DNA Encoding Sequences Research Articles

Chloroplast genomes of Vitis sp. samples from Nechaevsk population of the Krasnodar region

The presented study demonstrates the results of sequencing and analysis of wild grape plastomes assemblies located in the Nechaevsk population. Previously, the habitats of the wild forest grape V. vinifera subsp. silvestris were explored as an outcome of expeditions. As a result of repeated expeditions, samples were taken and used to isolate chloroplast DNA. Assembly and annotation of plastomes showed the presence of DNA encoding sequences. At the same time, the structure of the obtained plastomes varied. These expressed in the presence of DNA polymorphisms. Comparison of the aligned sequences made it possible to reveal the presence of the species V. vinifera subsp. sylvestris in the population, as well as hybrid specimens. This is also confirmed by the result of determining the taxonomy after depositing the archives of readings in the NCBI database.

A New Method for Color Image Encryption Using Chaotic System and DNA Encoding

Image encryption is an essential area of visual cryptography that helps protect images when they are shared over the internet. There are many cryptography algorithms applied for many years in encrypting images. In recent years, techniques from chaotic systems have been combined with DNA coding to help encrypt images and protect them from unauthorized use. In this study, we proposed a new method for image encryption based on a new four-dimensional chaotic system and DNA encoding. The proposed method consists of two stages: the pixel positions are scrambled depending on which chaotic sequences are generated from the new chaotic system; and then, an XOR operation is performed on the image scrambled by using the DNA encoding sequence to get the final encryption image. Analyses such as entropy, NPCR, UACI, and key space are used to evaluate the algorithm's performance. The algorithm attains average entropy of 7.99, which is close to the ideal value of 8 with NPCR and UACI of 99.64 and 33.02, respectively. In addition, the key space is 2627. The simulation results show that the proposed method offers high security, good encryption, and is resistant to many types of attacks

Chaotic-DNA system for efficient image encryption

In order to prevent unwanted access to sensitive data by unauthorized individuals, color images are encoded. Because chaotic-deoxyribonucleic acid (chaotic-DNA) encoding can make information highly secure, it is often employed in image encryption. In this study, a new image encryption technique has been proposed based on a new 4D-chaotic system and DNA computing. The algorithm consists of two phases: in the first phase, the pixel positions are permuted by chaotic sequences. In the second phase, according to the concept of DNA cryptography, a set of operations (like DNA addition, DNA XOR, DNA subtraction, shift right, and shift left) are performed on the DNA encoding sequence. The performance of the suggested algorithm is evaluated through analyses like correlation coefficient, entropy, histogram, and key space. The results show that the encryption method that was exhibited has good encryption performance and high security. For encrypted images, the histogram is fairly uniform, the correlation values between adjacent pixels are very small and close to zero, and the entropy is near to the ideal value of eight. In addition, the proposed system has a very large key space that is equal to 2627 keys, which makes it resistant to brute-force, differential, and statistical attacks.

Chaotic image encryption algorithm based on hybrid multi-objective particle swarm optimization and DNA sequence

This paper studies an image encryption algorithm based on multi-objective particle swarm optimization (MOPSO), DNA encoding sequence and one-dimensional Logistic map. First, the key of this paper consists of the sub-key sequence selected by particle swarm optimization (PSO), a hash value of the plaintext image, and a shuffle mark bit. Create random DNA mask images using Logistic map and DNA encoding. Then use it and the block-shuffled plaintext DNA encoding sequence to operate to form an encryption system. In PSO, the position value of a particle represents a position of the plaintext image, the iterative PSO algorithm is based on the information entropy and correlation coefficient. Finally, obtains the best ciphertext, and returns the value of the best particle at this time. Simulation experiment and security analysis show that the correlation coefficient and entropy of ciphertext are excellent, and it can resist all kinds of typical attacks and has better encryption effect.

