hydrologic and biodiversity assessments. At the intersection of two disciplines, our study provides complementary knowledge gains and identifies the next steps to be addressed for using eDNA to achieve complementary insights into Alpine water sources. Finally, we provide recommendations for future observation of eDNA in Alpine stream ecosystems.

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Omoregbee, Henry O., and Mabel U. Olanipekun. "Exploring the Intelligent Attributes of Industrial 4.0: The Next Revolution and Beyond." International Conference on Intelligent and Innovative Computing Applications 2022 (December 31, 2022): 30–39. http://dx.doi.org/10.59200/iconic.2022.004.

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Industry 4.0 places a strong emphasis on connection, automation, machine learning and real-time data. With these descriptions, intelligent/smart manufacturing that incorporates people, technology, and other resources has undergone a significant revolution leading the globe to the new era of Industry 5.0. Responding to disruption by employing intuition to decide what to do in a changing circumstance has grown to be highly attractive and exciting, even when it has never been utilized before. The domains of modern intelligent systems and computers have also made major strides in recent years. Examples include soft computing, computational intelligence, which encompasses evolutionary computing, neural networks, fuzzy systems, and the fusion of various paradigms. Others include immune-based systems, ambient intelligence, cognitive science, computational neuroscience and systems, perspective and vision, DNA, intelligent decision-making, and support etc. This technological breakthrough has also made room for new and emerging technologies that offer important advantages including extreme low latency, highly reliable connections, sufficient bandwidth, ample data storage, and powerful processing capabilities. This paper provides a comprehensive overview of what smart/intelligent systems include, as was observed in an ongoing project where such devices were designed, and what to anticipate from the 4.0, 5.0, and 6.0 industrial revolutions.

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Matange, Karishma, James M. Tuck, and Albert J. Keung. "DNA stability: a central design consideration for DNA data storage systems." Nature Communications 12, no. 1 (March 1, 2021). http://dx.doi.org/10.1038/s41467-021-21587-5.

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AbstractData storage in DNA is a rapidly evolving technology that could be a transformative solution for the rising energy, materials, and space needs of modern information storage. Given that the information medium is DNA itself, its stability under different storage and processing conditions will fundamentally impact and constrain design considerations and data system capabilities. Here we analyze the storage conditions, molecular mechanisms, and stabilization strategies influencing DNA stability and pose specific design configurations and scenarios for future systems that best leverage the considerable advantages of DNA storage.

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Journal articles on the topic 'DNA storage systems'

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