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Reverse Transcription (0):
Recent article
Reverse Transcription
Abstract
Moritella viscosa is considered to be the main aetiological agent of winter ulcer disease, primarily affecting farmed salmonid fish in cold marine waters. Transcription profiles of twelve M. viscosa genes, potentially involved in the pathogenesis, were studied during the course of an in vitro cell cu...
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PMID: 21334427
PDF is available here.
PDF is available here.
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Abstract
: Estrogen promoted the differentiation of hMSCs to osteoblasts in contrast to adipocytes, the former of which was mediated through the PI3K/SSH1L but not the mitogen-activated protein kinase pathway. CONCLUSION:: This study provides a novel mechanistic understanding of estrogen-related osteoporosis...
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PMID: 21289500
PDF is available here.
PDF is available here.
Abstract
The newly developed H3-RT-LAMP assay is simple, sensitive, rapid and can identify H3 subtype AIVs visually. Consequently, it will be a very useful screening assay for the surveillance of H3 subtype AIVs in underequipped laboratories as well as in field conditions....
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PMID: 21729297
PDF is available here.
PDF is available here.
Virus/Uirusu (60)2 2010
Abstract
We lately discovered endogenous elements homologous to the nucleoprotein of bornaviruses, a negative-strand RNA virus, in the genomes of many mammalian species, including humans. We also demonstrated that mRNA of extant mammalian bornavirus, Borna disease virus, is reverse-transcribed and integrated...
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PMID: 21488328
PDF is available here.
PDF is available here.
Abstract
We report a single-molecule study that monitors the dynamics of individual initiation complexes, comprised of vRNA, tRNA and HIV reverse transcriptase (RT). RT transitions between two opposite binding orientations on tRNA-vRNA complexes, and the prominent pausing events are related to RT binding in...
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PMID: 21102446
PDF is available here.
PDF is available here.
Abstract
We developed detects novel influenza A (H1N1) of swine origin and seasonal influenza A (H1N1 and H3N2) viruses. Individual primer sets targeting the HA gene for novel H1N1, H1N1, and H3N2 were newly designed to specifically detect these subtypes. No cross-reactions occurred among novel H1N1, H1N1, a...
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PMID: 20715552
PDF is available here.
PDF is available here.
Abstract
These results indicate that the RT-LAMP assay is specific for equine rotavirus and more sensitive than semi-nested RT-PCR. Because it is easy to manipulate without the need for a thermal cycler or gel electrophoresis, the RT-LAMP assay should be applicable to diagnosis of equine rotavirus infections...
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PMID: 20160420
PDF is available here.
PDF is available here.
Abstract
We report a next-generation sequencing technique designed to facilitate the inference of function of uncharacterized transcript forms by improving their coverage in sequencing libraries, in parallel with the detection of canonical mRNAs. We piloted this protocol, which is based on the capture of 3'...
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PMID: 20421314
PDF is available here.
PDF is available here.
Methods in Molecular Biology (629)629 2010
Abstract
We describe such a method that has been widely used for the validation of cloned small RNAs and also for quantitative analyses of small RNAs in both tissues and cells....
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PMID: 20387157
PDF is available here.
PDF is available here.
Methods in Molecular Biology (629)629 2010
Abstract
We describe a small RNA cloning method that can be used to generate small RNA cDNA libraries for both conventional and next generation (deep) sequencing. It can also be used for detection and quantitative analyses of small RNAs using PCR....
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PMID: 20387155
PDF is available here.
PDF is available here.
Methods in Molecular Biology (616)616 2010
Abstract
We describe the collection, isolation and activation of human peripheral blood-derived T lymphocytes and methods to examine the expression of CXCR3 and its atypical variants at both mRNA and protein levels, as well as protocols for exploring the biochemical and functional responses of T lymphocytes...
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PMID: 20379873
PDF is available here.
PDF is available here.
Abstract
A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay targeting the nucleocapsid phosphoprotein gene of infectious bronchitis virus (IBV) was developed. The detection limits for the IBV RT-LAMP assay were 10(1) 50% egg infection dose (EID(50)) per 50 microl of titrated virus...
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PMID: 19835950
PDF is available here.
PDF is available here.
