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Analysis of HBsAg Immunocomplexes and cccDNA Activity During and Persisting After NAP-Based Therapy.

Hepatol Commun 2021 Jul 10. Epub 2021 Jul 10.

Replicor Inc., Montreal, Canada.

Therapy with nucleic acid polymers (NAPs), tenofovir disoproxil fumarate (TDF), and pegylated interferon (pegIFN) achieve high rates of HBsAg loss/seroconversion and functional cure in chronic hepatitis B virus (HBV) infection. The role of hepatitis B surface antigen (HBsAg) seroconversion and inactivation of covalently closed circular DNA (cccDNA) in establishing functional cure were examined. Archived serum from the REP 401 study was analyzed using the Abbott ARCHITECT HBsAg NEXT assay (Chicago, IL), Abbott research use-only assays for HBsAg immune complexes (HBsAg ICs), circulating HBV RNA, and the Fujirebio assay for hepatitis B core-related antigen (HBcrAg; Malvern, PA). Read More

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Formation of Minimised Hairpin Template-transcribing Dumbbell Vectors for Small RNA Expression.

Bio Protoc 2017 Jun 5;7(11):e2313. Epub 2017 Jun 5.

Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Block MD4, Level 5, 5 Science Drive 2, Singapore 117597, Singapore.

A major barrier for using non-viral vectors for gene therapy is the short duration of transgene expression in postmitotic tissues. Previous studies showed transgene expression from conventional plasmid fell to sub-therapeutic level shortly after delivery even though the vector DNA was retained, suggesting transcription was silenced ( Nicol , 2002 ; Chen , 2004 ). Emerging evidence indicates that plasmid bacterial backbone sequences are responsible for the transcriptional repression and this process is independent of CpG methylation ( Chen , 2008 ). Read More

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Ultrasensitive Assay for Hepatitis B Core-Related Antigen Predicts Hepatocellular Carcinoma Incidences During Entecavir.

Hepatol Commun 2021 Sep 16. Epub 2021 Sep 16.

Department of Hepatology, Toranomon Hospital, Tokyo, Japan.

Serum hepatitis B core-related antigen (HBcrAg) and surface antigen (HBsAg) are surrogate markers of intrahepatic covalently closed circular DNA. The measurement range of the current HBcrAg assay is relatively narrow. Thus, we examined the potential of HBcrAg and HBsAg measured by ultrasensitive assays for predicting hepatocellular carcinoma (HCC) development in patients with chronic hepatitis B treated with entecavir (ETV). Read More

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September 2021

The Ongoing Evolution of Basal Insulin Therapy over 100 Years and its Promise for the Future.

Diabetes Obes Metab 2021 Sep 16. Epub 2021 Sep 16.

Leadership Sinai Centre for Diabetes, Mount Sinai Hospital, Toronto, Canada.

The evolution of basal insulin therapy over the past 100 years since the discovery of insulin is a testimony to the biomedical bench-to-bedside process, wherein incremental advances in the basic sciences are progressively translated over time into a series of enhancements in clinical care, each building upon the success of its predecessors. The emergence of recombinant DNA technology and the resultant biosynthesis of human insulin in the 1980's provided the critical capacity to bioengineer designer insulin analogues with pharmacokinetic and pharmacodynamic properties that can better mimic, though not fully replicate, the effects of endogenous insulin secretion. Through these efforts, basal insulin therapy has progressed over this time from first-generation analogues (glargine U-100, detemir) to second-generation analogues (glargine U-300, degludec) to ultra-long-acting formulations that are suitable for administration once weekly (icodec). Read More

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September 2021

Persistence of Hepatitis B Virus Infection: A Multi-Faceted Player for Hepatocarcinogenesis.

Front Microbiol 2021 30;12:678537. Epub 2021 Aug 30.

Centre for Liver Research, School of Digestive and Liver Diseases, Institute of Post Graduate Medical Education and Research, Kolkata, India.

Hepatitis B virus (HBV) infection has a multi-dimensional effect on the host, which not only alters the dynamics of immune response but also persists in the hepatocytes to predispose oncogenic factors. The virus exists in multiple forms of which the nuclear localized covalently closed circular DNA (cccDNA) is the most stable and the primary reason for viral persistence even after clearance of surface antigen and viral DNA. The second reason is the existence of pregenomic RNA (pgRNA) containing virion particles. Read More

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Development of red-shifted and fluorogenic nucleoside and oligonucleotide diarylethene photoswitches.

