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Добірка наукової літератури з теми "Data storage into DNA molecules"

Автор: Grafiati

Опубліковано: 14 грудня 2024

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Статті в журналах з теми "Data storage into DNA molecules"

Jiang, Jiao. "Application of gene editing technology to DNA digital data storage." Highlights in Science, Engineering and Technology 73 (November 29, 2023): 452–58. http://dx.doi.org/10.54097/hset.v73i.14051.

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While the archival digital storage industry is approaching its physical limits, demand is increasing significantly, so alternatives are emerging. The modern world is in dire need of durable, scalable and economical alternative storage media. Deoxyribonucleic acid (DNA), a promising storage medium, offers superior information durability, capacity and energy consumption, making it a promising candidate for long-term data storage. However, the design and realization of DNA digital data storage face many problems, but gene editing technology, as a technology that makes modifications to genes directly from the molecular level, provides a breakthrough in solving these problems. In this paper, I show some methods for designing DNA digital data storage based on gene editing technology. The method utilizes gene editing technology to modify DNA molecules to improve their storage capacity and stability. At the same time, this paper also introduces the application cases of gene editing technology in DNA bio storage devices and looks forward to its future development.

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Garafutdinov, R. R., A. R. Sakhabutdinova, and A. V. Chemeris. "Long-term room temperature storage of DNA molecules." Biomics 12, no. 4 (2020): 552–63. http://dx.doi.org/10.31301/2221-6197.bmcs.2020-49.

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The simplest and most common method of long-term storage of DNA samples at present is the storage of their frozen solutions, which, however, has a number of disadvantages, including the destruction of DNA molecules during freezing and thawing, as well as energy consumption and the likelihood of losing valuable samples in the event of possible accidents. In this regard, long-term storage of DNA samples at room temperature in a dried state is preferable, especially since an even greater increase in the number of stored DNA samples is planned due to the planned preservation of non-biological data in this molecule, which is recognized at the International Economic Forum 2019 among the 10 most important innovative technologies as “DNA Data Storage” of the near future of mankind. Such storage requires the exclusion of hydrolysis and oxidation of DNA molecules under the action of water and reactive oxygen species, which can be achieved by placing DNA in an inert anhydrous atmosphere, including in the presence of additional ingredients in the form of, for example, trehalose, imitating wildlife, since it is known that this simple disaccharide, capable of vitrification, protects a wide range of anhydrobiont organisms from adverse environmental conditions. Currently, there are a number of technologies that provide long-term storage of DNA at room temperature, including those available from commercial sources, but not all problems have yet been solved, which is reflected in this review article.

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Ceze, Luis, Jeff Nivala, and Karin Strauss. "Molecular digital data storage using DNA." Nature Reviews Genetics 20, no. 8 (May 8, 2019): 456–66. http://dx.doi.org/10.1038/s41576-019-0125-3.

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Zhang, Yun Peng, Feng Ying Tian, Man Hui Sun, Ding Yu, Fei Xiang Fan, and Wei Guo Liu. "Based on DNA OTP Key Generation and Management Research." Applied Mechanics and Materials 427-429 (September 2013): 2470–72. http://dx.doi.org/10.4028/www.scientific.net/amm.427-429.2470.

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With the development of molecular-bio technology, the feature of DNA molecules for ultra-large-scale data storage has created a new approach for data storage. This paper gives a way of strengthening key transport security. Through recombinant DNA technology, use only sender-receiver know restriction enzymes to combine the key DNA and the T vector, to form a recombinant plasmid, making the key DNA bio-hide, and then place the recombinant plasmid in implanted bacteria .

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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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Carmean, Douglas, Luis Ceze, Georg Seelig, Kendall Stewart, Karin Strauss, and Max Willsey. "DNA Data Storage and Hybrid Molecular–Electronic Computing." Proceedings of the IEEE 107, no. 1 (January 2019): 63–72. http://dx.doi.org/10.1109/jproc.2018.2875386.

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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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Solanki, Arnav, Zak Griffin, Purab Ranjan Sutradhar, Karisha Pradhan, Caiden Merritt, Amlan Ganguly, and Marc Riedel. "Neural network execution using nicked DNA and microfluidics." PLOS ONE 18, no. 10 (October 19, 2023): e0292228. http://dx.doi.org/10.1371/journal.pone.0292228.

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DNA has been discussed as a potential medium for data storage. Potentially it could be denser, could consume less energy, and could be more durable than conventional storage media such as hard drives, solid-state storage, and optical media. However, performing computations on the data stored in DNA is a largely unexplored challenge. This paper proposes an integrated circuit (IC) based on microfluidics that can perform complex operations such as artificial neural network (ANN) computation on data stored in DNA. We envision such a system to be suitable for highly dense, throughput-demanding bio-compatible applications such as an intelligent Organ-on-Chip or other biomedical applications that may not be latency-critical. It computes entirely in the molecular domain without converting data to electrical form, making it a form of in-memory computing on DNA. The computation is achieved by topologically modifying DNA strands through the use of enzymes called nickases. A novel scheme is proposed for representing data stochastically through the concentration of the DNA molecules that are nicked at specific sites. The paper provides details of the biochemical design, as well as the design, layout, and operation of the microfluidics device. Benchmarks are reported on the performance of neural network computation.

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Bhattarai-Kline, Santi, Sierra K. Lear, and Seth L. Shipman. "One-step data storage in cellular DNA." Nature Chemical Biology 17, no. 3 (January 26, 2021): 232–33. http://dx.doi.org/10.1038/s41589-021-00737-2.

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Zhang, Cheng, Ranfeng Wu, Fajia Sun, Yisheng Lin, Yuan Liang, Jiongjiong Teng, Na Liu, Qi Ouyang, Long Qian, and Hao Yan. "Parallel molecular data storage by printing epigenetic bits on DNA." Nature 634, no. 8035 (October 23, 2024): 824–32. http://dx.doi.org/10.1038/s41586-024-08040-5.

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Дисертації з теми "Data storage into DNA molecules"

Berton, Chloé. "Sécurité des données stockées sur molécules d’ADN." Electronic Thesis or Diss., Ecole nationale supérieure Mines-Télécom Atlantique Bretagne Pays de la Loire, 2024. http://www.theses.fr/2024IMTA0431.