Abstract
These results indicate that the developed RT-LAMP assay with uniquely designed primers is potentially useful in comprehensive avian influenza surveillance....
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PMID: 20032626
PDF is available here.
PDF is available here.
Methods in Molecular Biology (630)630 2010
Abstract
Reverse transcription (RT) is the synthesis of complementary deoxyribonucleic acids (DNA) from single-stranded ribonucleic acid (RNA) templates. This process is catalyzed by the reverse transcriptase enzyme, which is the replicating enzyme of retroviruses. Reverse transcriptase was discovered in 197...
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PMID: 20301003
PDF is available here.
PDF is available here.
Abstract
We explored the mechanism of the stabilization of Moloney murine leukaemia virus reverse transcriptase (MMLV RT) by eliminating RNase H activity. Without the template-primer (T/P) poly(rA)-p(dT)(15), the temperature reducing initial reverse-transcription activity by 50% over a 10-min incubation of t...
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PMID: 20139597
PDF is available here.
PDF is available here.
Abstract
We evaluated 10 licensed anti-HIV-1 compounds for their activity against XMRV, including protease inhibitors (PI), nucleoside reverse transcriptase (RT) inhibitors (NRTI), non-nucleoside RT inhibitors (NNRTI) and an integrase inhibitor. No PI affected XMRV production; even high concentrations of Rit...
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PMID: 19959199
PDF is available here.
PDF is available here.
Abstract
Our results suggest that HuR does not impact HIV-1 replication through a direct protein-protein interaction with the viral RT....
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PMID: 20459669
PDF is available here.
PDF is available here.
Abstract
We present here all of the techniques used to systematically determine if a gene possesses these types of control elements....
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PMID: 20033655
PDF is available here.
PDF is available here.
BMC Genomics (11) 2010
Abstract
We used an ongoing study of our laboratory aiming at identifying new biomarkers of graft rejection by the transcriptomic analysis of blood cells from brain-dead organ donors.
QPCR for ACTB performed on AA-aRNA from 15 donors provided Cq values 8 cycles higher than when original RNA was used (P < 0.0...
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PMID: 20929564
PDF is available here.
PDF is available here.
Abstract
Formalin-fixed, paraffin-embedded tissues are widely available for gene expression analysis using TaqMan PCR. Five methods, including 4 commercial kits, for recovering RNA from paraffin-embedded renal tumor tissue were compared. The MasterPure kit from Epicentre produced the highest RNA yield. Howev...
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PMID: 20008123
PDF is available here.
PDF is available here.
Abstract
We sought to identify structural determinants of this unique activity in the catalytic protein subunit telomerase reverse transcriptase (TERT) of telomerase. Residues within the highly conserved telomerase-specific T motif of human TERT were mutationally probed, leading to variant telomerases with i...
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PMID: 19917726
PDF is available here.
PDF is available here.
Journal of Virology (84)1 2010
Abstract
We previously demonstrated that the 5' cap proximity of the stem-loop structure (epsilon or epsilon), an encapsidation signal, is critically important for the encapsidation of the pgRNA (J. K. Jeong, G. S. Yoon, and W. S. Ryu, J. Virol. 74:5502-5508, 2000). Therefore, we speculated that the viral po...
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PMID: 19776122
PDF is available here.
PDF is available here.
Abstract
We found that T3 is needed for P to bind the viral RNA, the first step in DNA synthesis. A second motif, RT-1, was predicted to assist T3. T3 and RT-1 appear to form a composite RNA binding site because mutating T3 and RT-1 had similar effects on RNA binding, exposure of antibody epitopes on P, and...
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PMID: 19467554
PDF is available here.
PDF is available here.
Abstract
We employed reverse transcription of total RNA using primer S-D-Bact-0338-a-A-18. Length heterogeneity detected by slab gel analysis, denaturing high-performance liquid chromatography (DHPLC) was used to differentiate the 5' tail of the precursor from mature 16S rRNA, and the relative abundance of t...
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PMID: 19395563
PDF is available here.
PDF is available here.
Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui] (25)4 2009
Abstract
We have established an epsilon library and selected out a series of RNA aptamers with higher affinity to P protein based on the in vitro Systematic Evolution of Ligands by Exponential Enrichment (SELEX) in duck hepatitis B virus (DHBV) system. In order to study the structural elements within the eps...
