Towards the development of standardized methods for comparison
... confidence level. The analysis of SO correlation factors between different software tools reveals that correlations among the various programs can be small (Table 2). It is noteworthy to mention that SO values from HOMSTRAD alignments correlate poorly with those obtained from the other software tool ...
... confidence level. The analysis of SO correlation factors between different software tools reveals that correlations among the various programs can be small (Table 2). It is noteworthy to mention that SO values from HOMSTRAD alignments correlate poorly with those obtained from the other software tool ...
Evolutionary aspects of recombination in RNA viruses
... RNA viruses deserve their reputation as Nature’s swiftest evolvers. Their high rates of mutation and replication (Holland et al., 1982) allow them to move through sequence space at a pace that often makes their DNA-based hosts ’ evolution look glacial by comparison. Over the last two decades it has ...
... RNA viruses deserve their reputation as Nature’s swiftest evolvers. Their high rates of mutation and replication (Holland et al., 1982) allow them to move through sequence space at a pace that often makes their DNA-based hosts ’ evolution look glacial by comparison. Over the last two decades it has ...
RNA-based regulation of genes of tryptophan synthesis
... dedicating genetic material to regulatory purposes would be costly, and therefore a single regulatory protein might suffice for each group of functionally related genes. We now know that this view was an oversimplification, for regulated, balanced gene expression was clearly a much more important ob ...
... dedicating genetic material to regulatory purposes would be costly, and therefore a single regulatory protein might suffice for each group of functionally related genes. We now know that this view was an oversimplification, for regulated, balanced gene expression was clearly a much more important ob ...
Teacher Guide: Gene Expression. By Ann Brokaw.
... include up-to-date research, prompt students to process material, help reinforce textbook material, and stimulate discussions and explorations of current biological topics. For these reasons, I routinely use HHMI’s BioInteractive website and Holiday Lectures on Science DVDs in my classroom to highli ...
... include up-to-date research, prompt students to process material, help reinforce textbook material, and stimulate discussions and explorations of current biological topics. For these reasons, I routinely use HHMI’s BioInteractive website and Holiday Lectures on Science DVDs in my classroom to highli ...
Virp1 Is a Host Protein with a Major Role in Potato - IMBB
... Received 6 May 2007/Accepted 16 September 2007 ...
... Received 6 May 2007/Accepted 16 September 2007 ...
TNFα signals through specialized factories where responsive coding
... most active genes more likely to colocalize. A second, unsettled issue of interest to the field related to this topic of tx factories is that there seems to be a significant difference in the nature of the "tx factories" identified in the pioneering work of the Fraser and Cook laboratories. Whereas ...
... most active genes more likely to colocalize. A second, unsettled issue of interest to the field related to this topic of tx factories is that there seems to be a significant difference in the nature of the "tx factories" identified in the pioneering work of the Fraser and Cook laboratories. Whereas ...
Structural Energetics of a RNA-DNA Hybrid
... the bases A and G are classified as purines. A, C, and G bases are found in both DNA and RNA, but T is found mostly in DNA and U is found mostly in RNA. An example of a fragment of a DNA (or RNA) chain is shown in Figure 1.1.1. DNA typically exists as a double-stranded helix. The bases on one strand ...
... the bases A and G are classified as purines. A, C, and G bases are found in both DNA and RNA, but T is found mostly in DNA and U is found mostly in RNA. An example of a fragment of a DNA (or RNA) chain is shown in Figure 1.1.1. DNA typically exists as a double-stranded helix. The bases on one strand ...
Transcriptional Attenuation
... Once RNA polymerase leaves the pause site, the rate at which th ribosome synthesizes the remainder of the leader peptide and releases the mRNA, relative to the rate at which polymerase transcribes the at~ tenuator, determines the extent of attenuation. One of five outcomes can occur (Fig. 3). First, ...
... Once RNA polymerase leaves the pause site, the rate at which th ribosome synthesizes the remainder of the leader peptide and releases the mRNA, relative to the rate at which polymerase transcribes the at~ tenuator, determines the extent of attenuation. One of five outcomes can occur (Fig. 3). First, ...
Transition Bias
... I often say that when you can measure what you are speaking about, and express it in numbers, you know something about it; but when you cannot measure it, when you cannot express it in numbers, your knowledge is of a meagre and unsatisfactory kind; it may be the beginning of knowledge, but you have ...
... I often say that when you can measure what you are speaking about, and express it in numbers, you know something about it; but when you cannot measure it, when you cannot express it in numbers, your knowledge is of a meagre and unsatisfactory kind; it may be the beginning of knowledge, but you have ...
Identification of functional domains in Arabidopsis thaliana mRNA
... not regulated by the addition of cap analog competitor (7), again suggesting the importance of a short RNA region for preliminary binding. In addition, uncapped transcripts are efficient competitors for capped RNA, suggesting that binding of mRNA to hDcp2 is independent of the cap itself (17). A regio ...