Chemistry 2021 Sep 14. Epub 2021 Sep 14.

Universität Heidelberg, Inst. f. Pharmazie, Abt. Chemie, Im Neuenheimer Feld 364, 69120, Heidelberg, GERMANY.

The reversible modulation of fluorescence signals by light is of high interest for applications in super-resolution microscopy, especially on the DNA level. In this article we describe the systematic variation of the core structure in nucleoside-based diarylethenes (DAEs), in order to generate intrinsically fluorescent photochromes. The introduction of aromatic bridging units resulted in a bathochromic shift of the visible absorption maximum of the closed-ring form, but caused reduced thermal stability and switching efficiency. Read More

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September 2021

DMRT1: An Ancient Sexual Regulator Required for Human Gonadogenesis.

Sex Dev 2021 Sep 1:1-14. Epub 2021 Sep 1.

Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA.

Transcriptional regulators related to the invertebrate sexual regulators doublesex and mab-3 occur throughout metazoans and control sex in most animal groups. Seven of these DMRT genes are found in mammals, and mouse genetics has shown that one, Dmrt1, plays a crucial role in testis differentiation, both in germ cells and somatic cells. Deletions and, more recently, point mutations affecting human DMRT1 have demonstrated that its heterozygosity is associated with 46,XY complete gonadal dysgenesis. Read More

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September 2021

Complete mitochondrial genome of the Red Keelback ( Boulenger, 1906).

Mitochondrial DNA B Resour 2021 6;6(10):2830-2831. Epub 2021 Sep 6.

Laboratory of Amphibian Diversity Investigation, College of Ecology, Lishui University, Lishui, Zhejiang, China.

The Red Keelback ( Boulenger, 1906) is widely distributed in the southern of China. The complete mitochondrial genome (mitogenome) of was determined for the first time by using next-generation sequencing. The size of assembled mitogenome for was 19,150 bp, which included 13 protein coding genes (), 22 , two and two control regions (d1 and d2). Read More

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September 2021

Nano-sandwich composite by kinetic trapping assembly from protein and nucleic acid.

Nucleic Acids Res 2021 Sep 9. Epub 2021 Sep 9.

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

Design and preparation of layered composite materials alternating between nucleic acids and proteins has been elusive due to limitations in occurrence and geometry of interaction sites in natural biomolecules. We report the design and kinetically controlled stepwise synthesis of a nano-sandwich composite by programmed noncovalent association of protein, DNA and RNA modules. A homo-tetramer protein core was introduced to control the self-assembly and precise positioning of two RNA-DNA hybrid nanotriangles in a co-parallel sandwich arrangement. Read More

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September 2021

IFN-α inhibits HBV transcription and replication by promoting HDAC3-mediated de-2-hydroxyisobutyrylation of histone H4K8 on HBV cccDNA minichromosome in liver.

Acta Pharmacol Sin 2021 Sep 8. Epub 2021 Sep 8.

Department of Cancer Research, Institute of Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.

The epigenetic modification of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) plays a crucial role in cccDNA transcription and viral persistence. Interferon-α (IFN-α) is a pivotal agent against HBV cccDNA. However, the mechanism by which IFN-α modulates the epigenetic regulation of cccDNA remains poorly understood. Read More

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September 2021

Laboratory Stock Variants of the Archetype Silver Resistance Plasmid pMG101 Demonstrate Plasmid Fusion, Loss of Transmissibility, and Transposition of Tn// Into the Host Chromosome.

Front Microbiol 2021 19;12:723322. Epub 2021 Aug 19.

School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, United Kingdom.

Typhimurium carrying the multidrug resistance (MDR) plasmid pMG101 was isolated from three burns patients in Boston United States in 1973. pMG101 was transferrable into other spp. and hosts and carried what was a novel and unusual combination of AMR genes and silver resistance. Read More

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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies.

J Vis Exp 2021 Aug 20(174). Epub 2021 Aug 20.

Department of Biological Sciences, University of Texas at Dallas;

Complete genome sequences provide valuable data for the understanding of genetic diversity and unique colonization factors of urinary microbes. These data may include mobile genetic elements, such as plasmids and extrachromosomal phage, that contribute to the dissemination of antimicrobial resistance and further complicate treatment of urinary tract infection (UTI). In addition to providing fine resolution of genome structure, complete, closed genomes allow for the detailed comparative genomics and evolutionary analyses. Read More

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Bacterial DNA screening to characterize surgical site infection risk in orthopaedic patients.

