Introduction to Bioinformatics.
... * Therefore it is usefull to monitor the genome-wide expression of S. cerevisiae in time, including the diauxic shift. * Such a conveyor belt of coupled expressed genes is called a genetic pathway * This monitoring can be done with microarrays, the foremost important tools in bioinformatics. * Other ...
... * Therefore it is usefull to monitor the genome-wide expression of S. cerevisiae in time, including the diauxic shift. * Such a conveyor belt of coupled expressed genes is called a genetic pathway * This monitoring can be done with microarrays, the foremost important tools in bioinformatics. * Other ...
1st set of Journal Clubs this Wednesday!
... something causes it to be released.’ Positive control: ‘An activator causes the accelerator pedal to be pushed.’ Cis-acting sequence: Can only function if on same piece of DNA that its regulating Trans-acting factor: A gene product that can act in ‘trans’ i.e. diffuse to a location at a distance fro ...
... something causes it to be released.’ Positive control: ‘An activator causes the accelerator pedal to be pushed.’ Cis-acting sequence: Can only function if on same piece of DNA that its regulating Trans-acting factor: A gene product that can act in ‘trans’ i.e. diffuse to a location at a distance fro ...
Whole-genome expression analysis of snf swi mutants of
... cause repression of transcription by blocking transcription factor binding (1). In recent years, several studies have shown that the conserved protein complex, Snf兾Swi, can relieve this repression by perturbing the structure of nucleosomes (2). This remodeling probably allows transcription factors t ...
... cause repression of transcription by blocking transcription factor binding (1). In recent years, several studies have shown that the conserved protein complex, Snf兾Swi, can relieve this repression by perturbing the structure of nucleosomes (2). This remodeling probably allows transcription factors t ...
Monday March 10th in-class “assignment”: studying SRS and BWS
... -At the molecular level, BWS can be caused by a 160kb inverted duplication involving ICR2 and the 5` most 20kb region of the Kcnq1ot1. As a result the maternal copy of the ICR2 is hypomethylated because the duplicated ICR2 is not methylated. Kcnq1ot1 is transcribed usually only from the paternal chr ...
... -At the molecular level, BWS can be caused by a 160kb inverted duplication involving ICR2 and the 5` most 20kb region of the Kcnq1ot1. As a result the maternal copy of the ICR2 is hypomethylated because the duplicated ICR2 is not methylated. Kcnq1ot1 is transcribed usually only from the paternal chr ...
Activity of ribosomes and tmRNA of Streptomyces aureofaciens
... GDPNP can substitute GTP in the binding of fMet-tRNA to ribosomes, but increasing concentrations of UTP had no stimulation effect. To investigate whether the stimulatory effect of UTP possibly influences the correct position of fMet-tRNA on ribosome, the transfer of fMet-tRNA from 70S ribosomes to p ...
... GDPNP can substitute GTP in the binding of fMet-tRNA to ribosomes, but increasing concentrations of UTP had no stimulation effect. To investigate whether the stimulatory effect of UTP possibly influences the correct position of fMet-tRNA on ribosome, the transfer of fMet-tRNA from 70S ribosomes to p ...
Genome segment 5 of Antheraea mylitta cytoplasmic polyhedrosis
... and indicates importance of these residues at these sites. Thermodynamic analysis showed p65-GTP interaction was primarily driven by enthalpy (ΔH = −399.1 ± 4.1 kJ/mol) whereas the p65-RNA interaction by favorable entropy (0.043 ± 0.0049 kJ/ mol). Conclusion: Viral capping enzymes play a critical ro ...
... and indicates importance of these residues at these sites. Thermodynamic analysis showed p65-GTP interaction was primarily driven by enthalpy (ΔH = −399.1 ± 4.1 kJ/mol) whereas the p65-RNA interaction by favorable entropy (0.043 ± 0.0049 kJ/ mol). Conclusion: Viral capping enzymes play a critical ro ...
