A fluorescence method for homogeneous detection of influenza A DNA sequence based on guanine‐quadruplex‐N‐methylmesoporphyrin IX complex and assistance‐DNA inhibition

2019 ◽  
Vol 91 (6) ◽  
pp. 979-985 ◽  
Author(s):  
Yubin Li ◽  
Wanshan Liu ◽  
Yinling Zhu ◽  
Liping Diao
Keyword(s):  
Dna Sequence ◽  
Influenza A ◽  
Fluorescence Method ◽  
Guanine Quadruplex ◽  
Dna Inhibition

scholarly journals Computational Method for Classification of Avian Influenza A Virus Using DNA Sequence Information and Physicochemical Properties

2021 ◽  
Vol 12 ◽  
Author(s):  
Fahad Humayun ◽  
Fatima Khan ◽  
Nasim Fawad ◽  
Shazia Shamas ◽  
Sahar Fazal ◽  
...  
Keyword(s):  
Feature Selection ◽  
Decision Tree ◽  
Avian Influenza ◽  
Physicochemical Properties ◽  
Influenza A Virus ◽  
Dna Sequence ◽  
Influenza A ◽  
Feature Selection Method ◽  
Selection Method ◽  
Avian Influenza A Virus

Accurate and fast characterization of the subtype sequences of Avian influenza A virus (AIAV) hemagglutinin (HA) and neuraminidase (NA) depends on expanding diagnostic services and is embedded in molecular epidemiological studies. A new approach for classifying the AIAV sequences of the HA and NA genes into subtypes using DNA sequence data and physicochemical properties is proposed. This method simply requires unaligned, full-length, or partial sequences of HA or NA DNA as input. It allows for quick and highly accurate assignments of HA sequences to subtypes H1–H16 and NA sequences to subtypes N1–N9. For feature extraction, k-gram, discrete wavelet transformation, and multivariate mutual information were used, and different classifiers were trained for prediction. Four different classifiers, Naïve Bayes, Support Vector Machine (SVM), K nearest neighbor (KNN), and Decision Tree, were compared using our feature selection method. This comparison is based on the 30% dataset separated from the original dataset for testing purposes. Among the four classifiers, Decision Tree was the best, and Precision, Recall, F1 score, and Accuracy were 0.9514, 0.9535, 0.9524, and 0.9571, respectively. Decision Tree had considerable improvements over the other three classifiers using our method. Results show that the proposed feature selection method, when trained with a Decision Tree classifier, gives the best results for accurate prediction of the AIAV subtype.

scholarly journals OVX836 Heptameric Nucleoprotein Vaccine Generates Lung Tissue-Resident Memory CD8+ T-Cells for Cross-Protection Against Influenza

2021 ◽  
Vol 12 ◽  
Author(s):  
Judith Del Campo ◽  
Julien Bouley ◽  
Marion Chevandier ◽  
Carine Rousset ◽  
Marjorie Haller ◽  
...  
Keyword(s):  
T Cells ◽  
Recombinant Protein ◽  
Dna Sequence ◽  
Cd8 T Cells ◽  
Influenza A ◽  
Influenza Infection ◽  
Influenza Viruses ◽  
Protein Vaccine ◽  
Memory Cd8 T Cells

Tissue-resident memory (TRM) CD8+ T-cells play a crucial role in the protection against influenza infection but remain difficult to elicit using recombinant protein vaccines. OVX836 is a recombinant protein vaccine, obtained by the fusion of the DNA sequence of the influenza A nucleoprotein (NP) to the DNA sequence of the OVX313 heptamerization domain. We previously demonstrated that OVX836 provides broad-spectrum protection against influenza viruses. Here, we show that OVX836 intramuscular (IM) immunization induces higher numbers of NP-specific IFNγ-producing CD8+ T-cells in the lung, compared to mutant NP (NPm) and wild-type NP (NPwt), which form monomeric and trimeric structures, respectively. OVX836 induces cytotoxic CD8+ T-cells and high frequencies of lung TRM CD8+ T-cells, while inducing solid protection against lethal influenza virus challenges for at least 90 days. Adoptive transfer experiments demonstrated that protection against diverse influenza subtypes is mediated by NP-specific CD8+ T-cells isolated from the lung and spleen following OVX836 vaccination. OVX836 induces a high number of NP-specific lung CD8+ TRM-cells for long-term protection against influenza viruses.

scholarly journals A graph-theoretical approach to DNA similarity analysis

2021 ◽  
Author(s):  
Dong Quan Ngoc Nguyen ◽  
Lin Xing ◽  
Phuong Dong Tan Le ◽  
Lizhen Lin
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Influenza A ◽  
Cartesian Product ◽  
Space Structure ◽  
Similarity Analysis ◽  
Cartesian Products ◽  
Research Areas ◽  
Active Research ◽  
Cartesian Products Of Graphs

One of the very active research areas in bioinformatics is DNA similarity analysis. There are several approaches using alignment-based or alignment-free methods to analyze similarities/dissimilarities between DNA sequences. In this work, we introduce a novel representation of DNA sequences, using n-ary Cartesian products of graphs for arbitrary positive integers n. Each of the component graphs in the representing Cartesian product of each DNA sequence contain combinatorial information of certain tuples of nucleotides appearing in the DNA sequence. We further introduce a metric space structure to the set of all Cartesian products of graphs that represent a given collection of DNA sequences in order to be able to compare different Cartesian products of graphs, which in turn signifies similarities/dissimilarities between DNA sequences. We test our proposed method on several datasets including Human Papillomavirus, Human rhinovirus, Influenza A virus, and Mammals. We compare our method to other methods in literature, which indicates that our analysis results are comparable in terms of time complexity and high accuracy, and in one dataset, our method performs the best in comparison with other methods.

DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization

1992 ◽  
Vol 50 (1) ◽  
pp. 496-497
Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Dual Band ◽  
Nick Translation ◽  
Metaphase Chromosomes ◽  
Band Pass ◽  
Texas Red ◽  
Fluorescent Spot

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.

Phylogenetic relationships ofSalvia(Lamiaceae) in China: Evidence from DNA sequence datasets

2012 ◽  
pp. n/a-n/a
Author(s):  
Qian-Quan Li ◽  
Min-Hui Li ◽  
Qing-Jun Yuan ◽  
Zhan-Hu Cui ◽  
Lu-Qi Huang ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships
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