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La quantité de données numériques produites dans le monde chaque année augmente exponentiellement et les supports actuels de stockage atteignent leurs limites. Dans ce contexte, le stockage de données sur molécules d'ADN est très prometteur. Stockant jusqu’à 10¹⁸ octets par gramme d'ADN pour une consommation d'énergie quasi nulle, il a une durée de vie 100 fois plus longue que les disques durs. Cette technologie de stockage étant en développement, il est opportun d’y intégrer nativement des mécanismes pour sécuriser les données. C’est l’objet de cette thèse. Notre première contribution est une analyse des risques de l’ensemble de la chaîne de stockage, qui nous a permis d’identifier des vulnérabilités des procédés numériques et biologiques, en termes de confidentialité, d’intégrité, de disponibilité et de traçabilité. Une seconde contribution est l’identification d’opérateurs élémentaires permettant des manipulations simples de l’ADN. Avec ceux-ci, nous avons développé notre troisième contribution, une solution de chiffrement DNACipher qui impose un déchiffrement biomoléculaire des molécules avant de pouvoir lire les données correctement. Cette solution, qui repose sur des enzymes, a nécessité le développement d’un codage des données numériques en séquences ADN appelée DSWE ; notre quatrième contribution. Cet algorithme respecte les contraintes liées aux procédés biologiques (e.g. homopolymères) et à notre DNACipher. Enfin, notre dernière contribution est une validation expérimentale de notre chaîne de stockage sécurisée. C’est la première preuve de concept montrant qu’il est possible de sécuriser ce nouveau support de stockage sur la base de manipulations biomoléculaires
The volume of digital data produced worldwide every year is increasing exponentially, and current storage solutions are reaching their limits. In this context, data storage on DNA molecules holds great promise. Storing up to 10¹⁸ bytes per gram of DNA for almost no energy consumption, it has a lifespan 100 times longer than hard disks. As this storage technology is still under development, the opportunity presents itself to natively integrate data security mechanisms. This is the aim of this thesis. Our first contribution is a risk analysis of the entire storage chain, which has enabled us to identify vulnerabilities in digital and biological processes, particularly in terms of confidentiality, integrity, availability and traceability. A second contribution is the identification of elementary biological operators for simple manipulations of DNA. Using these operators, we have developed a DNACipher encryption solution that requires biomolecular decryption (DNADecipher) of the molecules before the data can be read correctly. This third contribution, based on enzymes, required the development of a coding algorithm for digital data into DNA sequences, a contribution called DSWE. This algorithm respects the constraints of biological processes (e.g. homopolymers) and our encryption solution. Our final contribution is an experimental validation of our secure storage chain. This is the first proof of concept showing that it is possible to secure this new storage medium using biomolecular manipulations

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Piretti, Mattia. "Synthetic DNA as a novel data storage solution for digital images." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2020. http://amslaurea.unibo.it/22028/.

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During the digital revolution there has been an explosion in the amount of data produced by humanity and the capacity of conventional storage devices has been struggling to keep up with this aggressive growth. This has highlighted the need for new means to store digital information, especially cold data. In this dissertations we will build upon the work done by the I3S MediaCoding team on utilizing DNA as a novel storage medium,thanks to its incredibly high information density and effectively infinite shelf life. We will expand on their previous works and adapt them to operate on the Nanopore MinIONsequencer, by increasing the noise resistance during the decoding process, and adding a post-processing step to repair the damage caused by the sequencing noise.

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Germishuizen, Willem Andreas. "Dielectrophoresis as an addressing mechanism in a novel data storage system based on DNA." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615680.

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Yanez, Ciceron. "SYNTHESIS OF NOVEL FLUORENE-BASED TWO-PHOTON ABSORBING MOLECULES AND THEIR APPLICATIONS IN OPTICAL DATA STORAGE, MICROFABRICATIO." Doctoral diss., University of Central Florida, 2009. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/3573.

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Two-photon absorption (2PA) has been used for a number of scientific and technological applications, exploiting the fact that the 2PA probability is directly proportional to the square of the incident light intensity (while one-photon absorption bears a linear relation to the incident light intensity). This intrinsic property of 2PA leads to 3D spatial localization, important in fields such as optical data storage, fluorescence microscopy, and 3D microfabrication. The spatial confinement that 2PA enables has been used to induce photochemical and photophysical events in increasingly smaller volumes and allowed nonlinear, 2PA-based, technologies to reach sub-diffraction limit resolutions. The primary focus of this dissertation is the development of novel, efficient 2PA, fluorene-based molecules to be used either as photoacid generators (PAGs) or fluorophores. A second aim is to develop more effective methods of synthesizing these compounds. As a third and final objective, the new molecules were used to develop a write-once-read many (WORM) optical data storage system, and stimulated emission depletion probes for bioimaging. In Chapter I, the microwave-assisted synthesis of triarylsulfonium salt photoacid generators (PAGs) from their diphenyliodonium counterparts is reported. The microwave-assisted synthesis of these novel sulfonium salts afforded reaction times 90 to 420 times faster than conventional thermal conditions, with photoacid quantum yields of new sulfonium PAGs ranging from 0.01 to 0.4. These PAGs were used to develop a fluorescence readout-based, nonlinear three-dimensional (3D) optical data storage system (Chapter II). In this system, writing was achieved by acid generation upon two-photon absorption (2PA) of a PAG (at 710 or 730 nm). Readout was then performed by interrogating two-photon absorbing dyes, after protonation, at 860 nm. Two-photon recording and readout of voxels was demonstrated in five and eight consecutive, crosstalk-free layers within a polymer matrix, generating a data storage capacity of up to 1.8 x 1013 bits/cm3. The possibility of using these PAGs in microfabrication is described in Chapter III, where two-photon induced cationic ring-opening polymerization (CROP) crosslinking of an SU8 resin is employed to produce free-standing microstructures. Chapter IV describes the investigation of one- and two-photon stimulated emission transitions by the fluorescence quenching of a sulfonyl-containing fluorene compound in solution at room temperate using a picosecond pump-probe technique. The nature of stimulated transitions under various fluorescence excitation and quenching conditions were analyzed theoretically, and good agreement with experimental data was demonstrated. Two-photon stimulated transitions S1 to S0 were shown at 1064 nm. The two-photon stimulated emission cross section of the sulfonyl fluorophore was estimated as aproximately 240 - 280 GM, making this compound a good candidate for use in two-photon stimulated emission depletion (STED) microscopy.
Ph.D.
Department of Chemistry
Sciences
Chemistry PhD

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Camerlengo, Terry Luke. "Techniques for Storing and Processing Next-Generation DNA Sequencing Data." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1388502159.