J Orthop 2021 Sep-Oct;27:56-62. Epub 2021 Aug 25.

University of Missouri, Thompson Laboratory for Regenerative Orthopaedics, Missouri Orthopaedic Institute, 1100 Virginia Ave., Columbia, MO, 65212, USA.

Purpose: To provide an initial characterization of relevant bacterial DNA profiles for patients undergoing closed-fracture fixation or total joint arthroplasties.

Patients And Methods: Swabs were collected and analyzed using Polymerase Chain Reaction from adult patients undergoing closed-fracture fixation or total shoulder, knee, or hip arthroplasties.

Results: Bacterial DNA profiles varied across the different orthopaedic patient populations, and produced uncharacteristic profile shifts with direct relevance to each clinical infection. Read More

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Towards eradication of HBV: Treatment approaches and status of clinical trials.

Curr Opin Pharmacol 2021 Aug 30;60:232-240. Epub 2021 Aug 30.

Department of Gastroenterology, Hepatology, and Endocrinology, Hannover Medical School Hannover, Germany; Centre for Individualised Infection Medicine (CiiM), a Joint Venture of Helmholtz Centre for Infection Research and Hannover Medical School, Hannover, Germany; German Center for Infection Research (DZIF), Partner-Site Hannover-Braunschweig, Hannover, Germany. Electronic address:

Chronic hepatitis B virus (HBV) infection and its sequelae remain a global health challenge. Current treatments are effective in controlling HBV replication, but complete eradication or 'cure' of HBV remains a rare event and is difficult to assess because of the intrahepatic reservoir of covalently closed circular DNA. Based on the understanding of the HBV life cycle and the deciphering of immune responses to HBV, therapeutic strategies to target HBV eradication are in principle possible. Read More

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On-treatment HBV RNA dynamic predicts entecavir-induced HBeAg seroconversion in children with chronic hepatitis B.

J Infect 2021 Aug 30. Epub 2021 Aug 30.

Department of Laboratory Medicine, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, China.

Background: Hepatitis B e antigen (HBeAg) seroconversion is an important intermediate outcome in HBeAg-positive chronic hepatitis B patients. This study aimed to explore whether hepatitis B virus (HBV) RNA serum levels can predict HBeAg seroconversion treated with entecavir.

Methods: Serum samples from HBeAg-positive children previously treated with entecavir were retrospectively analyzed. Read More

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The first complete plastome of (Fenzl) Makino: assembly, annotation and phylogenetic analysis.

Mitochondrial DNA B Resour 2021 25;6(9):2762-2763. Epub 2021 Aug 25.

Chongqing Shangyao Huiyuan Pharmaceutical Co. Ltd, Chongqing, China.

(Fenzl) Makino is one of the 'Square Bamboo' due to its square-shaped culm. However, as an edible bamboo, there is no genomic information reported so far. In this study, we reported and characterized the first plastome of based on Illumina Hiseq sequencing. Read More

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Spatial rearrangement of the Streptomyces venezuelae linear chromosome during sporogenic development.

Nat Commun 2021 09 1;12(1):5222. Epub 2021 Sep 1.

Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.

Bacteria of the genus Streptomyces have a linear chromosome, with a core region and two 'arms'. During their complex life cycle, these bacteria develop multi-genomic hyphae that differentiate into chains of exospores that carry a single copy of the genome. Sporulation-associated cell division requires chromosome segregation and compaction. Read More

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September 2021

Characterization of Episomal Replication of Bovine Papillomavirus Type 1 DNA in Long-Term Virion-Infected Saccharomyces Cerevisiae Culture.

Virol Sin 2021 Aug 30. Epub 2021 Aug 30.

Department of Obstetrics and Gynaecology, The Second Affiliated Hospital and Yuyin Children Hospital of Wenzhou Medical University, Wenzhou, 325035, China.

We have previously reported that bovine papillomavirus type 1 (BPV-1) DNA can replicate its genome and produce infectious virus-like particles in short term virion-infected S. cerevisiae (budding yeast) cultures (Zhao and Frazer 2002, Journal of Virology, 76:3359-64 and 76:12265-73). Here, we report the episomal replications of BPV-1 DNA in long term virion-infected S. Read More

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DNA Aptamers Block the Receptor Binding Domain at the Spike Protein of SARS-CoV-2.