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PMID: 19769164
PDF is available here.
PDF is available here.
Journal of Neurochemistry (109 Suppl 1) 2009
Abstract
We compared gene expression between LPS (lipopolysaccharide)/interferon (IFN)gamma-treated microglia from neonatal mixed glial cultures and similarly treated peritoneal macrophages. Fifteen molecules were identified by quantative PCR (qPCR) as being enriched from 2-fold to 250-fold in cultured neona...
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PMID: 19393017
PDF is available here.
PDF is available here.
Journal of General Virology (90)Pt 3 2009
Abstract
We show that PERVs are insensitive to restriction by divergent TRIM5alpha molecules despite the fact that they strongly restrict a variety of divergent lentiviruses. We also show that the human PERV A/C recombinant clone 14/220 reverse transcribes with increased efficiency in human cells, leading to...
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PMID: 19218217
PDF is available here.
PDF is available here.
Abstract
Knowledge about the structure of RNA is crucial to understanding its biological activities. Very often, the presence of unusually thermodynamically stable structural fragments in RNAs, such as hairpins, makes it impossible to apply primer extension to visualize the results of chemical mapping experi...
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PMID: 19119855
PDF is available here.
PDF is available here.
Biological Research (42)1 2009
Abstract
Our objective was to analyze the mRNA pro files of workers, queens, and intercastes of M. scutellaris through DDRT-PCR. Three hundred (300) pupae with white eyes were collected and externally identified according to the number of abdominal nerve ganglions: workers (5 ganglions), queens (4 ganglions)...
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PMID: 19621138
PDF is available here.
PDF is available here.
Abstract
Upon cell infection by a retrovirus, the viral DNA polymerase, called reverse transcriptase (RT), copies the genomic RNA to generate the proviral DNA flanked by two long terminal repeats (LTR). A discovery twenty years ago demonstrated that the structural viral nucleocapsid protein (NC) encoded by G...
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PMID: 19261185
PDF is available here.
PDF is available here.
Abstract
We conducted a DNA microarray analysis to detect critical factors that mediate fulminant pneumonia due to influenza virus and S. pneumoniae co-infection in mice. Among the factors detected, levels of PAF-acetyl hydrolase (PAF-AH), which functions as inactivated PAF, were significantly increased, and...
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PMID: 19168951
PDF is available here.
PDF is available here.
Abstract
We have modified molecular methods for RNA extraction, RNA quantification, reverse transcription, and quantitative PCR to work optimally in archived clinical samples in order to develop a clinically validated assay for breast cancer prognosis and prediction of patient response to hormonal and chemot...
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PMID: 19381955
PDF is available here.
PDF is available here.
Abstract
Much information can be obtained from knowledge of the relative expression level of each gene in the transcriptome. With the current advances in technology as little as a single cell is required as starting material for gene expression experiments. The mRNA from a single cell may be linearly amplifi...
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PMID: 19381966
PDF is available here.
PDF is available here.
Abstract
We describe three robust methods for target amplification from purified genomic DNA or pre-amplified DNA. The protocols include incorporation of biotin labels in the target molecules and allow for biotin/streptavidin chemistry to be utilized for flexibility in choice of visualization strategy....
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PMID: 19381981
PDF is available here.
PDF is available here.
Abstract
The availability of microarray technology for zebrafish research has enabled the expression of tens of thousands of genes to be studied simultaneously in one experiment. The experiment usually involves measuring and comparing the relative abundance of tens of thousands of mRNA species in experimenta...
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PMID: 19378105
PDF is available here.
PDF is available here.
Abstract
We also described the development of a reverse genetics system for HTNV strain 84FLi. The RNA polymerase I (pol I)-mediated transcription system was used to generate artificial viral RNA genome segments (minigenomes), which contained the chloramphenicol acetyltransferase (CAT) reporter gene in antis...
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PMID: 19133012
PDF is available here.
PDF is available here.
Abstract
We use a natural endogenous reverse transcriptase assay to show that, in cell-free virus particles, A3G is able to inhibit HIV-1 cDNA accumulation not only in the absence of hypermutation but also without the apparent need for any target cell factors. We find that although reverse transcription init...