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Yanez, Ciceron. "Synthesis of novel fluorene-based two-photon absorbing molecules and their applications in optical data storage, microfabrication, and stimulated emission depletion." Orlando, Fla. : University of Central Florida, 2009. http://purl.fcla.edu/fcla/etd/CFE0002913.

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Halladjian, Sarkis. "Spatially Integrated Abstraction of Genetic Molecules." Electronic Thesis or Diss., université Paris-Saclay, 2020. http://www.theses.fr/2020UPASG056.

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Le génome humain est principalement constitué d'ADN, une macromolécule constituée d'une longue séquence linéaire de bases, étroitement serrée pour s'insérer dans le noyau relativement petit. L'empaquetage donne lieu à de multiples niveaux hiérarchiques d'organisation. Des recherches récentes ont montré que, parallèlement à la séquence linéaire, l'agencement spatial du génome joue un rôle important dans la fonction et l'activité du génome. La visualisation des aspects li-né-aires et spatiaux des données du génome est donc nécessaire. Dans cette thèse, nous nous concentrons sur le concept d'abstraction visuelle continue pour les données multi-échelles, appliqué à la visualisation du génome humain. L'abstraction visuelle est un concept inspiré par des illustrations qui simplifie le travail de traitement visuel, en guidant l'attention du spectateur vers les aspects importants.Nous commençons par extraire les caractéristiques des données multi-échelles et faisons une comparaison parallèle entre le génome et les données astronomiques. Les différences existantes créent le besoin d'approches différentes. Un point commun cependant est la nécessité de transitions continues qui aident les spectateurs à saisir les relations et les différences de taille relative entre les échelles. Pour satisfaire aux conditions posées par les deux aspects des données génomiques multi-échelles, nous présentons deux cadres conceptuels, basés sur les mêmes données. Le premier cadre, ScaleTrotter, représente la structure spatiale du génome, à tous les niveaux disponibles. Il donne à l'utilisateur la liberté de voyager du noyau d'une cellule aux atomes des bases, en passant par les différents niveaux d'organisation du génome. Pour rendre possible l'exploration de la structure de tous les niveaux, des transitions temporelles fluides sont utilisées. Même si toutes les échelles ne sont pas visibles simultanément, la transition temporelle utilisée superpose deux représentations d'un même élément à des échelles consécutives, ce qui met en évidence leur relation. Pour garantir la compréhensibilité et l'interactivité des données, les parties inutiles des données sont extraites à l'aide d'une caméra dépendante de l'échelle. Le deuxième cadre, Multiscale Unfolding, se concentre sur des aspects qui ne sont pas visibles dans ScaleTrotter : la séquence linéaire et une vue d'ensemble simultanée de tous les niveaux organisationnels. Les données sont redressées pour déplier l’empaquetage qui se produit à plusieurs niveaux de manière à conserver la connectivité entre les éléments. Pour représenter tous les niveaux disponibles, nous utilisons des transitions spatiales douces entre les niveaux. Ces transitions spatiales sont basées sur le même concept que les transitions temporelles du cadre précédent, en superposant les échelles et en mettant l'accent sur leur relation et leur différence de taille. Nous introduisons une technique d'interaction appelée Multiscale Zliding qui permet l'exploration des données et met davantage l'accent sur les différences de taille entre les niveaux. Dans chaque cadre conceptuel, l'un des deux aspects linéaire ou spatial des données sur le génome est sacrifié pour mettre l'accent sur l'autre. La thèse se termine par une discussion sur la possibilité de combiner les deux cadres, en minimisant les sacrifices pour explorer les deux aspects du génome qui sont d'égale importance. Dans cette thèse, nous faisons un pas de plus vers la compréhension complète de l'activité du génome
The human genome consists mainly of DNA, a macromolecule consisting of a long linear sequence of bases, tightly packed to fit in the relatively small nucleus. The packing gives rise to multiple hierarchical organizational levels. Recent research has shown that, along with the linear sequence, the spatial arrangement of the genome plays an important role in the genome’s function and activity. The visualization of both linear and spatial aspects of genome data is therefore necessary. In this thesis, we focus on the concept of continuous visual abstraction for multiscale data, applied to the visualization of the human genome. Visual abstraction is a concept inspired by illustrations that makes the job of visual processing simpler, by guiding the attention of the viewer to important aspects. We first extract characteristics of multiscale data and makes a parallel comparison between genome and astronomical data. The existing differences create the need for different approaches. A common point however is the need for continuous transitions that helps viewers grasp the relationships and relative size differences between scales. To satisfy the conditions posed by the two aspects of the multiscale genome data, we present two conceptual frameworks, based on the same data. The first framework, ScaleTrotter, represents the spatial structure of the genome, on all available levels. It gives users the freedom to travel from the nucleus of a cell to the atoms of the bases, passing through the different organizational levels of the genome. To make the exploration of the structure of all levels possible, smooth temporal transitions are used. Even though all the scales are not simultaneously visible, the temporal transition used superimposes two representations of the same element at consecutive scales emphasizing their relationship. To ensure the understandability and interactivity of the data, unnecessary parts of the data are abstracted away with the use of a scale-dependent camera. The second framework, Multiscale Unfolding, focuses on aspects that are not visible in ScaleTrotter: the linear sequence and a simultaneous overview of all the organizational levels. The data is straightened to unfold the packing that occurs on several levels in a way that conserves the connectivity between the elements. To represent all the available levels, we use smooth spatial transitions between the levels. These spatial transitions are based on the same concept of the temporal transitions of the previous framework, superimposing scales and emphasizing on their relationship and size difference. We introduce an interaction technique called Multiscale Zliding that allows the exploration of the data and further emphasizes the size differences between the levels. In each framework, one of either linear of spatial aspect of genome data is sacrificed to emphasize the other. The thesis concludes with a discussion about the possibility of combining the two frameworks, minimizing the sacrifices to explore the two equally important aspects of the genome. In this thesis, we take a step closer to fully understanding the activity of the genome

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Favero, Francesco. "Development of two new approaches for NGS data analysis of DNA and RNA molecules and their application in clinical and research fields." Doctoral thesis, Università del Piemonte Orientale, 2019. http://hdl.handle.net/11579/102446.