Front Mol Biosci 2021 12;8:713003. Epub 2021 Aug 12.

University of Lille, CNRS UMR8576 UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France.

DNA aptamers are versatile molecular species obtained by the folding of short single-stranded nucleotide sequences, with highly specific recognition capabilities against proteins. Here we test the ability of DNA aptamers to interact with the spike (S-)protein of the SARS-CoV-2 viral capsid. The S-protein, a trimer made up of several subdomains, develops the crucial function of recognizing the ACE2 receptors on the surface of human cells, and subsequent fusioning of the virus membrane with the host cell membrane. Read More

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Microbiological load and preantral follicle preservation using different systems for ovarian tissue vitrification in the red-rumped agouti.

Cryobiology 2021 Aug 26. Epub 2021 Aug 26.

Laboratory on Animal Germplasm Conservation, Universidade Federal Rural Do Semi-Árido (UFERSA), BR 110, Km 47, Costa e Silva, 59625-900, Mossoró, RN, Brazil. Electronic address:

We evaluated the effect of open and closed systems used for ovarian tissue vitrification on the microbiological load and preservation of preantral follicles (PAFs) in the red-rumped agoutis. The ovaries from eight females were recovered and fragmented, with four cortexes fragments immediately fixed and evaluated (fresh group). The other fragments were processed for the solid-surface vitrification method (SSV) or an ovarian tissue cryosystem (OTC) using fetal calf serum, ethylene glycol, and sucrose as cryoprotectants, stored for two weeks, and rewarmed. Read More

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Mechanism of Hepatitis B Virus cccDNA Formation.

Viruses 2021 Jul 27;13(8). Epub 2021 Jul 27.

110 Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA.

Hepatitis B virus (HBV) remains a major medical problem affecting at least 257 million chronically infected patients who are at risk of developing serious, frequently fatal liver diseases. HBV is a small, partially double-stranded DNA virus that goes through an intricate replication cycle in its native cellular environment: human hepatocytes. A critical step in the viral life-cycle is the conversion of relaxed circular DNA (rcDNA) into covalently closed circular DNA (cccDNA), the latter being the major template for HBV gene transcription. Read More

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The complete mitochondrial genome of (Linnaeus, 1771) (Hemiptera: Scutelleridae) and its phylogenetic implications.

Mitochondrial DNA B Resour 2021 16;6(9):2660-2661. Epub 2021 Aug 16.

College of Life Science, China West Normal University, Nanchong, China.

The complete mitochondrial genome sequence of was sequenced and analyzed. The 16,524 bp mitogenome of contained 21 tRNA genes, two rRNA genes, 13 protein-coding genes (PCGs), and a control region. Most PCGs used standard ATG start codons and complete TAA ermination codons. Read More

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Optimization of Loop-Mediated Isothermal Amplification (LAMP) reaction mixture for biosensor applications.

MethodsX 2021 19;8:101282. Epub 2021 Feb 19.

Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey.

Genetically Modified (GM) foods are becoming the future of agriculture on surviving global natural disasters and climate change by their enhanced production efficiency and improved functional properties. On the other hand, their adverse health and environmental effects, ample evidence on transgene leakage of Genetically Modified Organisms (GMOs) to crops have raised questions on their benefits and risks. Consequently, low-cost, reliable, rapid, and practical detection of GMOs have been important. Read More

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February 2021

Differential nuclease sensitivity profiling uncovers a drought responsive change in maize leaf chromatin structure for two large retrotransposon derivatives, and .

Plant Direct 2021 Aug 16;5(8):e337. Epub 2021 Aug 16.

Department of Biological Science Florida State University Tallahassee Florida USA.

Plant chromatin dynamics are generally recognized as playing a role in the genomic response to environmental stress. Although stress-induced transcriptional activities of LTR-retrotransposons have been reported, whether the stress response can be detected at the level of chromatin structure for LTR-retrotransposons is largely unknown. Using differential nuclease sensitivity profiling, we identified that two out of 29 maize LTR-retrotransposon families change their chromatin structure in response to drought stress in leaf tissue. Read More

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Entry of hepatitis B virus: going beyond NTCP to the nucleus.

Curr Opin Virol 2021 Aug 21;50:97-102. Epub 2021 Aug 21.

