Data Hiding Based DNA Issues: A Review

يعد أمن المعلومات مصدر قلق رئيسي ، لا سيما مع نمو استخدام الإنترنت. بسبب هذا النمو ظهرت حالات اختراق للبيانات المرسلة منها الوصول غير المصرح به التي يتم التصدي له باستخدام تقنيات اتصال آمنة متنوعة  وهي ؛ التشفير وإخفاء البيانات. تتعلق الاتجاهات الحديثة بالحمض النووي المستخدم في التشفير وإخفاء البيانات كحامل للبيانات من خلال استغلال خصائصه الجزيئية الحيوية. تقدم هذه الورقة استبيانًا حول البحوث المنشورة المستندة إلى الحمض النووي لاخفاء البيانات المهمة  كحامي لها  والمنقولة عبر قناة غير آمنة  لمعرفة  نقاط القوة والضعف فيها. لمساعدة البحث المستقبلي في تصميم تقنيات أكثر كفاءة وأمانًا للاخفاء في الحمض نوويSecurity of Information are a key concern, particularly with the extension growth of internet usage. This growth comes the incidents of unauthorized access which are countered by the use of varied secure communication techniques, namely; cryptography and data hiding. More recent trends are concerned with DNA used for cryptography and data hiding as a carrier exploiting its bio-molecular properties. This paper provides a review about published DNA based data hiding techniques using the DNA as a safeguard to critical data that transmitted on an insecure channel, to find out the strength and weaknesses points of them. This will help the future research in designing of more efficient and secure data hiding techniques-based DNA

DNA nanotechnology: new adventures for an old warhorse

As the blueprint of life, the natural exploits of DNA are admirable. However, DNA should not only be viewed within a biological context. It is an elegantly simple yet functionally complex chemical polymer with properties that make it an ideal platform for engineering new nanotechnologies. Rapidly advancing synthesis and sequencing technologies are enabling novel unnatural applications for DNA beyond the realm of genetics. Here we explore the chemical biology of DNA nanotechnology for emerging applications in communication and digital data storage. Early studies of DNA as an alternative to magnetic and optical storage mediums have not only been promising, but have demonstrated the potential of DNA to revolutionize the way we interact with digital data in the future.United States. Defense Advanced Research Projects Agency (Contract FA8721-05-C-0002)National Institutes of Health (U.S.) (Grant 1R01EB017755)National Institutes of Health (U.S.) (Grant 1DP2OD008435)National Institutes of Health (U.S.) (Grant 1P50GM098792

DNA Computing Using Cryptographic and Steganographic Strategies

Information protection and secrecy are major concerns, especially regarding the internet’s rapid growth and widespread usage. Unauthorized database access is becoming more common and is being combated using a variety of encrypted communication methods, such as encryption and data hiding. DNA cryptography and steganography are used as carriers by utilizing the bio-molecular computing properties that have become more common in recent years. This study examines recently published DNA steganography algorithms, which use DNA to encrypt confidential data transmitted through an insecure communication channel. Several DNA-based steganography strategies will be addressed, with a focus on the algorithm’s advantages and drawbacks. Probability cracking, blindness, double layer of security, and other considerations are used to compare steganography algorithms. This research would help and create more effective and accurate DNA steganography strategies in the future

Enhancement to the patient's health care image encryption system, using several layers of DNA computing and AES (MLAESDNA)

Keeping patient health data private has been a big issue for decades, and this issue will not go away anytime soon. As an integral part of many developing technologies, cryptographic Internet communications ICs (e.g. fog computing and cloud computing) are a main focus of IoT research. Just keep trying all the potential keys until you find the correct one. New and future technologies must have a model of DNA cryptography in order to assure the efficient flow of these technologies. Public-key cryptography is also required to make DNA sequence testing devices for the Internet of Things interoperable. This method employs DNA layers and AES in such a way that it may be easier to design a trustworthy hybrid encryption algorithm that uses DNA layers and AES. In order to guard against brute-force decryption attacks, DNA sequences are encrypted using three keys: (I) the main key, which is the key to the AES encryption algorithm; (II) the rule 1 key, which is the base DNA structure; and (III) the rule 2 key, which is the DNA helical structure binding probability. This key was created with increased security in mind. multi-layered AES encryption and DNA computing were applied to "Covid 19" images in this research (MLAESDNA). With cloud computing, the MLAESDNA team was able to show that IoT signals could be enhanced with encrypted data

