Eukaryotic Deoxyribonucleic Acid Research Articles

ViBE: a hierarchical BERT model to identify eukaryotic viruses using metagenome sequencing data.

Viruses are ubiquitous in humans and various environments and continually mutate themselves. Identifying viruses in an environment without cultivation is challenging; however, promoting the screening of novel viruses and expanding the knowledge of viral space is essential. Homology-based methods that identify viruses using known viral genomes rely on sequence alignments, making it difficult to capture remote homologs of the known viruses. To accurately capture viral signals from metagenomic samples, models are needed to understand the patterns encoded in the viral genomes. In this study, we developed a hierarchical BERT model named ViBE to detect eukaryotic viruses from metagenome sequencing data and classify them at the order level. We pre-trained ViBE using read-like sequences generated from the virus reference genomes and derived three fine-tuned models that classify paired-end reads to orders for eukaryotic deoxyribonucleic acid viruses and eukaryotic ribonucleic acid viruses. ViBE achieved higher recall than state-of-the-art alignment-based methods while maintaining comparable precision. ViBE outperformed state-of-the-art alignment-free methods for all test cases. The performance of ViBE was also verified using real sequencing datasets, including the vaginal virome.

Splice-site identification for exon prediction using bidirectional LSTM-RNN approach

Machine learning methods played a major role in improving the accuracy of predictions and classification of DNA (Deoxyribonucleic Acid) and protein sequences. In eukaryotes, Splice-site identification and prediction is though not a straightforward job because of numerous false positives. To solve this problem, here, in this paper, we represent a bidirectional Long Short Term Memory (LSTM) Recurrent Neural Network (RNN) based deep learning model that has been developed to identify and predict the splice-sites for the prediction of exons from eukaryotic DNA sequences. During the splicing mechanism of the primary mRNA transcript, the introns, the non-coding region of the gene are spliced out and the exons, the coding region of the gene are joined. This bidirectional LSTM-RNN model uses the intron features that start with splice site donor (GT) and end with splice site acceptor (AG) in order of its length constraints. The model has been improved by increasing the number of epochs while training. This designed model achieved a maximum accuracy of 95.5%. This model is compatible with huge sequential data such as the complete genome.

A Bidirectional LSTM-RNN and GRU Method to Exon Prediction Using Splice-Site Mapping

Deep Learning techniques (DL) significantly improved the accuracy of predictions and classifications of deoxyribonucleic acid (DNA). On the other hand, identifying and predicting splice sites in eukaryotes is difficult due to many erroneous discoveries. To address this issue, we propose a deep learning model for recognizing and anticipating splice sites in eukaryotic DNA sequences based on a bidirectional Long Short-Term Memory (LSTM) Recurrent Neural Network (RNN) and Gated recurrent unit (GRU). The non-coding introns of the gene are spliced out, and the coding exons are joined during the splicing of the original mRNA transcript. This bidirectional LSTM-RNN-GRU model incorporates intron features in order of their length constraints, beginning with splice site donor (GT) and ending with splice site acceptor (AG). The performance of the model improves as the number of training epochs grows. The best level of accuracy for this model is 96.1 percent.

Role of cytokines in pathogenesis, diagnosis and efficiency evaluation of immunotherapy in various variants of sclerotic lichen in women

Our aim was to evaluate diagnostic and pathogenetic significance of plasma cytokines (IL-20, IL-23, IL-10, TNFα, IFNγ) in the patients with various clinical and histological variants of sclerotic lichen and to assess opportunity for their use as effectiveness criteria of immunotherapy for this disease using a drug based on eukaryotic deoxyribonucleic acid (Derinat). The prospective cohort study included assessment of the clinical manifestations (itching and dyspareunia) and measurement of blood cytokine contents (IL-20, IL-23, IL-10, TNFα, IFNγ) in women (n = 114) with various clinical variants of sclerotic lichen (atrophic, sclerotic and sclerotic-atrophic) before and after immunotherapy with a nucleic acid-based drug (Derinat). Derinat was chosen due to the fact of being an agonist of Toll-like receptors, and a number of immunoregulatory effects, including the ability to modulate cytokine production and to exert a positive influence upon regeneration processes. In addition, based on visual inspection, vulvoscopy and morphohistochemical examination results (evaluation criteria: skin thickness, number of collagen fibers, severity of fibrosis and sclerosis, etc.), the corresponding subgroups were classified within the II group, i.e., 2.1 (minimal sclerotic signs, n = 14), and 2.2 (pronounced sclerotic signs, n = 20). The control group consisted of conditionally healthy women, without history or presence of vulvar pathology (n = 30), with an age ranging from 20 to 50 years. Along with cytokine assessment by enzyme immunoassay, the study used the data of clinical examination (anamnesis collection, examination, palpation, vulvoscopy), as well as complex morphohistochemical evaluation of vulvar tissues. In atrophic variant, we have observed an increase in plasma IL-23 content, along with decreased TNFα; in lichen sclerosis, a maximal increase in IL-20, IL-23, and IFNγ was revealed; in sclerotic form of sclerotic lichen variant with severe sclerotic features, maximally enhanced IL-20, IL-23, TNFα, IFNγ, along with minimal levels of IL-10 was registered, as compared with other groups. Immunotherapy using Derinate resulted into significant reduction in the clinical manifestations in sclerotic lichen, i.e., itching of the vulva and dyspareunia, as well as normalization of cytokine indexes. Our studies have demonstrated an opportunity of using plasma concentrations of IL-20, IL-23, IL-10, TNFα, IFNγ as biomarkers of sclerotic lichen variants, and as laboratory criteria for efficiency of immunotherapy.