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The aim of this study is focused on two main areas of NGS analysis data: RNA-seq(with a specific interest in meta-transcriptomics) and DNA somatic mutations detection. We developed a simple and efficient pipeline for the analysis of NGS data derived from gene panels to identify DNA somatic point mutations. In particular we optimized a somatic variant calling procedure that was tested on simulated datasets and on real data. The performance of our system has been compared with currently available tools for variant calling reviewed in literature. For RNA-seq analysis, in this work we tested and optimized STAble, an algorithm developed originally in our laboratory for the de novo reconstruction of transcripts from non reference based RNA-seq data. At the beginning of this study, the first module of STAble was already been written. The first module is the one which reconstructs a list of transcripts starting from RNA-seq data. The aim of this study, particularly, consisted in adding a new module to STAble, developed in collaboration with Cambridge University, based on the flux-balance analysis in order to link the metatranscriptomic analysis to a metabolic approach. This goal has been achieved in order to study the metabolic fluxes of microbiota starting from metatranscriptomic data.

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Boukis, Andreas Christos [Verfasser], and M. A. R. [Akademischer Betreuer] Meier. "Moleküle als potentielle Datenspeichersysteme: Multikomponentenreaktionen sind der Schlüssel = Molecules as potential data storage systems: Multicomponent reactions are the key / Andreas Christos Boukis ; Betreuer: M. A. R. Meier." Karlsruhe : KIT-Bibliothek, 2018. http://d-nb.info/1164081071/34.

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Pearson, Anthony Craig. "Nanoscale Surface Patterning and Applications: Using Top-Down Patterning Methods to Aid Bottom-Up Fabrication." BYU ScholarsArchive, 2012. https://scholarsarchive.byu.edu/etd/3757.

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Bottom-up self-assembly can be used to create structures with sub-20 nm feature sizes or materials with advanced electrical properties. Here I demonstrate processes to enable such self-assembling systems including block copolymers and DNA origami, to be integrated into nanoelectronic devices. Additionally, I present a method which utilizes the high stability and electrical conductivity of graphene, which is a material formed using a bottom-up growth process, to create archival data storage devices. Specifically, I show a technique using block copolymer micelle lithography to fabricate arrays of 5 nm gold nanoparticles, which are chemically modified with a single-stranded DNA molecule and used to chemically attach DNA origami to a surface. Next, I demonstrate a method using electron beam lithography to control location of nanoparticles templated by block copolymer micelles, which can be used to enable precise position of DNA origami on a surface. To allow fabrication of conductive structures from a DNA origami template, I show a method using site-specific attachment of gold nanoparticles to and a subsequent metallization step to form continuous nanowires. Next, I demonstrate a long-term data storage method using nanoscale graphene fuses. Top-down electron beam lithography was used to pattern atomically thin sheets of graphene into nanofuses. To program the fuses, graphene is oxidized as the temperature of the fuse is raised via joule heating under a sufficiently high applied voltage. Finally, I investigate the effect of the fuse geometry and the electrical and thermal properties of the fuse material on the programming requirements of nanoscale fuses. Programming voltages and expected fuse temperatures obtained from finite element analysis simulations and a simple analytical model were compared with fuses fabricated from tellurium, a tellurium alloy, and tungsten.

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Книги з теми "Data storage into DNA molecules"

I, Bell George, and Marr Thomas G, eds. Computers and DNA: The proceedings of the Interface Between Computation Science and Nucleic Acid Sequencing Workshop, held Dec. 12 to 16, 1988 in Santa Fe, New Mexico. Redwood City, Calif: Addison-Wesley, 1990.

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Venter, J. Craig, Chris Fields, and Mark D. Adams. Automated DNA Sequencing and Analysis. Elsevier Science & Technology Books, 2012.

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(Editor), Mark D. Adams, Chris Fields (Editor), and J. Craig Venter (Editor), eds. Automated DNA Sequencing and Analysis. Academic Press, 1994.

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Shomorony, Ilan, and Reinhard Heckel. Information-Theoretic Foundations of DNA Data Storage. Now Publishers, 2022.

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Demidov, Vadim V. DNA Beyond Genes: From Data Storage and Computing to Nanobots, Nanomedicine, and Nanoelectronics. Springer, 2020.

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Demidov, Vadim V. DNA Beyond Genes: From Data Storage and Computing to Nanobots, Nanomedicine, and Nanoelectronics. Springer International Publishing AG, 2021.

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Data in Modern Biology (Codata Bulletin,). Elsevier Science Pub Co, 1985.

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Hilgurt, S. Ya, and O. A. Chemerys. Reconfigurable signature-based information security tools of computer systems. PH “Akademperiodyka”, 2022. http://dx.doi.org/10.15407/akademperiodyka.458.297.

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The book is devoted to the research and development of methods for combining computational structures for reconfigurable signature-based information protection tools for computer systems and networks in order to increase their efficiency. Network security tools based, among others, on such AI-based approaches as deep neural networking, despite the great progress shown in recent years, still suffer from nonzero recognition error probability. Even a low probability of such an error in a critical infrastructure can be disastrous. Therefore, signature-based recognition methods with their theoretically exact matching feature are still relevant when creating information security systems such as network intrusion detection systems, antivirus, anti-spam, and wormcontainment systems. The real time multi-pattern string matching task has been a major performance bottleneck in such systems. To speed up the recognition process, developers use a reconfigurable hardware platform based on FPGA devices. Such platform provides almost software flexibility and near-ASIC performance. The most important component of a signature-based information security system in terms of efficiency is the recognition module, in which the multipattern matching task is directly solved. It must not only check each byte of input data at speeds of tens and hundreds of gigabits/sec against hundreds of thousand or even millions patterns of signature database, but also change its structure every time a new signature appears or the operating conditions of the protected system change. As a result of the analysis of numerous examples of the development of reconfigurable information security systems, three most promising approaches to the construction of hardware circuits of recognition modules were identified, namely, content-addressable memory based on digital comparators, Bloom filter and Aho–Corasick finite automata. A method for fast quantification of components of recognition module and the entire system was proposed. The method makes it possible to exclude resource-intensive procedures for synthesizing digital circuits on FPGAs when building complex reconfigurable information security systems and their components. To improve the efficiency of the systems under study, structural-level combinational methods are proposed, which allow combining into single recognition device several matching schemes built on different approaches and their modifications, in such a way that their advantages are enhanced and disadvantages are eliminated. In order to achieve the maximum efficiency of combining methods, optimization methods are used. The methods of: parallel combining, sequential cascading and vertical junction have been formulated and investigated. The principle of multi-level combining of combining methods is also considered and researched. Algorithms for the implementation of the proposed combining methods have been developed. Software has been created that allows to conduct experiments with the developed methods and tools. Quantitative estimates are obtained for increasing the efficiency of constructing recognition modules as a result of using combination methods. The issue of optimization of reconfigurable devices presented in hardware description languages is considered. A modification of the method of affine transformations, which allows parallelizing such cycles that cannot be optimized by other methods, was presented. In order to facilitate the practical application of the developed methods and tools, a web service using high-performance computer technologies of grid and cloud computing was considered. The proposed methods to increase efficiency of matching procedure can also be used to solve important problems in other fields of science as data mining, analysis of DNA molecules, etc. Keywords: information security, signature, multi-pattern matching, FPGA, structural combining, efficiency, optimization, hardware description language.