National Institute of Biological Science, Beijing, 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 102206, China. Electronic address:

Hepatitis B virus (HBV) infection remains a major cause of liver diseases and hepatocellular carcinoma. HBV infection begins by low-affinity attachment to hepatocytes and subsequent binding with a specific receptor sodium taurocholate cotransporting polypeptide (NTCP) on sinusoidal-basolateral side of liver parenchymal cells. Following internalization with an unclear mechanism, HBV undergoes uncoating, capsid disassembling and culminates in delivering its genome into the nucleus and forms the covalently closed circular (ccc) DNA. Read More

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Phylogenetic analysis of kinetoplast DNA: kDNA of Leishmania tropica in Thi-Qar province, Iraq.

Comp Immunol Microbiol Infect Dis 2021 Oct 12;78:101696. Epub 2021 Aug 12.

Department of Medical Laboratory Techniques, Nasiriyah Technical Institute, Southern Technical University, Nasiriyah 64001, Iraq.

Introduction: Cutaneous leishmaniasis (CL) is one of wobbling endemic disease in Iraq, that cause intracellular obligate protistan parasite returned to the genusLeishmania. This study is aimed to identify epidemiology of CL, detect the prevalence of Leishmania tropica and find the phylogenetic relationship.

Methodology: The current study was conducted in the main hospitals of Thi-Qar province-south of Iraq for period from November 2018 to October 2019. Read More

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October 2021

Evidence for long-term association of virion-delivered HBV core protein with cccDNA independently of viral protein production.

JHEP Rep 2021 Oct 8;3(5):100330. Epub 2021 Jul 8.

CIRI - Centre International de Recherche en Infectiologie, Univ Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, F-69007 Lyon, France.

Background & Aims: HBV persists in the nucleus of infected hepatocytes as a covalently closed circular DNA (cccDNA) episome that constitutes the template for viral RNA and protein synthesis. Both HBx and HBc (core) viral proteins associate with cccDNA but, while HBx is required for viral transcription, the role of HBc is still unclear. The aim of this study was to determine if HBc derived from incoming nucleocapsid can associate with cccDNA before the onset of viral transcription and protein production. Read More

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October 2021

Comparison of open and a novel closed vitrification system with slow freezing for human ovarian tissue cryopreservation.

J Assist Reprod Genet 2021 Aug 16. Epub 2021 Aug 16.

Laboratory of Molecular Reproduction and Fertility Preservation, Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, 333 Cedar Street, FMB 224, New Haven, CT, 06520, USA.

Purpose: To investigate the differences concerning post-thawing/warming follicle survival, DNA damage and apoptosis in human ovarian tissues cryopreserved by slow freezing, open, or closed vitrification methods.

Methods: A total of 50 pieces of 5 × 5 × 1 mm ovarian cortical pieces were harvested (5 donor ovaries; mean age 31 ± 6.62 years). Read More

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Mechanical Stimulation after Centrifuge-Free Nano-Electroporative Transfection Is Efficient and Maintains Long-Term T Cell Functionalities.

Small 2021 Sep 15;17(38):e2103198. Epub 2021 Aug 15.

Department of Materials Science and Engineering, Stanford University, Stanford, CA, 94305, USA.

Transfection is an essential step in genetic engineering and cell therapies. While a number of non-viral micro- and nano-technologies have been developed to deliver DNA plasmids into the cell cytoplasm, one of the most challenging and least efficient steps is DNA transport to and expression in the nucleus. Here, the magnetic nano-electro-injection (MagNEI) platform is described which makes use of oscillatory mechanical stimulation after cytoplasmic delivery with high aspect-ratio nano-structures to achieve stable (>2 weeks) net transfection efficiency (efficiency × viability) of 50% in primary human T cells. Read More

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September 2021

Methylation profile of hepatitis B virus is not influenced by interferon α in human liver cancer cells.

Mol Med Rep 2021 Oct 13;24(4). Epub 2021 Aug 13.

Department of Medicine, Seoul National University Bundang Hospital, Seongnam, Gyeonggi 13620, Republic of Korea.

Interferon (IFN) α is used for the treatment of chronic hepatitis B virus (HBV) infection, but the molecular mechanisms underlying its antiviral effect have not been fully elucidated. Epigenetic modifications regulate the transcriptional activity of covalently closed circular DNA (cccDNA) in cells with chronic HBV infection. IFN‑α has been shown to modify cccDNA‑bound histones, but it is not known whether the anti‑HBV effect of IFN‑α involves methylation of cccDNA. Read More

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October 2021