Wireless Security Protocol in DNA Bio-Inspired Network

The 21st century communications have evolved rapidly and spread all over the world using the Wi-Fi network which has provided benefits of connection which become more desirable for users to connect to the internet. These benefits are driving the world to a major internet security issues that links to harm their own sensitive data and it resulting for generates encouragement for attackers to drill the legitimate user’s Wi-Fi connection to access to where they want to organize and eavesdropping the data passed to hack them through and revealing it to check whether it is useful for them, hence exploiting packets travelling through the user’s Wi-Fi and using of the powerful of super sniffer techniques by the hackers to break in to such as malware and sniffing software that allows them to crack on the Wi-Fi to steal the data of the user who uses the eavesdropper Wi-Fi without their knowledge, these sniffers open to the hackers access to the user’s data like bank details and other data, it could be using their details for a crime such as find their identity which make the world more concerns about their personal information and they are looking for the latest security protocols to protect their Wi-Fi network. Wi-Fi security introduces a number of vulnerabilities that give hackers an opportunity to cause harm to the Wi-Fi users by stealing information, accessing the Wi-Fi network to compromise the Wi-Fi network as a way to access the enterprise network which is used by some security protocols. This would allow a hacker to use sniffers to access the Wi-Fi enterprise network which is used in coffee shops across the world and other trading premises by probing the SSID of their Wi-Fi. Near by the hackers would be able to crack the security protocols such as WPA or WPA2 which are the latest protocol that users use for their Wi-Fi security keys. In our research we have taken different security methods to secure the Wi-Fi network using the bio-inspired DNA is the idea comed from the Deoxyribonucleic Acid DNA because that DNA have several important features including the random nature of the sequences denoted by alphapet characters A, C, G and T to perform encoded unique DNA sequences that is transmitting the secrets and the DNA encryption comes from the biology of the DNA science of the human and animals. Our research has achieved basic steps which encrypt the user’s static data to DNA sequence to use it for a security access key this work is functioning successfully to DNA bases and experimentation prove in the implementation at chapter 5, and we used the symmetric cryptographic keys in DNA sequence encryption to be similar at both parties with the admin(Wi-Fi) and clients and this is the basic step for this project and it needs to implement the dynamic DNA to make the keys more secure for each user and we have explained how we can match and mismatch these encrypted data and how they need to updated automatically to new security keys with the dynamic DNA sequence in future work [1]. The achievements of our research are proposed to convert user data to a DNA security sequence to use it in the same way as the existing security protocols such as WPA2 but in DNA format with the dynamic key and static user data will keep the security key rubost durig the automatic updates, hence the static data and dynamic data can be updated automatically when adding the dynamic data to the project in future work for the user access key and this can be suitable for multi-users to form an autonomous Wi-Fi connection and DNA security key to mitigating some flaws of that existing security protocols techniques has such as sharing the same security key on the same Wi-Fi network users

A new color image encryption technique using DNA computing and Chaos-based substitution box

In many cases, images contain sensitive information and patterns that require secure processing to avoid risk. It can be accessed by unauthorized users who can illegally exploit them to threaten the safety of people’s life and property. Protecting the privacies of the images has quickly become one of the biggest obstacles that prevent further exploration of image data. In this paper, we propose a novel privacy-preserving scheme to protect sensitive information within images. The proposed approach combines deoxyribonucleic acid (DNA) sequencing code, Arnold transformation (AT), and a chaotic dynamical system to construct an initial S-box. Various tests have been conducted to validate the randomness of this newly constructed S-box. These tests include National Institute of Standards and Technology (NIST) analysis, histogram analysis (HA), nonlinearity analysis (NL), strict avalanche criterion (SAC), bit independence criterion (BIC), bit independence criterion strict avalanche criterion (BIC-SAC), bit independence criterion nonlinearity (BIC-NL), equiprobable input/output XOR distribution, and linear approximation probability (LP). The proposed scheme possesses higher security wit NL = 103.75, SAC ≈ 0.5 and LP = 0.1560. Other tests such as BIC-SAC and BIC-NL calculated values are 0.4960 and 112.35, respectively. The results show that the proposed scheme has a strong ability to resist many attacks. Furthermore, the achieved results are compared to existing state-of-the-art methods. The comparison results further demonstrate the effectiveness of the proposed algorithm

