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152 results for “DNA viruses”
Figure 2 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 2 Phenolic (trans-ferulic) acid and its vicinity after docking procedure. The amino acid residues of HSV-1 DNA polymerase active site, mostly involved in interaction with ligands, are represented as follows: Lis928 is basic amino acid right from the ligand, Glu 927 is above it, basic amino acid on the left is Lis 939 and Asp 886 is in its right.
Supplementary material 1 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Tables S1–S3 and Figures S1–S4
Figure 8 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 8 Complex of acyclovir triphosphate and amino acids from DNA polymerase active site, optimized at B3LYP/6-31+G(d,p) level.
Figure 7 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 7 Complexes of phenolic acids from GP phenolic fraction "C" and amino acids from DNA polymerase active site, optimized at B3LYP/6-31+G(d,p) level.
Figure 5 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 5 Structures of hydroxybenzoic acids from GP phenolic fraction "C", optimized at B3LYP/6-31+G(d,p) level.
Data from: Advanced characterization of DNA molecules in rAAV vector preparations by single-stranded virus next-generation sequencing
Recent successful clinical trials with recombinant adeno-associated viral vectors (rAAVs) have led to a renewed interest in gene therapy. However, despite extensive developments to improve vector-manufacturing processes, undesirable DNA contaminants in rAAV preparations remain a major safety concern. Indeed, the presence of DNA fragments containing antibiotic resistance genes, wild-type AAV, and packaging cell genomes has been found in previous studies using quantitative polymerase chain reaction (qPCR) analyses. However, because qPCR only provides a partial view of the DNA molecules in rAAV preparations, we developed a method based on next-generation sequencing (NGS) to extensively characterize single-stranded DNA virus preparations (SSV-Seq). In order to validate SSV-Seq, we analyzed three rAAV vector preparations produced by transient transfection of mammalian cells. Our data were consistent with qPCR results and showed a quasi-random distribution of contaminants originating from the packaging cells genome. Finally, we found single-nucleotide variants (SNVs) along the vector genome but no evidence of large deletions. Altogether, SSV-Seq could provide a characterization of DNA contaminants and a map of the rAAV genome with unprecedented resolution and exhaustiveness. We expect SSV-Seq to pave the way for a new generation of quality controls, guiding process development toward rAAV preparations of higher potency and with improved safety profiles.
Effects of Telbivudine and Tenofovir Disoproxil Fumarate Treatment on the Hepatitis B Virus DNA Kinetics in CHB
ClinicalTrials.gov study NCT00805675. IPD Sharing: Not stated. Countries: 1. Publications: 0.
A Study on Using Cell-Free Tumor DNA (ctDNA) Testing to Decide When to StartRoutine Treatment in People With Human Papilloma Virus (HPV)- Associated Oropharynx Cancer (OPC)
ClinicalTrials.gov study NCT05307939. IPD Sharing: YES. Countries: 1. Publications: 0.
Phase 2a Immunogenicity Study of Hantaan/Puumala Virus DNA Vaccine for Prevention of Hemorrhagic Fever
ClinicalTrials.gov study NCT02116205. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses
Open the record for dataset details and reuse information.
Data from: Advanced characterization of DNA molecules in rAAV vector preparations by single-stranded virus next-generation sequencing
Open the record for dataset details and reuse information.
The Epstein-Barr virus B-ZIP protein Zta recognizes specific DNA sequences containing 5-methylcytosine and 5-hydroxymethylcytosine [Zta_5mCG]
GEO Series GSE100869. human gammaherpesvirus 4; synthetic construct; Mus musculus. 16 samples. Type: Other.
Aberrant DNA methylation epigenotype expanding to non-polycomb target genes, induced by Epstein-Barr virus infection in human gastric cancer [Illumina Methylation]
GEO Series GSE31788. Homo sapiens. 80 samples. Type: Methylation profiling by array.
Evaluation of DNA array sensitivity to detect viruses in clinical samples following propidium monoazide treatment
GEO Series GSE62910. Sus scrofa; Viruses. 80 samples. Type: Other.
Aberrant DNA methylation in hepatitis B and C virus-related hepatocellular carcinoma
GEO Series GSE19665. Homo sapiens. 20 samples. Type: Expression profiling by array.
Genome-wide DNA methylation analysis of liver tissue samples obtained from patients with hepatitis virus-related hepatocellular carcinomas
GEO Series GSE89852. Homo sapiens. 74 samples. Type: Methylation profiling by genome tiling array.
The Effect of Epstein Barr Virus Latency on Cellular DNA Methylation Profile of DiffuseLarge B Cell Lymphoma
GEO Series GSE306846. Homo sapiens. 48 samples. Type: Methylation profiling by array.
The Adeno-Associated Virus 2 (AAV2) genome and Rep 68/78 proteins interact with cellular sites of DNA damage.
GEO Series GSE178316. Homo sapiens. 48 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Maternal Zika virus infection alters epigenetic DNA modifications and leads to transgenerational behavioral changes in offspring mice (RNA-Seq)
GEO Series GSE163266. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Circular DNA tumor viruses make circular RNAs
GEO Series GSE117798. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing; Other.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.