DeF-GPU: Efficient and effective deletions finding in hepatitis B viral genomic DNA using a GPU architecture

Methods ◽  
2016 ◽  
Vol 111 ◽  
pp. 56-63 ◽  
Author(s):  
Chun-Pei Cheng ◽  
Kuo-Lun Lan ◽  
Wen-Chun Liu ◽  
Ting-Tsung Chang ◽  
Vincent S. Tseng
Keyword(s):  
Hepatitis B ◽  
Genomic Dna ◽  
Gpu Architecture

scholarly journals Nuclear Covalently Closed Circular Viral Genomic DNA in the Liver of Hepatocyte Nuclear Factor 1α-Null Hepatitis B Virus Transgenic Mice

2001 ◽  
Vol 75 (6) ◽  
pp. 2900-2911 ◽  
Author(s):  
Anneke K. Raney ◽  
Carrie M. Eggers ◽  
Eric F. Kline ◽  
Luca G. Guidotti ◽  
Marco Pontoglio ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Transgenic Mice ◽  
Genomic Dna ◽  
Nuclear Factor ◽  
Hepatocyte Nuclear Factor ◽  
B Virus ◽  
Hepatocyte Nuclear Factor 1Α ◽  
Replication Intermediates

ABSTRACT The role of hepatocyte nuclear factor 1α (HNF1α) in the regulation of hepatitis B virus (HBV) transcription and replication in vivo was investigated using a HNF1α-null HBV transgenic mouse model. HBV transcription was not measurably affected by the absence of the HNF1α transcription factor. However, intracellular viral replication intermediates were increased two- to fourfold in mice lacking functional HNF1α protein. The increase in encapsidated cytoplasmic replication intermediates in HNF1α-null HBV transgenic mice was associated with the appearance of nonencapsidated nuclear covalently closed circular (CCC) viral genomic DNA. Viral CCC DNA was not readily detected in HNF1α-expressing HBV transgenic mice. This indicates the synthesis of nuclear HBV CCC DNA, the proposed viral transcriptional template found in natural infection, is regulated either by subtle alterations in the levels of viral transcripts or by changes in the physiological state of the hepatocyte in this in vivo model of HBV replication.

scholarly journals Prevalence of Serologic Hepatitis B Markers in Blood Donors From Puebla, Mexico: The Association of Relatively High Levels of Anti-Core Antibodies With the Detection of Surface Antigen and Genomic DNA

2016 ◽  
Vol 16 (6) ◽  
Author(s):  
Francisca Sosa-Jurado ◽  
Nora Hilda Rosas-Murrieta ◽  
Belinda Guzman-Flores ◽  
Cintia Perez Zempoaltecalt ◽  
Ana Patricia Sanchez Torres ◽  
...  
Keyword(s):  
Hepatitis B ◽  
Surface Antigen ◽  
Genomic Dna ◽  
Blood Donors

scholarly journals Hepatitis B virus nucleocapsid envelopment does not occur without genomic DNA synthesis.

1996 ◽  
Vol 70 (7) ◽  
pp. 4269-4274 ◽  
Author(s):  
T Gerelsaikhan ◽  
J E Tavis ◽  
V Bruss
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Dna Synthesis ◽  
Genomic Dna ◽  
B Virus

scholarly journals Electrochemical Biosensor for Sensitive Detection of Hepatitis B in Human Plasma

2021 ◽  
Author(s):  
Ana Graci Brito-Madurro ◽  
Ana Cristina Honorato Castro ◽  
Leandro Toshio Kochi ◽  
José Manuel Rodrigueiro Flauzino ◽  
Marcia Maria Costa Nunes Soares ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Blood Plasma ◽  
Genomic Dna ◽  
Point Of Care ◽  
Electrochemical Techniques ◽  
Reference Method ◽  
Sample Volume ◽  
Graphite Electrodes ◽  
B Virus

Abstract In this work we report the construction of an electrochemical device for molecular diagnosis of hepatitis B virus in the blood plasma of infected patients, using graphite electrodes functionalized with poly(4-aminophenol) and sensitized with specific DNA probe. The recognition of genomic DNA was evaluated by electrochemical techniques (DPV and EIS) and scanning electron microscopy. The genosensor was efficient in detecting genomic DNA with a linear range from 1.176 μg.ml-1 to 4.825 μg.ml-1 and detection limit of 35.69 ng.ml-1 (4.63 UI.ml-1 or 25.93 copies.ml-1), which is better than 10.00 UI.ml-1 limit of reference method, real- time PCR, used in point of care. EIS analysis shows that the genosensor resistence increased exponentially with the concentration of the genomic DNA target. The developed platform has inherent advantages to its applicability in real samples, such as good sensitivity, selectivity, and low sample volume, being interesting for application in diagnosis of hepatitis B virus in blood plasma.

Detecting exact breakpoints of deletions with diversity in hepatitis B viral genomic DNA from next-generation sequencing data

Methods ◽  
2017 ◽  
Vol 129 ◽  
pp. 24-32 ◽  
Author(s):  
Ji-Hong Cheng ◽  
Wen-Chun Liu ◽  
Ting-Tsung Chang ◽  
Sun-Yuan Hsieh ◽  
Vincent S. Tseng
Keyword(s):  
Next Generation Sequencing ◽  
Hepatitis B ◽  
Genomic Dna ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

scholarly journals Hepatitis B virus genomic nucleic acid in the activation and maturation of bone marrow-derived dendritic cells

2021 ◽  
pp. 109-119
Author(s):  
Chean Ring Leong ◽  
Tsukasa Seya ◽  
Woei Yenn Tong ◽  
Wen-Nee Tan
Keyword(s):  
Bone Marrow ◽  
Immune Response ◽  
Hepatitis B Virus ◽  
Nucleic Acid ◽  
Hepatitis B ◽  
Genomic Dna ◽  
Innate Immune ◽  
Adaptive Immune ◽  
B Virus

Hepatitis B virus (HBV) is the etiological agent that causes a self-limiting or chronic infection in the hepatocytes of about 250 million people worldwide. The role of adaptive immune system during HBV infection has been well studied. However, the innate immune system's responses against HBV during the early stage of infection largely remain unclear. In this study, we found that HBV genomic DNA or Salmon Sperm DNA (SSD) was able to induce the innate immune response in the macrophages cell line RAW264.7 but not the hepatocyte cell line, HepG2, indicating that hepatocytes may lack of a functional DNA-sensing pathway and hence are unable to respond to the presence of foreign DNA in the cytosol with type 1 IFN response. Thus, we hypothesized that non-parenchymal cells like the Antigen Presenting Cells (APC) might be crucial in triggering the initial immune response to suppress the virus replication and link the innate and adaptive responses. Using bone marrow-derived DCs (BMDC) as a model, this study demonstrated that HBV genomic DNA is able to induce cytokines like TNF-alpha, IL-6, and IL-12p40 secretion. We also examined the activation and maturation of BMDCs when exposed to the HBV genomic DNA intracellularly and extracellularly. A significant shift of CD86+ and CD40+ cell populations was observed during extracellular exposure of BMDC to Poly I:C and HBV genomic DNA, indicating that TLRs may be vital in the uptake of the extracellular viral DNA to activate the BMDCs. Moreover, transfection of intracellular nucleic acid stimuli, including HBV genomic DNA as well induced BMDCs maturation. Our findings highlight the critical function of DCs in antiviral response as a potential connection between the innate and adaptive immune systems during HBV pathogenesis. Nevertheless, further study is required to determine the role of cytosol DNA sensing pathway in DCs during HBV infection.

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