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Частини книг з теми "Data storage into DNA molecules"

Chen, Yuan-Jyue, and Georg Seelig. "Scaling Up DNA Computing with Array-Based Synthesis and High-Throughput Sequencing." In Natural Computing Series, 281–93. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-19-9891-1_16.

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AbstractIt was 40 years ago today, when Ned taught DNA to play [32]. When Ned Seeman began laying the theoretical foundations of what is now DNA nanotechnology, he likely did not imagine the entire diversity and scale of molecular structures, machines, and computing devices that would be enabled by his work. While there are many reasons for the success of the field, not least the creativity shown by Ned and the community he helped build, such progress would not have been possible without breakthroughs in DNA synthesis and molecular analysis technology. Here, we argue that the technologies that will enable the next generation of DNA nanotechnology have already arrived but that we have not yet fully taken advantage of them. Specifically, we believe that it will become possible, in the near future, to dramatically scale up DNA nanotechnology through the use of array-synthesized DNA and high-throughput DNA sequencing. In this article, we provide an example of how DNA logic gates and circuits can be produced through enzymatic processing of array-synthesized DNA and can be read out by sequencing in a massively parallel format. We experimentally demonstrate processing and readout of 380 molecular gates in a single reaction. We further speculate that in the longer term, very large-scale DNA computing will find applications in the context of molecular diagnostics and, in particular, DNA data storage.

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Singh, Baljinder. "DNA Digital Data Storage: Breakthroughs in Biomedical Research." In Biomedical Translational Research, 135–40. Singapore: Springer Nature Singapore, 2022. http://dx.doi.org/10.1007/978-981-16-4345-3_9.

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Jenifer, P., and T. Kirthiga Devi. "Enhancing Data Security Using DNA Algorithm in Cloud Storage." In Artificial Intelligence Techniques for Advanced Computing Applications, 19–26. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-5329-5_3.

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Kim, Raphael. "DNA as Digital Data Storage: Opportunities and Challenges for HCI." In Communications in Computer and Information Science, 225–32. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-60700-5_29.

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Siddaramappa, V., and K. B. Ramesh. "DNA-Based XOR Operation (DNAX) for Data Security Using DNA as a Storage Medium." In Integrated Intelligent Computing, Communication and Security, 343–51. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-8797-4_36.

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Kruglik, S. G., C. Otto, A. G. Shvedko, V. V. Ermolenkov, V. A. Orlovich, V. S. Chirvony, and P. Y. Turpin. "New Raman Data on Photoinduced Porphyrin Translocation and Exciplex Formation in Cu(TMpy-P4) — DNA Complex." In Spectroscopy of Biological Molecules: Modern Trends, 395–96. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-011-5622-6_177.

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Yatribi, Anouar, Mostafa Belkasmi, and Fouad Ayoub. "An Efficient and Secure Forward Error Correcting Scheme for DNA Data Storage." In Proceedings of the Tenth International Conference on Soft Computing and Pattern Recognition (SoCPaR 2018), 226–37. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-17065-3_23.

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Satz, Alexander L., and Weiren Cui. "Analysis of DNA-Encoded Library Screening Data: Selection of Molecules for Synthesis." In Methods in Molecular Biology, 195–205. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2545-3_23.

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Rasool, Abdur, Qiang Qu, Qingshan Jiang, and Yang Wang. "A Strategy-based Optimization Algorithm to Design Codes for DNA Data Storage System." In Algorithms and Architectures for Parallel Processing, 284–99. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-95388-1_19.

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Pragaladan, R., and S. Sathappan. "A Secure Cloud Data Storage Combining DNA Structure and Multi-aspect Time-Integrated Cut-off Potential." In Advances in Intelligent Systems and Computing, 361–74. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-7200-0_33.

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Тези доповідей конференцій з теми "Data storage into DNA molecules"

Ghosh, Nishant, N. Anushka Reddy, VNS Sasank, K. Suvarchala, and Sushma Patkar. "Preserving History with Synthetic DNA: An Innovative Data Storage Solution." In 2024 IEEE International Conference on Electronics, Computing and Communication Technologies (CONECCT), 1–6. IEEE, 2024. http://dx.doi.org/10.1109/conecct62155.2024.10677101.

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En-Nattouh, Youssef, and Reda Jourani. "Improved storage of Big Data in DNA using the PCA algorithm." In 2024 International Conference on Circuit, Systems and Communication (ICCSC), 1–5. IEEE, 2024. http://dx.doi.org/10.1109/iccsc62074.2024.10616520.

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Srivastava, Shubham, Krishna Gopal Benerjee, and Adrish Banerjee. "Efficient Bidirectional RNNs for Substitution Error Correction in DNA Data Storage." In 2024 IEEE International Conference on Machine Learning for Communication and Networking (ICMLCN), 434–39. IEEE, 2024. http://dx.doi.org/10.1109/icmlcn59089.2024.10625179.

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Yuvarani, R., and R. Mahaveerakannan. "Enhanced Cloud Security Through DNA-based Authentication for Data Storage and Transactions." In 2024 5th International Conference on Electronics and Sustainable Communication Systems (ICESC), 589–94. IEEE, 2024. http://dx.doi.org/10.1109/icesc60852.2024.10689928.