A New Fuzzy-DNA Image Encryption and Steganography Technique

Image encryption and steganography techniques are receiving a lot of interest and investigations due to their high importance in multimedia communication systems. A novel highly efficient image encryption and steganography technique are presented in this paper. For the first time, the proposed technique uses hybrid DNA encoding and Choquet's Fuzzy Integral sequences. At first, a confused version of the image, using a simple chaotic map, is encoded using DNA's bases. Four coded images are generated using the four DNA bases, namely AT, CG, GC, and TA. Parallel to that, a Choquet's fuzzy Integral sequence is generated and DNA encoded similarly to obtain four pseudo-random sequences. Secondly, the resulting four fuzzy/DNA sequences are used to diffuse the four DNA encoded images using the complementary DNA XOR rule, according to certain control code. Finally, the wavelet fusion algorithm is then used to fuse the resulting four fuzzy-DNA encoded images, to get the encrypted image. For added security, a new steganography approach is used. In particular, the encrypted image is divided into four sub-images, each of which is hidden in a different carrier image selected from a known group of carrier images according to a given key. The simulation results and security analysis confirmed the efficiency of the proposed image encryption algorithm as well as the steganography approach used for enhanced security. Ten different images with a size of 256 x 256 are used to test the proposed method. The results show that the proposed algorithm has a higher key sensitivity. The pixel correlation coefficient values are very small (between 5.3220e-04 and 0.0011 horizontally, between 8.7670e-04 and 0.0022 vertically and between 0.0002 and 0.0045 diagonally). Furthermore, the measured information entropy of the encrypted images is between 7.9970 and 7.9979 which are very close to the ideal value of 8. Additionally, the measured unified average changing intensity and number of pixels change rate values take the values between 33.46 and 33.39 and between 99.61 and 99.64, respectively, which are again closed to the ideal values. The steganography test shows that the hidden encrypted images are almost invisible at high values of SNR and are characterized by good NCC values under different types of attacks. The performance of the new proposed algorithm is proved to overcomes many other previously published image encryption techniques.

P40 and P75 Are Singular Functional Muramidases Present in the Lactobacillus casei /paracasei/rhamnosus Taxon.

Lactobacillus casei and Lactobacillus rhamnosus proteins P40 and P75 belong to a large family of secreted cell wall proteins that contain a carboxy(C)-terminal CHAP or NlpC/P60 superfamily domains. In addition to their peptidoglycan hydrolases activity, proteins in this family are specific antigens of pathogens, frequently responsible of interactions with the host. L. rhamnosus GG and L. casei BL23 purified P40 and P75 proteins have antiapoptotic activity by inducing the EGF/Akt pathway. The aim of this work was to study the genetics, phylogeny and dissemination of this family of proteins in the genus Lactobacillus as well as their characteristics and likely function. The scrutiny of their DNA encoding sequences revealed the presence of minisatellite DNA in the P75 encoding gene of L. casei/paracasei strains (cmuB) with intraspecific indels that gave raise to four different alleles (cmuB1–4), which are exclusive of this species. Phylogenic analyses suggest that both proteins are present mainly in the L. casei and Lactobacillus sakei phylogenomic groups. A P40 ancestral gene was possibly present in the common ancestor of Enterococcaceae, Lactobacillaceae and Streptococcaceae. P75 is also present in L. casei and L. sakei groups, but its evolution is difficult to explain only by vertical transmission. Antibodies raised against the N-terminal regions of P40 and P75 improved their immunological detection in culture supernatants as they recognized almost exclusively proteins of L. casei/paracasei/rhamnosus strains, highlighting their structural similarity, that allowed to detect them in different fermented dairy products that contained probiotic L. casei strains. Purified P40 and P75 proteins showed no evident lytic activity but they complemented L. casei BL23 cmuA and cmuB defective mutants, respectively, thus proving that they actively participate in cell division.

Recombinant laccase from Pediococcus acidilactici CECT 5930 with ability to degrade tyramine.