Towards Understanding Helicase and Chaperone Activities in the RNA Degradosome

The E. coli RNA degradosome is a complex multi-enzyme machine which is central to the post-transcriptional regulation of the cell. Some of its functions include maturing and processing sRNA, rRNA, and tRNA, as well as degrading mRNA. The key components of the RNA degradosome include the endoribonuclease RNase E, the DEAD-box RNA helicase RhlB, the glycolytic enzyme enolase, and the phosphorolytic exoribonuclease PNPase. The degradosome has also been previously shown to associate with the RNA chaperone Hfq to form a small RNA guided machinery that targets defined transcripts. This thesis attempts to investigate several characteristics of the degradosome, including the importance of RhlB, the structure of a portion of the RNase E C-terminal domain that recruits enolase and helicase, and the association between Hfq, ChiX and the RNase E C-terminus. The thesis also explored structural details regarding the small domain of RNase E involved in both RNA binding and oligomerisation and its relationship to the RNA binding KH domains. Utilizing a point mutation in the DEAD box of RhlB, I have found increased RNA affinity to mutant RhlB, the potential structure of Hfq — an RNA chaperone — bound to the sRNA ChiX, and a structural correlation between the RNase E small domain and other KH domains. Preliminary models of Hfq and ChiX structure show a novel binding mode for class II sRNAs as the majority of ChiX associating with the distal face of Hfq. Bioinformatic studies reveal evolutionary roots between the KH domains and the RNase E small domain, supporting the hypothesis that the RNase E small domain may be involved in a novel mode of RNA binding and recognition

Attributes of the [4Fe4S] Cofactor Coordinated by UvrC, a DNA Repair Enzyme

Protein-bound iron sulfur clusters are critical in cells and allow proteins to carry out many essential functions as electron carriers, catalysts for challenging organic reactions, and sensors of cellular environments. A wide range of protein families are known to coordinate iron sulfur clusters, and a growing category includes proteins involved in maintenance of the genome. Within the last three decades, iron sulfur clusters have been demonstrated to be important for enzymes that function in DNA repair, DNA replication, and transcription pathways. To date, iron sulfur clusters in the cubane [4Fe4S] geometry with all cysteine ligands have been exclusively reported for DNA repair and replication enzymes. In contrast to enzymes where the cofactor is necessary for active site chemistry or directly-linked to protein function, the [4Fe4S] cluster in the overwhelming majority of repair and replication enzymes is not involved in the catalytic modification of DNA substrates. Rather, the role of the cofactor appears to vary in function from protein to protein, and has been demonstrated to be important for protein stability, in the assembly of multisubunit proteins, and for substrate recognition, among other roles. Through investigations of the redox chemistry of the cofactor, our group has found that these enzymes participate in DNA-mediated charge transport chemistry, the process through which electrons rapidly migrate through well-stacked, duplex DNA. Long-range, DNA-mediated redox signaling provides a means of rapid communication among DNA-processing proteins for organizing repair and replication activities across the nucleus. Notably, the first observations of the [4Fe4S] cofactor associated with repair and replications enzymes has consistently occurred well after the first biochemical studies of these enzymes. In some cases, the demonstration of a [4Fe4S] center has taken place decades later after initial work. Some proteins have required use of anaerobic methods in order to detect the cofactor, perhaps explaining why in some cases the metal center had eluded observation. Analysis of protein sequences might be expected to help accelerate identification of new iron sulfur centers in repair and replication enzymes. However, even with the abundance of sequencing data available in the post-genomic era, prediction of a metal center based on sequences alone has been challenging. This is in large part because the spacing of the coordinating cysteine residues can be quite irregular, leading to a weak bioinformatic signature. Identifying proteins with overlooked [4Fe4S] cofactors poses an exciting challenge, and there are some elegant examples in the literature where data from genetics assays has been used in combination with careful sequence analysis to predict and discover iron sulfur centers in repair and replication enzymes. Described here is the evolution of our studies on one well-known repair enzyme from Escherichia coli, UvrC. UvrC is part of the nucleotide excision repair pathway in the Bacteria domain which is responsible for addressing the wide class of bulky, helix-distorting lesions that can form after exposure to sources such as ultraviolet light, cigarette smoke, chemotherapeutics, and protein-DNA crosslinks. UvrC, an excision nuclease with two distinct active sites that incise the phosphodiester backbone on either side of the site of damage, has been historically challenging to study. Given how essential UvrC is in repairing damaged substrates, new insight has been greatly needed. Through integration of several key reports from the literature regarding the sequence of UvrC and evidence that pointed to a cofactor from genetics assays, our group predicted that UvrC is a [4Fe4S] protein. Development of a new overexpression system and an anaerobic purification method allowed for isolation of UvrC in holo form. We used spectroscopic techniques to confirm that the cluster type was [4Fe4S], and a combination of spectroscopy and chromatography to demonstrate that the UvrC-bound cofactor is susceptible to oxidative degradation. We also found that loss of the cofactor, either through aerobic degradation or mutation of coordinating cysteines, is associated with aggregation of apoprotein. Importantly, in its holo form with the cofactor bound, UvrC forms high affinity complexes with duplexed DNA substrates; the apparent dissociation constants to well-matched and damaged duplex substrates are 100 ± 20 nM and 80 ± 30 nM, respectively. This high affinity DNA binding contrasts reports made for isolated protein lacking the cofactor. Moreover, using DNA electrochemistry, we find that the cluster coordinated by UvrC is redox-active and participates in DNA-mediated charge transport chemistry with DNA-bound midpoint potential of 90 mV vs. NHE. The work detailed in this dissertation has highlighted how critical the [4Fe4S] center is for UvrC, where the cofactor has been implicated in protein stabilization, substrate binding, and redox signaling on DNA. Handling an apo form of UvrC may have led to the previous challenges catalogued by researchers. Through the development of entirely new methods to study UvrC under anaerobic conditions, many opportunities are now available to study UvrC and the NER pathway anew in vitro and in vivo. Such work will contribute additional insight on how iron sulfur clusters are essential for enzymes that maintain genomic integrity.</p