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Palunčić, Filip, Daniella Palunčić, and B. T. Maharaj. "Capacity of Runlength-Limited and GC-Content Constrained Codes for DNA Data Storage." In 2024 IEEE International Symposium on Information Theory (ISIT), 1937–42. IEEE, 2024. http://dx.doi.org/10.1109/isit57864.2024.10619166.

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Martens, Koen, David Barge, Lijun Liu, Sybren Santermans, Colin Stoquart, Jacobus Delport, Kherim Willems, et al. "The Nanopore-FET as a High-Throughput Barcode Molecule Reader for Single-Molecule Omics and Read-out of DNA Digital Data Storage." In 2022 IEEE International Electron Devices Meeting (IEDM). IEEE, 2022. http://dx.doi.org/10.1109/iedm45625.2022.10019451.

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Heller, Michael J., Carl Edman, Don Ackley, WJ Kitchen, Christian Gurtner, and Rachel Formosa. "ELECTRIC FIELD ASSISTED SELF-ASSEMBLY OF DNA BASED MOLECULAR CHROMOPHORE COMPONENTS FOR OPTICAL DATA STORAGE AND OTHER NANOTECHNOLOGY APPLICATIONS." In Spatial Light Modulators and Integrated Optoelectronic Arrays. Washington, D.C.: OSA, 1999. http://dx.doi.org/10.1364/slm.1999.stua2.

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Patel, Radhika, Dweepna Garg, Milind Shah, Safeya Dharmajwala, Kush Jindal, and Amit Nayak. "DNA Archives: Revolutionizing Data Storage." In 2023 3rd International Conference on Innovative Mechanisms for Industry Applications (ICIMIA). IEEE, 2023. http://dx.doi.org/10.1109/icimia60377.2023.10426397.

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Weide-Zaage, Kirsten. "Technical Implementation of DNA Data-Storage." In 2024 International Conference on Electronics Packaging (ICEP). IEEE, 2024. http://dx.doi.org/10.23919/icep61562.2024.10535600.

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Mansuripur, Masud. "DNA, human memory, and the storage technology of the 21st century." In Optical Data Storage, edited by Terril Hurst and Seiji Kobayashi. SPIE, 2002. http://dx.doi.org/10.1117/12.453368.

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Звіти організацій з теми "Data storage into DNA molecules"

Iudicone, Daniele, and Marina Montresor. Omics community protocols. EuroSea, 2023. http://dx.doi.org/10.3289/eurosea_d3.19.

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The aim of the WP3 “Network Integration and Improvements” is to coordinate and enhance key aspects of integration of European observing technology (and related data flows) for its use in the context of international ocean monitoring activities. One of the dimensions of the integrations is the constitution of thematic networks, that is, networks whose aim is to address specific observational challenges and thus to favor innovation, innovation that will ultimately support the Blue economy. In this context, the specific aim of Task 3.8 is to accelerate the adoption of molecular methods such as genomic, transcriptomic (and related “omics”) approaches, currently used as monitoring tools in human health, to the assessment of the state and change of marine ecosystems. It was designed to favor the increase the capacity to evaluate biological diversity and the organismal metabolic states in different environmental conditions by the development of “augmented observatories”, utilizing state-of-art methodologies in genomic-enabled research at multidisciplinary observatories at well-established marine LTERs, with main focus on a mature oceanographic observatory in Naples, NEREA. In addition, an effort is dedicated to connecting existing observatories that intend to augment their observations with molecular tools. Molecular approaches come with many different options for the protocols (size fractioning, sample collection and storage, sequencing etc). One main challenge in systematically implementing those approaches is thus their standardization across observatories. Based on a survey of existing methods and on a 3-year experience in collecting, sequencing and analyzing molecular data, this deliverable is thus dedicated to present the SOPs implemented and tested at NEREA. The SOPs consider a size fractioning of the biological material to avoid biases toward more abundant, smaller organisms such as bacteria. They cover both the highly stable DNA and the less stable RNA and they are essentially an evolution of the ones developed for the highly successful Tara Oceans Expedition and recently updated for the Expedition Mission Microbiomes, an All-Atlantic expedition organised and executed by the EU AtlantECO project. Importantly, they have only slight variations with respect the ones adopted by the network of genomic observatories EMOBON. Discussions are ongoing with EMOBON to perfectly align the protocols. The SOPs are being disseminated via the main national and international networks. (EuroSea Deliverable, D3.19)

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Heifetz, Yael, and Michael Bender. Success and failure in insect fertilization and reproduction - the role of the female accessory glands. United States Department of Agriculture, December 2006. http://dx.doi.org/10.32747/2006.7695586.bard.

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The research problem. Understanding of insect reproduction has been critical to the design of insect pest control strategies including disruptions of mate-finding, courtship and sperm transfer by male insects. It is well known that males transfer proteins to females during mating that profoundly affect female reproductive physiology, but little is known about the molecular basis of female mating response and no attempts have yet been made to interfere with female post-mating responses that directly bear on the efficacy of fertilization. The female reproductive tract provides a crucial environment for the events of fertilization yet thus far those events and the role of the female tract in influencing them are poorly understood. For this project, we have chosen to focus on the lower reproductive tract because it is the site of two processes critical to reproduction: sperm management (storage, maintenance, and release from storage) and fertilization. E,fforts during this project period centered on the elucidation of mating responses in the female lower reproductive tract The central goals of this project were: 1. To identify mating-responsive genes in the female lower reproductive tract using DNA microarray technology. 2. In parallel, to identify mating-responsive genes in these tissues using proteomic assays (2D gels and LC-MS/MS techniques). 3. To integrate proteomic and genomic analyses of reproductive tract gene expression to identify significant genes for functional analysis. Our main achievements were: 1. Identification of mating-responsive genes in the female lower reproductive tract. We identified 539 mating-responsive genes using genomic and proteomic approaches. This analysis revealed a shift from gene silencing to gene activation soon after mating and a peak in differential gene expression at 6 hours post-mating. In addition, comparison of the two datasets revealed an expression pattern consistent with the model that important reproductive proteins are pre-programmed for synthesis prior to mating. This work was published in Mack et al. (2006). Validation experiments using real-time PCR techniques suggest that microarray assays provide a conservativestimate of the true transcriptional activity in reproductive tissues. 2.lntegration of proteomics and genomics data sets. We compared the expression profiles from DNA microarray data with the proteins identified in our proteomic experiments. Although comparing the two data sets poses analyical challenges, it provides a more complete view of gene expression as well as insights into how specific genes may be regulated. This work was published in Mack et al. (2006). 3. Development of primary reproductive tract cell cultures. We developed primary cell cultures of dispersed reproductive tract cell types and determined conditions for organ culture of the entire reproductive tract. This work will allow us to rapidly screen mating-responsive genes for a variety of reproductive-tract specifi c functions. Scientific and agricultural significance. Together, these studies have defined the genetic response to mating in a part of the female reproductive tract that is critical for successful fertllization and have identified alarge set of mating-responsive genes. This work is the first to combine both genomic and proteomic approaches in determining female mating response in these tissues and has provided important insights into insect reproductive behavior.