Against the Central Dogma
... in the control of gene expression. Xist is an lncRNA that suppresses the inactive, non‐coding X chromosome (Xi) in female cells. In all, 7 ncRNAs are found as part of the X inactivation center on the X chromosome, including Xist. Initially, Xist and its antisense transcript Tsix are expressed on bot ...
... in the control of gene expression. Xist is an lncRNA that suppresses the inactive, non‐coding X chromosome (Xi) in female cells. In all, 7 ncRNAs are found as part of the X inactivation center on the X chromosome, including Xist. Initially, Xist and its antisense transcript Tsix are expressed on bot ...
TNFα signals through specialized factories where responsive coding
... A major question is whether the observed associations relate to clustering of highly active genes per se rather than genes which are coregulated by p65. In fact the discussion seems to suggest a model in which at early time points, at least, association begins at generic tx factories which then beco ...
... A major question is whether the observed associations relate to clustering of highly active genes per se rather than genes which are coregulated by p65. In fact the discussion seems to suggest a model in which at early time points, at least, association begins at generic tx factories which then beco ...
not a plastid specific promoter but is also capable of
... being that deletion of either box would significanfly reduce PAT expression, thus supporting their functional importance. On pGSC54 two chimaeric genes producing respectively PAT and NPTII, and both under the control of the psbA promoter, are placed in a head to tail configuration. In order to avoid ...
... being that deletion of either box would significanfly reduce PAT expression, thus supporting their functional importance. On pGSC54 two chimaeric genes producing respectively PAT and NPTII, and both under the control of the psbA promoter, are placed in a head to tail configuration. In order to avoid ...
Polyamines and other charged amines bind to RNA by hydrogen
... proposed models for spermine and spermidine, NH 2 (CH 2 ) NH(CH2) NH2,binding to DNA in which phosphate groups interact with each positively charged amino group, the tetramethylene portion of the polyamine bridges the narrow (minor) groove of the helix between the two strands and the trimethylene po ...
... proposed models for spermine and spermidine, NH 2 (CH 2 ) NH(CH2) NH2,binding to DNA in which phosphate groups interact with each positively charged amino group, the tetramethylene portion of the polyamine bridges the narrow (minor) groove of the helix between the two strands and the trimethylene po ...
Historical review: Deciphering the genetic code – a personal account
... regulation. I thought that in the absence of cysteine the synthesis of penicillinase might proceed, whereas synthesis of most other proteins might be reduced. In England, Pollock [2] had shown that penicillinase is inducible in Bacillus cerus and had isolated mutants that differed in the regulation ...
... regulation. I thought that in the absence of cysteine the synthesis of penicillinase might proceed, whereas synthesis of most other proteins might be reduced. In England, Pollock [2] had shown that penicillinase is inducible in Bacillus cerus and had isolated mutants that differed in the regulation ...
Strong association between mRNA folding strength and protein
... with real-time high-resolution measurements of single ribosomes’ translation rates (for example, see ref. 23). We propose the following experiment for determining the dominant mechanism that associates mF strength and expression levels: Generate a highly expressed library of a heterologous green flu ...
... with real-time high-resolution measurements of single ribosomes’ translation rates (for example, see ref. 23). We propose the following experiment for determining the dominant mechanism that associates mF strength and expression levels: Generate a highly expressed library of a heterologous green flu ...
Chapt. 14 Eukaryotic mRNA processing I: splicing 14.1 Genes are in
... • Most ‘higher eukaryotic’ genes coding for mRNA and tRNA (some rRNA) are interrupted by introns • Exons surround introns: contain sequences that finally appear in the mature RNA product – Genes for mRNAs have 0 to 362 exons (titin) – tRNA genes have either 0 or 1 exon Introns present in genes, not ...
... • Most ‘higher eukaryotic’ genes coding for mRNA and tRNA (some rRNA) are interrupted by introns • Exons surround introns: contain sequences that finally appear in the mature RNA product – Genes for mRNAs have 0 to 362 exons (titin) – tRNA genes have either 0 or 1 exon Introns present in genes, not ...