Biogenic amines degradation by bacterial laccases is little known, so we have cloned and heterologously expressed, in E. coli, a new laccase from Pediococcus acidilactici CECT 5930 (Lpa5930), a lactic acid bacterium commonly found in foods able to degrade tyramine. The recombinant enzyme has been characterized by physical and biochemical assays. Here we report the optimization of expression and purification procedures of this laccase. DNA encoding sequence of laccase from P. acidilactici was amplified by PCR and cloned into the expression plasmid pET28a for induction by isopropyl-β-D-thiogalactoipyranoside. Protein expression was performed in E. coli BL21(DE3) harboring pGro7 plasmid expressing a chaperone folding assistant induced by arabinose. Purification was performed by column metal-chelating chromatography on Ni-NTA-agarose. The laccase enzyme obtained has an apparent molecular mass of ∼60 kDa, an optimum temperature activity toward 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) of 28°C, and was quickly inactivated at temperatures higher than 70°C. The apparent Km value for ABTS was 1.7 mM and the Vmax obtained was 24 U/mg. In addition to ABTS, recombinant Lpa5930 laccase degraded the biogenic amine tyramine at pH 9.5 and pH 4.0 with or without ABTS as a mediator. Tyramine degradation by laccases could solve the problems generated in food due to the presence of this toxic compound.

PirAB protein from Xenorhabdus nematophila HB310 exhibits a binary toxin with insecticidal activity and cytotoxicity in Galleria mellonella.

PirAB (Photorhabdus insect-related proteins, PirAB) toxin was initially found in the Photorhabdus luminescens TT01 strain and has been shown to be a binary toxin with high insecticidal activity. Based on GenBank data, this gene was also found in the Xenorhabdus nematophila genome sequence. The predicted amino acid sequence of pirA and pirB in the genome of X. nematophila showed 51% and 50% identity with those gene sequences from P. luminescens. The purpose of this experiment is to identify the relevant information for this toxin gene in X. nematophila. The pirA, pirB and pirAB genes of X. nematophila HB310 were cloned and expressed in Escherichia coli BL21 (DE3) using the pET-28a vector. A PirAB-fusion protein (PirAB-F) was constructed by linking the pirA and pirB genes with the flexible linker (Gly)4 DNA encoding sequence and then efficiently expressed in E. coli. The hemocoel and oral insecticidal activities of the recombinant proteins were analyzed against the larvae of Galleria mellonella. The results show that PirA/B alone, PirA/B mixture, co-expressed PirAB protein, and PirAB-F all had no oral insecticidal activity against the second-instar larvae of G. mellonella. Only PirA/B mixture and co-expressed PirAB protein had hemocoel insecticidal activity against G. mellonella fifth-instar larvae, with an LD50 of 2.718μg/larva or 1.566μg/larva, respectively. Therefore, we confirmed that PirAB protein of X. nematophila HB310 is a binary insecticidal toxin. The successful expression and purification of PirAB laid a foundation for further studies on the function, insecticidal mechanism and expression regulation of the binary toxin.

Multi-modulus algorithm based on global artificial fish swarm intelligent optimization of DNA encoding sequences.

Aimed to address the defects of the large mean square error (MSE), and the slow convergence speed in equalizing the multi-modulus signals of the constant modulus algorithm (CMA), a multi-modulus algorithm (MMA) based on global artificial fish swarm (GAFS) intelligent optimization of DNA encoding sequences (GAFS-DNA-MMA) was proposed. To improve the convergence rate and reduce the MSE, this proposed algorithm adopted an encoding method based on DNA nucleotide chains to provide a possible solution to the problem. Furthermore, the GAFS algorithm, with its fast convergence and global search ability, was used to find the best sequence. The real and imaginary parts of the initial optimal weight vector of MMA were obtained through DNA coding of the best sequence. The simulation results show that the proposed algorithm has a faster convergence speed and smaller MSE in comparison with the CMA, the MMA, and the AFS-DNA-MMA.