DNA Damage Tolerance by Eukaryotic DNA Polymerase and Primase PrimPol.

PrimPol is a human deoxyribonucleic acid (DNA) polymerase that also possesses primase activity and is involved in DNA damage tolerance, the prevention of genome instability and mitochondrial DNA maintenance. In this review, we focus on recent advances in biochemical and crystallographic studies of PrimPol, as well as in identification of new protein-protein interaction partners. Furthermore, we discuss the possible functions of PrimPol in both the nucleus and the mitochondria.

Inhibition of topoisomerase II alpha subunit de novo synthesis by specific antisense oligonucleotides suppresses human glioma T98G cell growth.

Deoxyribonucleic acid (DNA) topoisomerases are enzymes which resolve topological problems in eukaryotic DNA, and may be involved in cell proliferation. The involvement of topoisomerase II in cell proliferation was examined in the human glioma cell line T98G. The growth rate of T98G cells was suppressed by treatment with topoisomerase II antisense oligonucleotides dose-dependently, with significant suppression at concentrations greater than of 0.1 mM. The growth rate of T98G treated with control oligonucleotide was suppressed at concentrations greater than 3.0 mM. The activity of topoisomerase II in T98G cells treated with 0.5 mM topoisomerase II antisense oligonucleotide was one fourth of that in cells treated with control oligonucleotide. When topoisomerase II translation was suppressed, the activity of topoisomerase I was increased. These results suggest that de novo synthesis of the topoisomerase II protein is required to maintain a normal growth rate in cultured T98G cells. These topoisomerases may be functionally related, and might provide compensatory mechanisms in the case of compromised function.

Identification of an immunogenic histone-like protein (HLPMt) ofMycobacterium tuberculosis

We report the identification of the first histone-like protein ofMycobacterium tuberculosis(MTB) (HLPMt). The T cell blot assay was used to identify antigens of MTB associated with human immune response in healthy contacts. Fraction 21 corresponding to proteins in the molecular weight range of approximately 30 kDa were found to be immunogenic in tuberculin reactors. None of the fractions were found to be immunogenic by this assay in non-reactors to tuberculin. All sera, irrespective of the source, showed reactivity with MTB antigen(s) over a wide molecular weight range (205 16 kDa). In the present study fraction 21 was processed for the generation of murine polyclonal sera and amino acid sequencing. The sequence of a 16-amino acid long peptide showed a 100% homology with an open reading frame (ORF) in the translated sequence of cosmid cY349 (Sanger Centre, Cambridge, UK). The ORF was predicted to code for a protein of 214 amino acids. Oligonucleotide primers were synthesized based on the nucleotide sequence located at the 5′ and 3′ regions of the gene. The gene encoding the predicted protein was PCR-amplified, cloned, sequenced and expressed inEscherichia colias a protein of 28 kDa. The expressed HLPMtprotein was shown to react with the polyclonal murine sera originally raised against fraction 21. Human immune response to the recombinant HLPMtprotein was demonstrated by its ability to induce lymphoproliferation in peripheral blood derived mononuclear cells, and the presence of anti-HLPMtantibodies in pooled patient sera by immunoblot. The recombinant HLPMtprotein elicited a vigorous lymphoproliferative response especially in healthy tuberculin reactors compared to non-reactors and patients of tuberculosis, (P⪡ 0.05). The protein has unique dual domains with homology to both bacterial histone-like proteins (HU) and eukaryotic histone H1. Homology to prokaryotic and eukaryotic deoxyribonucleic acid (DNA)-binding proteins suggested that HLPMtcould bind DNA. DNA-binding properties were confirmed by South-Western analysis strongly suggesting an interaction between HLPMtand the MTB chromosome.