A framework for visual analysis of protein structure states

Proteins are involved in most molecular processes in living organisms, and their study, therefore, finds use in many applications. The 3D structure plays a fundamental role in the protein's ability to bind other molecules and thus participate in biological processes. However, the structure of a protein can change over time; for example, the binding of a molecule can result in conformational change. The goal of the work is to create a software framework that would, for a set of proteins, store information about their different conformations, to extract and visualize this data via a web application. The entire system will be applied to an existing set of conformations for structures from the PDB, but at the same time will be general enough to allow analysis of new datasets. 1Proteiny se podílí na většině molekulárních procesů v žívých organismech a jejich studium proto nachází uplatnění v mnoha aplikacích. 3D struktura hraje zásadní roli ve schopnosti proteinu vázat se na další molekuly a tím se podílet na biologických procesech. Nicméně struktura proteinu se může v čase měnit v závislosti na externích faktorech, jako je třeba navázání molekuly, která může způsobit změnu konformace. Cílem práce je vytvořit softwarový framework, který by umožnil udržovat pro sadu proteinů informace o jejich konformacích, tyto data vytěžovat a vizualizovat ve webovém prostředí. Celý systém bude aplikován na existující sadu konformací pro struktury z PDB, ale zároveň bude dostatečně obecný, aby umožnil nahrání a analýzu nových datových sad. 1Department of Software EngineeringKatedra softwarového inženýrstvíFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult

Advances in Parvovirus Research 2020

Viruses of the Parvoviridae family constitute a most diverse and intriguing field of research. Parvoviruses can differ widely in their structure, genome organization and expression, virus–cell interactions, and impact on hosts. The translational implication of research on parvoviruses is relevant, since many viruses are important human and veterinary pathogens, while other viruses can be engineered as tools for oncolytic therapy or as sophisticated gene delivery vectors. Exploring the diversity and inherent complexity in the biology of these apparently simple viruses is a still challenging topic for the scientific community. The Special Issue of Viruses is a collection of recent contributions in the field of parvovirus research, encompassing many aspects of basic and translational research on viruses of the family Parvoviridae, including on their structure, replication, and gene expression in addition to virus–host interactions and the development of vaccines and viral vectors