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Ron, Eliora, and Eugene Eugene Nester. Global functional genomics of plant cell transformation by agrobacterium. United States Department of Agriculture, March 2009. http://dx.doi.org/10.32747/2009.7695860.bard.

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The aim of this study was to carry out a global functional genomics analysis of plant cell transformation by Agrobacterium in order to define and characterize the physiology of Agrobacterium in the acidic environment of a wounded plant. We planed to study the proteome and transcriptome of Agrobacterium in response to a change in pH, from 7.2 to 5.5 and identify genes and circuits directly involved in this change. Bacteria-plant interactions involve a large number of global regulatory systems, which are essential for protection against new stressful conditions. The interaction of bacteria with their hosts has been previously studied by genetic-physiological methods. We wanted to make use of the new capabilities to study these interactions on a global scale, using transcription analysis (transcriptomics, microarrays) and proteomics (2D gel electrophoresis and mass spectrometry). The results provided extensive data on the functional genomics under conditions that partially mimic plant infection and – in addition - revealed some surprising and significant data. Thus, we identified the genes whose expression is modulated when Agrobacterium is grown under the acidic conditions found in the rhizosphere (pH 5.5), an essential environmental factor in Agrobacterium – plant interactions essential for induction of the virulence program by plant signal molecules. Among the 45 genes whose expression was significantly elevated, of special interest is the two-component chromosomally encoded system, ChvG/I which is involved in regulating acid inducible genes. A second exciting system under acid and ChvG/Icontrol is a secretion system for proteins, T6SS, encoded by 14 genes which appears to be important for Rhizobium leguminosarum nodule formation and nitrogen fixation and for virulence of Agrobacterium. The proteome analysis revealed that gamma aminobutyric acid (GABA), a metabolite secreted by wounded plants, induces the synthesis of an Agrobacterium lactonase which degrades the quorum sensing signal, N-acyl homoserine lactone (AHL), resulting in attenuation of virulence. In addition, through a transcriptomic analysis of Agrobacterium growing at the pH of the rhizosphere (pH=5.5), we demonstrated that salicylic acid (SA) a well-studied plant signal molecule important in plant defense, attenuates Agrobacterium virulence in two distinct ways - by down regulating the synthesis of the virulence (vir) genes required for the processing and transfer of the T-DNA and by inducing the same lactonase, which in turn degrades the AHL. Thus, GABA and SA with different molecular structures, induce the expression of these same genes. The identification of genes whose expression is modulated by conditions that mimic plant infection, as well as the identification of regulatory molecules that help control the early stages of infection, advance our understanding of this complex bacterial-plant interaction and has immediate potential applications to modify it. We expect that the data generated by our research will be used to develop novel strategies for the control of crown gall disease. Moreover, these results will also provide the basis for future biotechnological approaches that will use genetic manipulations to improve bacterial-plant interactions, leading to more efficient DNA transfer to recalcitrant plants and robust symbiosis. These advances will, in turn, contribute to plant protection by introducing genes for resistance against other bacteria, pests and environmental stress.

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Rodriguez Muxica, Natalia. Open configuration options Bioinformatics for Researchers in Life Sciences: Tools and Learning Resources. Inter-American Development Bank, February 2022. http://dx.doi.org/10.18235/0003982.

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The COVID-19 pandemic has shown that bioinformatics--a multidisciplinary field that combines biological knowledge with computer programming concerned with the acquisition, storage, analysis, and dissemination of biological data--has a fundamental role in scientific research strategies in all disciplines involved in fighting the virus and its variants. It aids in sequencing and annotating genomes and their observed mutations; analyzing gene and protein expression; simulation and modeling of DNA, RNA, proteins and biomolecular interactions; and mining of biological literature, among many other critical areas of research. Studies suggest that bioinformatics skills in the Latin American and Caribbean region are relatively incipient, and thus its scientific systems cannot take full advantage of the increasing availability of bioinformatic tools and data. This dataset is a catalog of bioinformatics software for researchers and professionals working in life sciences. It includes more than 300 different tools for varied uses, such as data analysis, visualization, repositories and databases, data storage services, scientific communication, marketplace and collaboration, and lab resource management. Most tools are available as web-based or desktop applications, while others are programming libraries. It also includes 10 suggested entries for other third-party repositories that could be of use.

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Epel, Bernard, and Roger Beachy. Mechanisms of intra- and intercellular targeting and movement of tobacco mosaic virus. United States Department of Agriculture, November 2005. http://dx.doi.org/10.32747/2005.7695874.bard.