Photorhabdus luminescens PirAB-fusion protein exhibits both cytotoxicity and insecticidal activity.

The binary toxin 'Photorhabdus insect-related' proteins (PirAB) produced by Photorhabdus luminescens have been reported to possess both injectable and oral activities against a range of insects. Here, PirAB-fusion protein was constructed by linking pirA and pirB genes with the flexible linker (Gly4 Ser)3 DNA encoding sequence and then efficiently expressed in Escherichia coli. To better understand the role of PirAB toxin played in the process of invasion, its cytotoxicity against insect midgut CF-203 cells was investigated. Application of purified PirAB-fusion protein as well as PirA/PirB mixture caused loss of viability of CF-203 cells after 24 h incubation. CF-203 cells treated by PirAB-fusion protein displayed morphological changes typical of apoptosis, such as cell shrinkage, cell membrane blebbing, nuclear condensation and DNA fragmentation. Moreover, PirAB-fusion protein also exhibited injectable insecticidal activity against Spodoptera exigua larvae. The bodies of S. exigua fourth-instar larvae injected with PirAB-fusion protein turned completely black. Thus, we concluded that PirAB-fusion protein possessed similar biological activity (cytotoxicity and insecticidal activity) to PirA/PirB mixture, which would enable it to be used as an efficient agent for pest control.

Nanobiotechnological Approaches to Delivery of DNA Vaccine Against Fungal Infection

Vaccines play an essential role in keeping humans healthy. Innovative approaches to their use include the utilization of plasmid DNA encoding sequences to express foreign antigens. DNAhsp65 from Mycobacterium leprae is suitable for this purpose due to its ability to elicit a powerful immune response. Controlled release systems represent a promising approach to delivering vaccines. In this work, we used liposomes or PLGA systems to deliver DNAhsp65 to treat the pulmonary fungal infection Paracoccidioidomycosis. Both formulations modulated a protective immune response and reduced the pulmonary fungal burden even in the groups receiving less than four times the amount of the DNAhps65 entrapped within the nanoparticles. Although both systems had the same effective therapeutic results, the advantage of the liposome formulation was that it was administered intranasally, which may be more easily accepted by patients. These systems are a great alternative to be considered as adjuvant vaccine therapy for systemic mycosis.

Hierarchy Evolutionary Searching Algorithm for DNA Encoding Sequence

DNA sequence design is the basic and important step for DNA computing. Good codeword could avoid some error may possibly occurred in practical computing. Therefore, much work has focused on designing the DNA sequences to make the molecular computation more reliable. In this paper, a new hierarchy evolutionary searching algorithm is proposed to obtain good DNA encoding sequences, this approach is based on combinatorial constraints which affect the molecular reaction process, and can provide some reliable and effective encoding sequences for controllable DNA computing.

DNA immunization--a new chance in vaccine research?

A novel class of vaccines, based on the immunization with "naked" DNA, may hold the promise of protecting against human disease without the disadvantages associated with vaccines presently used, and may help to prevent infections which are not curable today. Direct intramuscular or intradermal inoculation of plasmid DNA encoding sequences of viral proteins results in the synthesis of these proteins, causing humoral and/or cellular immune responses in the recipient. Several advantages are associated with DNA immunization, e.g., cheap to produce, heat stability, amenable to genetic manipulation, mimic viral infection, and no risk of reversion to pathogenicity. Nevertheless, some concerns remain regarding their safety, e.g., the possible integration of plasmid DNA into host chromosomes. In summary, the results concerning the efficiency of DNA vaccination demonstrate clearly that these new vaccines may have a promising future in human immunization.