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PMID: 19057663
PDF is available here.
PDF is available here.
Journal of Molecular Biology (383)5 2008
Abstract
The human immunodeficiency virus type 1 nucleocapsid protein (NCp7) plays an important role in the second strand transfer during reverse transcription. It promotes annealing of the 18-nucleotide complementary DNA primer-binding site (PBS) sequences at the 3' ends of (-)DNA and (+)DNA. NMR studies sh...
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PMID: 18773912
PDF is available here.
PDF is available here.
Abstract
We used single-molecule fluorescence resonance energy transfer to probe the interactions between RT and nucleic acid substrates in real time. RT was observed to slide on nucleic acid duplexes, rapidly shuttling between opposite termini of the duplex. Upon reaching the DNA 3' terminus, RT can spontan...
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PMID: 19008444
PDF is available here.
PDF is available here.
Abstract
We describe the cloning and isolation of HCV replicon-bearing cells, the extraction of total RNA, the generation of cDNA, and the amplification of specific HCV replicon sequences for sequence analysis. The methods we describe permit rapid and robust determination of HCV RNA sequences from cell cultu...
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PMID: 19009260
PDF is available here.
PDF is available here.
Abstract
We sought to determine which components of the retrovirus are responsible for this loss in bioactivity and to obtain a quantitative characterization of their stability. To this end, we focused on RNA and viral proteins, two major components that we hypothesized may undergo degradation and negatively...
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PMID: 18706668
PDF is available here.
PDF is available here.
Journal of Virology (82)19 2008
Abstract
We report here that several HIV-1 NC mutants, which we previously identified as being replication defective, contain abnormally high levels of intravirion DNA. These findings were further reinforced by the inability of these NC mutants to perform endogenous reverse transcription (ERT), in contrast t...
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PMID: 18667500
PDF is available here.
PDF is available here.
Abstract
We have investigated the expression profile of 27 chondrocyte-associated genes from both osteoarthritic cartilage tissue and healthy passaged human articular chondrocytes by quantitative real-time PCR. Our results indicate that the gene expression levels of matrix proteins and proteases in chondrocy...
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PMID: 18404652
PDF is available here.
PDF is available here.
Oral Diseases (14)6 2008
Abstract
Among the 54 675 tested transcripts, 47 transcripts were upregulated at least twofold in the parotid gland compared with the submandibular gland, including tumor-associated genes (pleiotrophin, WNT5A, ABCC1) and transport-associated genes (SLCO1A2, SLC13A5, KCNJ15). Ninety-eight transcripts were upr...
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PMID: 18826381
PDF is available here.
PDF is available here.
Journal of Virology (82)18 2008
Abstract
We characterize a novel mechanism in which human immunodeficiency virus type 1 (HIV-1) infection preferentially depletes peripheral memory CD4+ T cells before the completion of reverse transcription. Using a recombinant HIV-1 carrying the green fluorescent protein reporter gene, we demonstrate that...
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PMID: 18596085
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)35 2008
Abstract
We describe a structural element in TER1 that defines the 5' boundary of the template. Disruption of a predicted long range base pairing interaction between template-adjacent nucleotides and a sequence further upstream resulted in reverse transcription beyond the template region and caused telomere...
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PMID: 18574244
PDF is available here.
PDF is available here.
Journal of Virology (82)15 2008
Abstract
We tested whether the additional positive-strand DNA synthesis initiation of human immunodeficiency virus type 1 (HIV-1) from the central polypurine tract (cPPT) facilitates efficient completion of kinetically disturbed proviral DNA synthesis induced by dysfunctional reverse transcriptase (RT) mutan...
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PMID: 18495776
PDF is available here.
PDF is available here.
Journal of Virology (82)15 2008
Abstract
We generated a series of site-specific point mutants of vpx and examined their phenotypes. The resultant five mutants, with no infectivity for MDMs, showed, without exception, the same defect as the vpx-defective mutant. Our results here clearly demonstrated that the entire Vpx protein is critical f...
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PMID: 18495778
PDF is available here.
PDF is available here.