Interaction of Sesbania Mosaic Virus Movement Protein
... poly protein 2a, and ORF 2b for the RNA dependent RNA polymerase (RdRp) that is translated by a frame shift mechanism to yield poly protein 2ab. The 39- proximal ORF codes for the CP which is expressed via a sub genomic RNA [16]. The domain arrangement in poly protein 2a and 2ab was recently shown t ...
... poly protein 2a, and ORF 2b for the RNA dependent RNA polymerase (RdRp) that is translated by a frame shift mechanism to yield poly protein 2ab. The 39- proximal ORF codes for the CP which is expressed via a sub genomic RNA [16]. The domain arrangement in poly protein 2a and 2ab was recently shown t ...
RNA 3`-terminal phosphate cyclases and cyclase
... Early biochemical studies of the human cyclase, partially or highly (~6’000-fold) purified from extracts of HeLa cells, revealed that the enzyme acts as a monomer of Mr ~40’000. The pH optimum of cyclisation of RNA substrates was between 8.0 and 9.0, and Mg++ was the preferred divalent cation. ATP s ...
... Early biochemical studies of the human cyclase, partially or highly (~6’000-fold) purified from extracts of HeLa cells, revealed that the enzyme acts as a monomer of Mr ~40’000. The pH optimum of cyclisation of RNA substrates was between 8.0 and 9.0, and Mg++ was the preferred divalent cation. ATP s ...
Biochimica et Biophysica Acta
... This two-plasmid strategy was applied to the L30e protein and its target RNA. Although the initial two-plasmid constructs produced very low repression ratios, following optimization of the reporter construct and conditions for protein expression, a 450-fold repression of the reporter construct by L3 ...
... This two-plasmid strategy was applied to the L30e protein and its target RNA. Although the initial two-plasmid constructs produced very low repression ratios, following optimization of the reporter construct and conditions for protein expression, a 450-fold repression of the reporter construct by L3 ...
SGD sample annotations
... annotation to “NOT RNA-3’-phosphate cyclase activity” with the evidence code NAS. While the authors mention the use of a direct assay, it is only in passing in the Discussion section and no experiment is shown. Thus, we have used the evidence code NAS, to indicate that this annotation is based on a ...
... annotation to “NOT RNA-3’-phosphate cyclase activity” with the evidence code NAS. While the authors mention the use of a direct assay, it is only in passing in the Discussion section and no experiment is shown. Thus, we have used the evidence code NAS, to indicate that this annotation is based on a ...
PowerPoint 演示文稿
... A major difference in the production of mRNA depends on the locations where transcription and translation occur: In bacteria, mRNA is transcribed and translated in the single cellular compartment; and the two processes are so closely linked that they occur simultaneously. Since ribosomes attach t ...
... A major difference in the production of mRNA depends on the locations where transcription and translation occur: In bacteria, mRNA is transcribed and translated in the single cellular compartment; and the two processes are so closely linked that they occur simultaneously. Since ribosomes attach t ...
m.se.hccs.edu
... Codons: Triplets of Bases • The flow of information from gene to protein is based on a triplet code: a series of nonoverlapping, three-nucleotide words • These triplets are the smallest units of uniform length that can code for all the amino acids • Example: AGT at a particular position on a DNA st ...
... Codons: Triplets of Bases • The flow of information from gene to protein is based on a triplet code: a series of nonoverlapping, three-nucleotide words • These triplets are the smallest units of uniform length that can code for all the amino acids • Example: AGT at a particular position on a DNA st ...
Chapter 17
... Codons: Triplets of Bases • The flow of information from gene to protein is based on a triplet code: a series of nonoverlapping, three-nucleotide words • These triplets are the smallest units of uniform length that can code for all the amino acids • Example: AGT at a particular position on a DNA st ...
... Codons: Triplets of Bases • The flow of information from gene to protein is based on a triplet code: a series of nonoverlapping, three-nucleotide words • These triplets are the smallest units of uniform length that can code for all the amino acids • Example: AGT at a particular position on a DNA st ...