Prostatitis: what is the role of infection

Although bacterial prostatitis is a common diagnosis, well documented infections of the prostate are uncommon. Culture studies of prostate tissue led our group to hypothesize that bacterial colonization/invasion of the prostate gland might occur more commonly than is appreciated by standard microbiological techniques. Specific polymerase chain reaction (PCR) assays were used for each of the pathogens previously implicated in chronic prostatitis as well as broad-spectrum PCR assays to identify tetracycline resistance genes and bacterial ribosomal-encoding genes (16S rDNAs), followed by cloning and sequencing of the PCR products. Only ten (8%) of the 135 patients with chronic prostatitis had positive specific PCR assays including: Mycoplasma genitalium in four men, Chlamydia trachomatis in three and Trichomonas vaginalis in two, as well as one man positive for both M. genitalium and C. trachomatis. In contrast to the specific probes, the broad-spectrum PCR assays had a substantial proportion of positives. We found evidence of tetracycline resistance in 25% of patients. 16S rDNA-encoding sequences in 77% of the subjects. The tetracycline resistance positives were a subset of the 16S rDNA positive patients. Patients with 16S rDNA-encoding sequences were significantly more likely to have expressed prostatic secretion leukocytes. Many patients with chronic prostatitis/chronic pelvic pain syndrome have a wide variety of bacterial DNA-encoding sequences despite extensive negative microbiological investigations. Understanding the precise role of infection in this syndrome may well lead to better methods to elucidate the microbiology of the prostate in health and disease.

How Many Ruminal Bacteria Are There?

With the development of strictly anaerobic techniques and habitat-simulating media, a variety of bacteria were isolated from the rumen in the 1940s and 1950s. Based on standard morphological and physiological characteristics, the microbial ecosystem of the rumen contains a very complex population of bacteria. In recent years, ruminal bacteria have been re-evaluated with newer, more objective, and genetically valid methods of classification. Ribosomes are complicated structures, and their DNA-encoding sequences are relatively free from selective pressure. Because ribosomes have evolved slowly, they provide a long-term natural history of evolution. The invariable and hypervariable regions of rRNA genes can be used to group bacteria into kingdoms, genera, and species. The 16s rRNA sequences have provided a basis for renaming some ruminal species (Bacteroides amylophilus is now Ruminobacter amylophilus and Bacteroides succinogenes is now Fibrobacter succinogenes) and for classifying at least one recently isolated ruminal bacterium (e.g., Clostridium aminophilum). The DNA:DNA hybridization is a more sensitive method of assessing bacterial relatedness than is 16S rRNA. Bacterial strains within a species should have a high degree of DNA:DNA homology, but some species of ruminal bacteria (e.g., Prevotella ruminicola and Butyrivibrio fibrisolvens) had highly unrelated strains. Studies of 16S rRNA and DNA:DNA hybridization indicate that the diversity of ruminal bacteria has been greatly underestimated. Traditional studies of phylogeny of ruminal bacteria were stymied by the fastidious growth requirements of many ruminal bacteria, and enumeration was tedious and inaccurate. Modern methods of bacterial classification do not require in vitro culture and have the potential of detecting even a single cell.

Cyclic 3′5′-adenosine monophosphate synthesis in Rhizobium: Identification of a cloned sequence from Rhizobium meliloti coding for adenyl cyclase

Cloned segments of Rhizobium genomic DNA encoding sequences for cyclic AMP synthesis (Adenyl cyclase) were identified from a gene bank of R. meliloti. The cloned DNA weakly complemented Escherichia coli Δcya mutants, promoting the expression of adenyl cyclase activity and the accumulation of cAMP. The complemented Δcya clones were also capable of inducing a number of cAMP dependent carbon utilization operons but displayed an altered pattern of catabolite repression control. A common 5.4 Kb Bg/II DNA fragment, with internal EcoR1, BamH1 and PstI sites and inserted in different orientations was identified in the complementing recombinant plasmids. The identification of this DNA sequence will be a useful tool in elucidating the role of cAMP in these agronomically important bacteria.