Molecules and Cells (25)4 2008
Abstract
We have previously shown that the 5' cap is indispensable for encapsidation of the pgRNA. A speculative extension of the above finding is that the cap contributes to encapsidation via its interaction with the poly(A) tail, possibly involving eIF4E-eIF4G-PABP interaction. To test this hypothesis, pol...
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PMID: 18460902
PDF is available here.
PDF is available here.
Experimental Parasitology (119)2 2008
Abstract
Haemonchus contortus is a blood-feeding nematode which parasitizes the abomasum of sheep and represents a serious constraint to sheep production. Anthelmintics are currently the most common method of worm control but the worldwide development of multiple-drug resistance and issues of residues in the...
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PMID: 18329022
PDF is available here.
PDF is available here.
Abstract
We developed a two-step isothermal amplification assay system, which achieved the detection of norovirus (NoV) genomes in oysters with a sensitivity similar to that of reverse transcription-seminested PCR. The time taken for the amplification of NoV genomes from RNA extracts was shortened to about 3...
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PMID: 18456857
PDF is available here.
PDF is available here.
Virus Research (134)1-2 2008
Murine leukemia virus reverse transcriptase: structural comparison with HIV-1 reverse transcriptase.
Abstract
We will review the similarities and differences between MoMLV RT and HIV-1 RT via structural analysis, and propose working models for the MoMLV RT based upon that information....
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PMID: 18294720
PDF is available here.
PDF is available here.
Virus Research (134)1-2 2008
Abstract
This review compares the well-studied RNase H activities of human immunodeficiency virus, type 1 (HIV-1) and Moloney murine leukemia virus (MoMLV) reverse transcriptases. The RNase H domains of HIV-1 and MoMLV are structurally very similar, with functions assigned to conserved subregions like the RN...
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PMID: 18261820
PDF is available here.
PDF is available here.
Virus Research (134)1-2 2008
Abstract
Human immunodeficiency virus type 1 (HIV-1) and other retroviruses replicate through reverse transcription, a process in which the single stranded RNA of the viral genome is converted to a double stranded DNA. The virally encoded reverse transcriptase (RT) mediates reverse transcription through DNA...
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PMID: 18279992
PDF is available here.
PDF is available here.
Virus Research (134)1-2 2008
Abstract
The ability of members of the APOBEC3 (A3) family of proteins to confer intrinsic immunity to retroviral infection was recognized in several studies. More specifically, A3 proteins are cytidine deaminases (CDAs) that cause hypermutations of nascent retroviral genomes by deamination of cytidine resid...
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PMID: 18262674
PDF is available here.
PDF is available here.
Virus Research (134)1-2 2008
Abstract
The role of nucleocapsid protein (NC) in the early steps of retroviral replication appears largely that of a facilitator for reverse transcription and integration. Using a wide variety of cell-free assay systems, the properties of mature NC proteins (e.g. HIV-1 p7(NC) or MLV p10(NC)) as nucleic acid...
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PMID: 18279991
PDF is available here.
PDF is available here.
Virus Research (134)1-2 2008
Abstract
Virus Research (134)1-2 2008
Abstract
Hepatitis B virus (HBV), the causative agent of B-type hepatitis in humans, is the type member of the Hepadnaviridae, hepatotropic DNA viruses that replicate via reverse transcription. Beyond long-established differences to retroviruses in gene expression and overall replication strategy newer work...
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PMID: 18339439
PDF is available here.
PDF is available here.
Virus Research (134)1-2 2008
Abstract
We describe recent developments concerning the initiation step of this complex, multi-step reaction. During initiation of reverse transcription, a cellular tRNA primer is placed onto a complementary sequence in the viral genome, called the primer binding site or PBS. The viral enzyme reverse transcr...
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PMID: 18255184
PDF is available here.
PDF is available here.
Virus Research (134)1-2 2008
Abstract
A number of abundant mobile genetic elements called retrotransposons reverse transcribe RNA to generate DNA for insertion into eukaryotic genomes. Four major classes of retrotransposons are described here. First, the long-terminal-repeat (LTR) retrotransposons have similar structures and mechanisms...
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PMID: 18261821
PDF is available here.
PDF is available here.