Conclusions Synapsin IIa is expressed in the brain of adult zebrafish
... Figure 1: RT-PCR analysis of Synapsin IIa from zebrafish embryos. The SynIIa gene was amplified from zebrafish brain, 24 hpf, and 72 hpf. The primers used encompassed the predicted ATG start codon and stop codon to produce an amplicon of 1420 base pairs ...
... Figure 1: RT-PCR analysis of Synapsin IIa from zebrafish embryos. The SynIIa gene was amplified from zebrafish brain, 24 hpf, and 72 hpf. The primers used encompassed the predicted ATG start codon and stop codon to produce an amplicon of 1420 base pairs ...
PG1005 Lecture 18 Translation
... enzyme (too large=excluded) 2) The correct tRNA is associated with the enzyme by fit of anti-codon sequences into 3 adjacent nucleotide binding pockets 3) Adenylated AA is shunted to a new site following tRNA binding. If it fits, it is hydrolysed (=removed) ...
... enzyme (too large=excluded) 2) The correct tRNA is associated with the enzyme by fit of anti-codon sequences into 3 adjacent nucleotide binding pockets 3) Adenylated AA is shunted to a new site following tRNA binding. If it fits, it is hydrolysed (=removed) ...
Deconstructing host-pathogen interactions in Drosophila
... Activated Hop phosphorylates receptor-bound signal transducer and activator of transcription (STAT; STAT92E in flies), which then dimerizes, enters the nucleus and activates transcription of effector target genes such as totA (Agaisse and Perrimon, 2004; Folsch et al., 2003). (D)RNAi pathway. Once ...
... Activated Hop phosphorylates receptor-bound signal transducer and activator of transcription (STAT; STAT92E in flies), which then dimerizes, enters the nucleus and activates transcription of effector target genes such as totA (Agaisse and Perrimon, 2004; Folsch et al., 2003). (D)RNAi pathway. Once ...
RNA interference
RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecules. Historically, it was known by other names, including co-suppression, post-transcriptional gene silencing (PTGS), and quelling. Only after these apparently unrelated processes were fully understood did it become clear that they all described the RNAi phenomenon. Andrew Fire and Craig C. Mello shared the 2006 Nobel Prize in Physiology or Medicine for their work on RNA interference in the nematode worm Caenorhabditis elegans, which they published in 1998.Two types of small ribonucleic acid (RNA) molecules – microRNA (miRNA) and small interfering RNA (siRNA) – are central to RNA interference. RNAs are the direct products of genes, and these small RNAs can bind to other specific messenger RNA (mRNA) molecules and either increase or decrease their activity, for example by preventing an mRNA from producing a protein. RNA interference has an important role in defending cells against parasitic nucleotide sequences – viruses and transposons. It also influences development.The RNAi pathway is found in many eukaryotes, including animals, and is initiated by the enzyme Dicer, which cleaves long double-stranded RNA (dsRNA) molecules into short double-stranded fragments of ~20 nucleotide siRNAs. Each siRNA is unwound into two single-stranded RNAs (ssRNAs), the passenger strand and the guide strand. The passenger strand is degraded and the guide strand is incorporated into the RNA-induced silencing complex (RISC). The most well-studied outcome is post-transcriptional gene silencing, which occurs when the guide strand pairs with a complementary sequence in a messenger RNA molecule and induces cleavage by Argonaute, the catalytic component of the RISC complex. In some organisms, this process spreads systemically, despite the initially limited molar concentrations of siRNA.RNAi is a valuable research tool, both in cell culture and in living organisms, because synthetic dsRNA introduced into cells can selectively and robustly induce suppression of specific genes of interest. RNAi may be used for large-scale screens that systematically shut down each gene in the cell, which can help to identify the components necessary for a particular cellular process or an event such as cell division. The pathway is also used as a practical tool in biotechnology, medicine and insecticides.