... not regulated by the addition of cap analog competitor (7), again suggesting the importance of a short RNA region for preliminary binding. In addition, uncapped transcripts are efficient competitors for capped RNA, suggesting that binding of mRNA to hDcp2 is independent of the cap itself (17). A regio ...
silicon nanowire biosensor for studying nuclear hormone receptor
... Estrogen receptors (ERs) are members of a superfamily of nuclear receptors that function as ligand-modulated transcriptional regulators. The ERs mainly function as a DNA binding transcription factor that regulates gene expression. They play a key role in many normal physiological processes, but prom ...
... Estrogen receptors (ERs) are members of a superfamily of nuclear receptors that function as ligand-modulated transcriptional regulators. The ERs mainly function as a DNA binding transcription factor that regulates gene expression. They play a key role in many normal physiological processes, but prom ...
Cotranscriptional coupling of splicing factor recruitment and
... (Fig. 3b–d). Comparing the induced to the uninduced signals, Interactions between Pol II and splicing factors U1-70K, U2AF65 and U5-116K are, respectively, about 4.5-, 6- and It has previously been proposed that direct binding to Pol II leads to 12-fold enriched at their peaks in the presence of cam ...
... (Fig. 3b–d). Comparing the induced to the uninduced signals, Interactions between Pol II and splicing factors U1-70K, U2AF65 and U5-116K are, respectively, about 4.5-, 6- and It has previously been proposed that direct binding to Pol II leads to 12-fold enriched at their peaks in the presence of cam ...
The energetic basis of the DNA double helix: a
... that the AT and GC base pair contributions to the total heat capacity of the duplex are similar and additive. As expected, the presence of AT base pairs decreases duplex stability significantly, however, absolutely unexpected is the observation that unfolding/dissociation of the less thermostable AT ...
... that the AT and GC base pair contributions to the total heat capacity of the duplex are similar and additive. As expected, the presence of AT base pairs decreases duplex stability significantly, however, absolutely unexpected is the observation that unfolding/dissociation of the less thermostable AT ...
Chapter25_Outline
... • The reading frame may be influenced by the sequence of mRNA and the ribosomal environment. • recoding – Events that occur when the meaning of a codon or series of codons is changed from that predicted by the genetic code. – It may involve altered interactions between aminoacyl-tRNA and mRNA that a ...
... • The reading frame may be influenced by the sequence of mRNA and the ribosomal environment. • recoding – Events that occur when the meaning of a codon or series of codons is changed from that predicted by the genetic code. – It may involve altered interactions between aminoacyl-tRNA and mRNA that a ...
Against the Central Dogma
... For the last few decades of the 20th century, the underlying dogma of molecular biology has been that the purpose of RNA is to direct the assembly of proteins from amino acids. A few exceptions to this paradigm were known (for example, ribosomal RNA and transfer RNA, which are functional RNA macromo ...
... For the last few decades of the 20th century, the underlying dogma of molecular biology has been that the purpose of RNA is to direct the assembly of proteins from amino acids. A few exceptions to this paradigm were known (for example, ribosomal RNA and transfer RNA, which are functional RNA macromo ...
Transcripts of the MHM region on the chicken Z chromosome
... Recently, the ASW/Wpkci gene was found in the distal non-hetrochromatic region on the short arm of the chicken W chromosome (O'Neill et al. 2000, Hori et al. 2000). Wpkci is actively transcribed during the early embryonic stage and encodes an altered form of PKCI (protein kinase C interacting protei ...
... Recently, the ASW/Wpkci gene was found in the distal non-hetrochromatic region on the short arm of the chicken W chromosome (O'Neill et al. 2000, Hori et al. 2000). Wpkci is actively transcribed during the early embryonic stage and encodes an altered form of PKCI (protein kinase C interacting protei ...
Translation Section 1 From Genes to Proteins Chapter 10
... Decoding the Information in DNA, continued • RNA differs from DNA in three ways: 1. RNA consists of a single strand of nucleotides instead of the two strands found in DNA. 2. RNA nucleotides contain the five-carbon sugar ribose rather than the sugar deoxyribose, which is found in DNA nucleotides. 3. ...
... Decoding the Information in DNA, continued • RNA differs from DNA in three ways: 1. RNA consists of a single strand of nucleotides instead of the two strands found in DNA. 2. RNA nucleotides contain the five-carbon sugar ribose rather than the sugar deoxyribose, which is found in DNA nucleotides. 3. ...
Slides
... §Successful information-based system involves conservation and transfer §DNA - stable structure that maximizes storage and duplication §RNA - more reactive with numerous roles in protein synthesis and gene expression regulation ...