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To cause disease, plant viruses must replicate and spread locally and systemically within the host. Cell-to-cell virus spread is mediated by virus-encoded movement proteins (MPs), which modify the structure and function of plasmodesmata (Pd), trans-wall co-axial membranous tunnels that interconnect the cytoplasm of neighboring cells. Tobacco mosaic virus (TMV) employ a single MP for cell- cell spread and for which CP is not required. The PIs, Beachy (USA) and Epel (Israel) and co-workers, developed new tools and approaches for study of the mechanism of spread of TMV that lead to a partial identification and molecular characterization of the cellular machinery involved in the trafficking process. Original research objectives: Based on our data and those of others, we proposed a working model of plant viral spread. Our model stated that MPᵀᴹⱽ, an integral ER membrane protein with its C-terminus exposed to the cytoplasm (Reichel and Beachy, 1998), alters the Pd SEL, causes the Pd cytoplasmic annulus to dilate (Wolf et al., 1989), allowing ER to glide through Pd and that this gliding is cytoskeleton mediated. The model claimed that in absence of MP, the ER in Pd (the desmotubule) is stationary, i.e. does not move through the Pd. Based on this model we designed a series of experiments to test the following questions: -Does MP potentiate ER movement through the Pd? - In the presence of MP, is there communication between adjacent cells via ER lumen? -Does MP potentiate the movement of cytoskeletal elements cell to cell? -Is MP required for cell-to-cell movement of ER membranes between cells in sink tissue? -Is the binding in situ of MP to RNA specific to vRNA sequences or is it nonspecific as measured in vitro? And if specific: -What sequences of RNA are involved in binding to MP? And finally, what host proteins are associated with MP during intracellular targeting to various subcellular targets and what if any post-translational modifications occur to MP, other than phosphorylation (Kawakami et al., 1999)? Major conclusions, solutions and achievements. A new quantitative tool was developed to measure the "coefficient of conductivity" of Pd to cytoplasmic soluble proteins. Employing this tool, we measured changes in Pd conductivity in epidermal cells of sink and source leaves of wild-type and transgenic Nicotiana benthamiana (N. benthamiana) plants expressing MPᵀᴹⱽ incubated both in dark and light and at 16 and 25 ᵒC (Liarzi and Epel, 2005 (appendix 1). To test our model we measured the effect of the presence of MP on cell-to-cell spread of a cytoplasmic fluorescent probe, of two ER intrinsic membrane protein-probes and two ER lumen protein-probes fused to GFP. The effect of a mutant virus that is incapable of cell-to-cell spread on the spread of these probes was also determined. Our data shows that MP reduces SEL for cytoplasmic molecules, dilates the desmotubule allowing cell-cell diffusion of proteins via the desmotubule lumen and reduces the rate of spread of the ER membrane probes. Replicase was shown to enhance cell-cell spread. The data are not in support of the proposed model and have led us to propose a new model for virus cell-cell spread: this model proposes that MP, an integral ER membrane protein, forms a MP:vRNAER complex and that this ER-membrane complex diffuses in the lipid milieu of the ER into the desmotubule (the ER within the Pd), and spreads cell to cell by simple diffusion in the ER/desmotubule membrane; the driving force for spread is the chemical potential gradient between an infected cell and contingent non-infected neighbors. Our data also suggests that the virus replicase has a function in altering the Pd conductivity. Transgenic plant lines that express the MP gene of the Cg tobamovirus fused to YFP under the control the ecdysone receptor and methoxyfenocide ligand were generated by the Beachy group and the expression pattern and the timing and targeting patterns were determined. A vector expressing this MPs was also developed for use by the Epel lab . The transgenic lines are being used to identify and isolate host genes that are required for cell-to-cell movement of TMV/tobamoviruses. This line is now being grown and to be employed in proteomic studies which will commence November 2005. T-DNA insertion mutagenesis is being developed to identify and isolate host genes required for cell-to-cell movement of TMV.

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Lichter, Amnon, Gopi K. Podila, and Maria R. Davis. Identification of Genetic Determinants that Facilitate Development of B. cinerea at Low Temperature and its Postharvest Pathogenicity. United States Department of Agriculture, March 2011. http://dx.doi.org/10.32747/2011.7592641.bard.

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Botrytis cinerea is the postharvest pathogen of many agricultural produce with table grapes, strawberries and tomatoes as major targets. The high efficiency with which B. cinerea causes disease on these produce during storage is attributed in part due to its exceptional ability to develop at very low temperature. Our major goal was to understand the genetic determinants which enable it to develop at low temperature. The specific research objectives were: 1. Identify expression pattern of genes in a coldenriched cDNA library. 2. Identify B. cinerea orthologs of cold-induced genes 3. Profile protein expression and secretion at low temperature on strawberry and grape supplemented media. 4. Test novel methods for the functional analysis of coldresponsive genes. Objective 1 was modified during the research because a microarray platform became available and it allowed us to probe the whole set of candidate genes according to the sequence of 2 strains of the fungus, BO5.10 and T4. The results of this experiment allowed us to validate some of our earlier observations which referred to genes which were the product of a SSH suppression-subtraction library. Before the microarray became available during 2008 we also analyzed the expression of 15 orthologs of cold-induced genes and some of these results were also validated by the microarray experiment. One of our goals was also to perform functional analysis of cold-induced genes. This goal was hampered for 3 years because current methodology for transformation with ‘protoplasts’ failed to deliver knockouts of bacteriordopsin-like (bR) gene which was our primary target for functional analysis. Consequently, we developed 2 alternative transformation platforms, one which involves an air-gun based technique and another which involves DNA injection into sclerotia. Both techniques show great promise and have been validated using different constructs. This contribution is likely to serve the scientific community in the near future. Using these technologies we generated gene knockout constructs of 2 genes and have tested there effect on survival of the fungus at low temperature. With reference to the bR genes our results show that it has a significant effect on mycelial growth of the B. cinerea and the mutants have retarded development at extreme conditions of ionic stress, osmotic stress and low temperature. Another gene of unknown function, HP1 is still under analysis. An ortholog of the yeast cold-induced gene, CCH1 which encodes a calcium tunnel and was shown to be cold-induced in B. cinerea was recently cloned and used to complement yeast mutants and rescue them from cold-sensitivity. One of the significant findings of the microarray study involves a T2 ribonuclease which was validated to be cold-induced by qPCR analysis. This and other genes will serve for future studies. In the frame of the study we also screened a population of 631 natural B. cinerea isolates for development at low temperature and have identified several strains with much higher and lower capacity to develop at low temperature. These strains are likely to be used in the future as candidates for further functional analysis. The major conclusions from the above research point to specific targets of cold-induced genes which are likely to play a role in cold tolerance. One of the most significant observations from the microarray study is that low temperature does not induce ‘general stress response in B. cinerea, which is in agreement to its exceptional capacity to develop at low temperature. Due to the tragic murder of the Co-PI Maria R. Davis and GopiPodila on Feb. 2010 it is impossible to deliver their contribution to the research. The information of the PI is that they failed to deliver objective 4 and none of the information which relates to objective 3 has been delivered to the PI before the murder or in a visit to U. Alabama during June, 2010. Therefore, this report is based solely on the IS data.

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