Mobius DNA, the paper tiger

Deoxyribonucleic acid (DNA), the biological molecule that determines the evolutionary architecture of all known life forms has been largely ignored as regards its own evolution from the prokaryotic cell (cells without nuclear membranes), to the eukaryotic cell (cells with nuclear membranes). In addition, the properties of prokaryotic DNA, have in some cases, been imposed on eukaryotic DNA resulting in the loss of evolutionary continuity of DNA. Regardless of the source of DNA, only small sections are usually examined as a salt extract. It is devoid of its associated proteins, which in the eukaryotic cell are responsible for the packing of DNA into chromosomes, and from its intimate connections with the nuclear membrane. From such studies various structures for DNA have been proposed which have not found general acceptance. Thus, any hypothesis on the structure of DNA must be able to incorporate most, if not all, other reported structures. Similarly, any structure proposed for DNA must be considered in terms of its own evolution as distinct from its phenotypic evolutionary expression. A single strand of DNA has opposite terminal ends, a 3′OH group and a 5′ phosphate group. These ends may join by a 5′ - 3′ phosphate linkage forming circular DNA. Both these single stranded linear and circular forms of DNA are considered to belong to “primitive” prokaryotic cells. A higher order of circular prokaryotic DNA may be formed if at one end, a single strand of DNA is turned through 180°, resulting in the 3−OH and 5′ phosphate groups being diagonally opposite each other ( 3′ 5′ ). This circular DNA has a continuous phosphate backbone and a discontinuous base sequence, Mobius circular DNA. The discontinuous base sequence may provide a start/stop signal for DNA and RNA polymerase. This Mobius DNA (M. 1.) may give rise to single circular, double linear or double circular DNA. During the replication of M. 1. DNA it may be possible for the two complementary strands to form one continuous Mobius DNa circle (M. 2. DNA) by two 5′ 3′ phosphate linkages. Thus, there are two start/stop signals for DNA and RNA polymerase, therefore DNA replication would occur as two separate strands and require splicing together. In addition, M. 2. DNA may be the first example of gene duplication and represent the first “primitive” eukaryotic DNA. Another form of Mobius DNA may be derived from M. 1., which represents the higher order in eukaryotic cells. This may be formed by two complementary strands of M. 1. forming a Mobius DNA circle (M. 3. DNA) by 5′ - 3′ and 5′ 3′ phosphate linkages. This will result in a double right handed α helical configuration which can be formed into a linear side-by-side configuration with a double loop at one end, which is a left handed helix. The side-by-side configuration allows base pairing, but in the double loop, the bases are facing in the same direction and are displaced, therefore they cannot base pair. Thus, single stranded DNA is existing with based paired DNA. It is proposed that the single stranded DNA represents unique copy and the base paired DNA repetitive copy, and that a number of these M. 3. DNA's constitute a gene. The DNA of eukaryotic cells is wound around a number of histone cores. Between each core there is a linking region of DNA upon which the histone H1 is attached. The core plus linker, represents a nucleosome, and under the electronmicroscope resembles beads on a string. A number of configurations have been proposed for these core histones which enable DNA to be packed to form chromosomes. The various configurations proposed for the histones can be achieved by considering each histone as a Mobius circle. The association of these Mobius histones results in the formation of cores in the form of wedge-shaped cylinders, which associate to form an helical spring-like solenoid with a central hole, when M. 3. DNA undergoes compaction.

Interaction of netropsin and distamycin with deoxyribonucleic acid: electric dichroism study.

We report dichroism and equilibrium binding studies of netropsin (Net) and distamycin A3 (Dist) binding to deoxyribonucleic acid (DNA). We show that at low degrees of binding (r) to calf thymus DNA, Net induces a considerable increase in the apparent DNA length (14 A/drug molecule bound), closely analogous to the results reported earlier for Dist. In addition, we show that chicken erythrocyte DNA shows length changes similar to those of calf thymus DNA upon distamycin binding. DNA length reaches a maximum at 1 bound drug/20-30 base pairs and then decreases to its initial value by r = 0.1. This effect is not seen for two other DNAs with nearly identical A + T base pair content and may therefore arise from the details of base sequence or base modification in eukaryotic DNA. We also show that Dist binding to calf thymus DNA at low r values is positively cooperative and shows a DNA affinity which is primarily nonionic. We demonstrate that independent of the DNA to which they are bound, the Net and Dist transition moments are inclined by 43 +/- 3 degrees from the helix axis, consistent with the idea that both drugs bind inside and parallel to the DNA small groove. From dichroism measurements, we show that the conformational change induced in calf thymus DNA by Dist does not kink or bend the helix and does not substantially alter the average inclination of the bases. Finally, we outline a statistical mechanical theory for calculation of binding isotherms when binding is coupled to a DNA structural change.