... §Successful information-based system involves conservation and transfer §DNA - stable structure that maximizes storage and duplication §RNA - more reactive with numerous roles in protein synthesis and gene expression regulation ...
Enzyme Mechanisms - Illinois Institute of Technology
... Cross-shaped structures arise from palindromic structures, including interrupted palindromes like this example These are less stable than regular duplexes but they are common, and they do create recognition sites for DNA-binding proteins, including restriction enzymes ...
... Cross-shaped structures arise from palindromic structures, including interrupted palindromes like this example These are less stable than regular duplexes but they are common, and they do create recognition sites for DNA-binding proteins, including restriction enzymes ...
Transition bias and substitution models
... I often say that when you can measure what you are speaking about, and express it in numbers, you know something about it; but when you cannot measure it, when you cannot express it in numbers, your knowledge is of a meagre and unsatisfactory kind; it may be the beginning of knowledge, but you have ...
... I often say that when you can measure what you are speaking about, and express it in numbers, you know something about it; but when you cannot measure it, when you cannot express it in numbers, your knowledge is of a meagre and unsatisfactory kind; it may be the beginning of knowledge, but you have ...
Evolutionary dynamics of RNA-like replicator systems
... reactions occurring in the cell. Nevertheless, RNA molecules are the actual catalyst of protein synthesis, one of the most vital reactions for life. It seems as if this role of RNA is a historical contingency. The second implication is that not only proteins, but also RNA can function as an efficien ...
... reactions occurring in the cell. Nevertheless, RNA molecules are the actual catalyst of protein synthesis, one of the most vital reactions for life. It seems as if this role of RNA is a historical contingency. The second implication is that not only proteins, but also RNA can function as an efficien ...
Improving Virus C type 4 Interferon using Bioinformatics Techniques
... After having discussed DNA and the various RNAs, the stage has been set for protein synthesis. The basic reaction of protein synthesis is the controlled formation of a peptide bond between two amino acids. This reaction is repeated many times, as each amino acid in turn is added to the growing polyp ...
... After having discussed DNA and the various RNAs, the stage has been set for protein synthesis. The basic reaction of protein synthesis is the controlled formation of a peptide bond between two amino acids. This reaction is repeated many times, as each amino acid in turn is added to the growing polyp ...
PPR2263, a DYW-Subgroup Pentatricopeptide
... is further subdivided into three subclasses on the basis of the successive addition of the E, E+, and DYW domain at the C terminus (Lurin et al., 2004). Independently of the subclass, three-quarters of the PPR proteins are predicted to be targeted to either mitochondria or chloroplasts, whereas no c ...
... is further subdivided into three subclasses on the basis of the successive addition of the E, E+, and DYW domain at the C terminus (Lurin et al., 2004). Independently of the subclass, three-quarters of the PPR proteins are predicted to be targeted to either mitochondria or chloroplasts, whereas no c ...
Structural basis for the inhibition of human alkyladenine Please share
... (⑀C)5 and 1,N6-ethenoadenine (⑀A) are endogenously generated when DNA is attacked by reactive aldehydes. These reactive compounds are generated as byproducts of lipid peroxidation that is induced by reactive oxygen and nitrogen species. Neutrophils and macrophages generate large quantities of reacti ...
... (⑀C)5 and 1,N6-ethenoadenine (⑀A) are endogenously generated when DNA is attacked by reactive aldehydes. These reactive compounds are generated as byproducts of lipid peroxidation that is induced by reactive oxygen and nitrogen species. Neutrophils and macrophages generate large quantities of reacti ...
Sequence Alignment - Bilkent University
... Schematic representation of the multiple alignment of the mRNAs of a microsomal glutathione transferase homolog gene with the genomic sequence. Three GenBank mRNAs (blue) align to the same genomic locus on chromosome 9, NT_008541 (red). Three ESTs that map to this locus are presented (purple), 38 ot ...
... Schematic representation of the multiple alignment of the mRNAs of a microsomal glutathione transferase homolog gene with the genomic sequence. Three GenBank mRNAs (blue) align to the same genomic locus on chromosome 9, NT_008541 (red). Three ESTs that map to this locus are presented (purple), 38 ot ...
Nucleic acid tertiary structure
The tertiary structure of a nucleic acid is its precise three-dimensional structure, as defined by the atomic coordinates. RNA and DNA molecules are capable of diverse functions ranging from molecular recognition to catalysis. Such functions require a precise three-dimensional tertiary structure. While such structures are diverse and seemingly complex, they are composed of recurring, easily recognizable tertiary structure motifs that serve as molecular building blocks. Some of the most common motifs for RNA and DNA tertiary structure are described below, but this information is based on a limited number of solved structures. Many more tertiary structural motifs will be revealed as new RNA and DNA molecules are structurally characterized.