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Heron HBV RNA Encapsidation Signal Epsilon
The Avian HBV RNA encapsidation signal epsilon (AHBV epsilon) is an RNA structure that is shown to facilitate encapsidation of the pregenomic RNA required for viral replication. There are two main classes of encapsidation signals in avian hepatitis B viruses - ''Duck hepatitis B virus'' (DHBV) and ''Heron hepatitis B virus'' (HHBV) like. DHBV is used as a model to understand human '' Hepatitis B virus''. Although studies have shown that the HHBV epsilon has less pairing in the upper stem than DHBV, this pairing is not absolutely required for DHBV infection in ducks. DHBV epsilon consists of a stem structure, a bulge and an apical loop (Fig. 1). The RNA structure was determined by chemical probing, NMR analysis and by mutagenesis. HHBV epsilon also consists of a stem structure, a bulge and an apical loop (Fig. 2). The RNA structure has been determined by chemical probing and by mutagenesis. However, it has less base pairing in the upper stem than DHBV epsilon. Recent NMR ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heron Hepatitis B Virus
''Avihepadnavirus'' is a genus of viruses, in the family ''Hepadnaviridae''. Birds serve as natural hosts. There are three species in this genus. Diseases associated with this genus include: hepatitis, hepatocellular carcinomas (chronic infections), and cirrhosis. Taxonomy The genus contains the following species: * ''Duck hepatitis B virus'' * '' Heron hepatitis B virus'' * ''Parrot hepatitis B virus'' Structure Viruses in the genus ''Avihepadnavirus'' are enveloped, with spherical geometries, and T=4 symmetry. The diameter is around 42 nm. Genomes are circular, around 3.2kb in length. The genome codes for 7 proteins. Life cycle Viral replication is nucleo-cytoplasmic. Replication follows the dsDNA(RT) replication model. DNA-templated transcription, specifically dsDNA-RT transcription, with some alternative splicing mechanism is the method of transcription. Translation takes place by ribosomal shunting Ribosome shunting is a mechanism of translation initiation in which ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
HBV RNA Encapsidation Signal Epsilon
The HBV RNA encapsidation signal epsilonHBV_epsilon is an element essential for HBV virus replication. It is an RNA structure situated near the 5' end of the HBV pregenomic RNA. The structure consists of a lower stem, a bulge region, an upper stem and a tri-loop. The structure was determined and refined through enzymatic probing and NMR spectroscopy. The closure of the tri-loop was not predicted by RNA structure prediction programs but observed in the NMR structure. The regions shown to be critical for encapsidation of the RNA in the viral lifecycle are the bulge, upper stem and tri-loop which interact with the terminal protein domain of the HBV viral polymerase. See also *Heron HBV RNA encapsidation signal epsilon The Avian HBV RNA encapsidation signal epsilon (AHBV epsilon) is an RNA structure that is shown to facilitate encapsidation of the pregenomic RNA required for viral replication. There are two main classes of encapsidation signals in avian he ... * Duck HB ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acid Secondary Structure
Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. The secondary structures of biological DNAs and RNAs tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar. In a non-biological context, secondary structure is a vital consideration in the nucleic acid design of nucleic acid structures for DNA nanotechnology and DNA computing, since the pattern of basepairing ultimately determines the overall structure of the molecules. Fundamental concepts Base pairing In molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Covariation Model
{{More footnotes, date=July 2021 Harold Kelley's covariation model (1967, 1971, 1972, 1973) is an attribution theory in which people make causal inferences to explain why other people and ourselves behave in a certain way. It is concerned with both social perception and self-perception (Kelley, 1973). The covariation principle states that, "an effect is attributed to the one of its possible causes with which, over time, it covaries" (Kelley, 1973:108). That is, a certain behaviour is attributed to potential causes that appear at the same time. This principle is useful when the individual has the opportunity to observe the behaviour over several occasions.see also Kelley's discounting principle (1971, 1972): single observation Causes of an outcome can be attributed to the person (internal), the stimulus (external), the circumstance, or some combination of these factors (Hewstone et al., 1973). Attributions are made based on three criteria: Consensus, Distinctiveness, and Consistency ( ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rfam
Rfam is a database containing information about non-coding RNA (ncRNA) families and other structured RNA elements. It is an annotated, open access database originally developed at the Wellcome Trust Sanger Institute in collaboration with Janelia Farm, and currently hosted at the European Bioinformatics Institute. Rfam is designed to be similar to the Pfam database for annotating protein families. Unlike proteins, ncRNAs often have similar secondary structure without sharing much similarity in the primary sequence. Rfam divides ncRNAs into families based on evolution from a common ancestor. Producing multiple sequence alignments (MSA) of these families can provide insight into their structure and function, similar to the case of protein families. These MSAs become more useful with the addition of secondary structure information. Rfam researchers also contribute to Wikipedia's RNA WikiProject. Uses The Rfam database can be used for a variety of functions. For each ncRNA f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tetraloop
Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. There are many variants of the tetraloop. The published ones include ANYA, CUYG, GNRA, UNAC and UNCG. Three types of tetraloops are common in ribosomal RNA: GNRA, UNCG and CUUG, in which the N could be either uracil, adenine, cytosine, or guanine, and the R is either guanine or adenine. These three sequences form stable and conserved tetraloops that play an important role in structural stability and biological function of 16S rRNA. * GNRA ** The GNRA tetraloop has a guanine-adenine base-pair where the guanine is 5' to the helix and the adenine is 3' to the helix. Tetraloops with the sequence UMAC have essentially the same backbone fold as the GNRA tetraloop, but may be less likely to form tetraloop-receptor interactions. They may therefore be a better choice for closing stems when designing artificial RNAs. ** The presence of the GNRA tetraloop provides an exceptional ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mutagenesis
Mutagenesis () is a process by which the genetic information of an organism is changed by the production of a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using laboratory procedures. A mutagen is a mutation-causing agent, be it chemical or physical, which results in an increased rate of mutations in an organism's genetic code. In nature mutagenesis can lead to cancer and various heritable diseases, and it is also a driving force of evolution. Mutagenesis as a science was developed based on work done by Hermann Muller, Charlotte Auerbach and J. M. Robson in the first half of the 20th century. History DNA may be modified, either naturally or artificially, by a number of physical, chemical and biological agents, resulting in mutations. Hermann Muller found that "high temperatures" have the ability to mutate genes in the early 1920s, and in 1927, demonstrated a causal link to mutation upon exper ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NMR Spectroscopy
Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic field and the NMR signal is produced by excitation of the nuclei sample with radio waves into nuclear magnetic resonance, which is detected with sensitive radio receivers. The intramolecular magnetic field around an atom in a molecule changes the resonance frequency, thus giving access to details of the electronic structure of a molecule and its individual functional groups. As the fields are unique or highly characteristic to individual compounds, in modern organic chemistry practice, NMR spectroscopy is the definitive method to identify monomolecular organic compounds. The principle of NMR usually involves three sequential steps: # The alignment (polarization) of the magnetic nuclear spins in an applied, constant magnetic field B0. # The p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stem Loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures. As an important secondary structure of RNA, it can direct RNA folding, protect structural stability for messenger RNA (mRNA), provide recognition sites for RNA binding proteins, and serve as a substrate for enzymatic reactions. Formation and stability The formation of a stem-loop structure is dependent on the stability of the resulting helix and loop regions. The first prerequisite is the presence of a sequence that can fold back on itself to form a paired double helix. The stability of this helix is determined by its length, the number of mismatches or bulges it ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hepatitis B Virus
''Hepatitis B virus'' (HBV) is a partially double-stranded DNA virus, a species of the genus '' Orthohepadnavirus'' and a member of the '' Hepadnaviridae'' family of viruses. This virus causes the disease hepatitis B. Disease Despite there being a vaccine to prevent Hepatitis B, HBV remains a global health problem. Hepatitis B can be acute and later become chronic, leading to other diseases and health conditions. In addition to causing hepatitis, infection with HBV can lead to cirrhosis and hepatocellular carcinoma. It has also been suggested that it may increase the risk of pancreatic cancer. Roles in disease Viral infection by ''Hepatitis B virus'' (HBV) causes many hepatocyte changes due to the direct action of a protein encoded by the virus, HBx, and to indirect changes due to a large increase in intracellular reactive oxygen species (ROS) after infection. HBx appears to dysregulate a number of cellular pathways. HBx causes dysregulation in part by binding to genomic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Duck Hepatitis B Virus
''Duck hepatitis B virus'', abbreviated DHBV, is part of the genus '' Avihepadnavirus'' of the '' Hepadnaviridae'', and is the causal agent of duck hepatitis B. DHBV is a small DNA virus with a diameter of 40–45 nm. The viral envelope is made up from host cell lipid, with viral surface antigens (DHBsAg). The icosahedral nucleocapsid within, is composed of the virus core antigen (DHBcAg) and surrounds the DNA genome and viral polymerase. The viral genome is a circular double stranded DNA molecule about 3000 base pairs long. The genome has three overlapping open reading frames or ORFs: * C-ORF – encoding the core antigen and pre-core protein which are processed and secreted as DHBcAg * S-ORF – codes for the surface antigen DHBsAg * P-ORF – encoding the viral polymerase. On binding and entry of the virus to the host cell, the genome is transported to the nucleus to be transcribed. Novel viral RNA is then transferred to the cytoplasm for translation and sub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
