ELSI Learning Objective
... Copyright © 2015 by AM Campbell, LJ Heyer, CJ Paradise. All rights reserved. ...
... Copyright © 2015 by AM Campbell, LJ Heyer, CJ Paradise. All rights reserved. ...
Biochemistry
... The controller molecule attaches to the repressor removing it from the operator and transcription proceeds. 1.Structure and catabolite of glucose The molecular mechanisms responsible for the regulation of the genes involved in the metabolism of lactose are now among the best-understood in any organi ...
... The controller molecule attaches to the repressor removing it from the operator and transcription proceeds. 1.Structure and catabolite of glucose The molecular mechanisms responsible for the regulation of the genes involved in the metabolism of lactose are now among the best-understood in any organi ...
Document
... Overview: Conducting the Genetic Orchestra • genetic and biochemical work in bacteria identified two things – 1. protein-binding regulatory sequences associated with genes – 2. proteins that can bind these regulatory sequences – either activating or repressing gene expression ...
... Overview: Conducting the Genetic Orchestra • genetic and biochemical work in bacteria identified two things – 1. protein-binding regulatory sequences associated with genes – 2. proteins that can bind these regulatory sequences – either activating or repressing gene expression ...
Connections between mRNA 3( end processing and transcription
... robust crosslinking of polyadenylation factors normally seen at 30 ends of genes is no longer observed in strains lacking Ctk1 [10]. Third, in vivo inhibition of Cdk9 in Drosophila cells leads to defects in polyadenylation [17]. Finally, in vitro binding of Pcf11 (a subunit of the yeast polyadenyl ...
... robust crosslinking of polyadenylation factors normally seen at 30 ends of genes is no longer observed in strains lacking Ctk1 [10]. Third, in vivo inhibition of Cdk9 in Drosophila cells leads to defects in polyadenylation [17]. Finally, in vitro binding of Pcf11 (a subunit of the yeast polyadenyl ...
Engineering Learning in Unicellular Organisms
... Sigmoidal activation function is sequence programmable but hard wired. ...
... Sigmoidal activation function is sequence programmable but hard wired. ...
RNAi Rescue using Precision LentiORF
... analysis. However, in addition to gene-specific silencing through perfect complementarity to the target transcript, siRNA-mediated silencing can also lead to regulation of unintended transcripts through seed-region complementarity. This off-targeted regulation can potentially cause phenotypic effect ...
... analysis. However, in addition to gene-specific silencing through perfect complementarity to the target transcript, siRNA-mediated silencing can also lead to regulation of unintended transcripts through seed-region complementarity. This off-targeted regulation can potentially cause phenotypic effect ...
BIOL 504: Molecular Evolution
... copies are still under purifying selection c) Functionally distinct copies often arise from positive selection ...
... copies are still under purifying selection c) Functionally distinct copies often arise from positive selection ...
B. Eukaryotic RNA polymerases
... B. Rate of Elongation 1. RNA polymerase can lay down and connect about 40 nucleotides a second a) It takes about 25 seconds to transcribe an average length gene of 1000 nucleotides 2. RNA polymerase proceeds at different rates down the DNA molecule in different regions a) Slow downs are referred to ...
... B. Rate of Elongation 1. RNA polymerase can lay down and connect about 40 nucleotides a second a) It takes about 25 seconds to transcribe an average length gene of 1000 nucleotides 2. RNA polymerase proceeds at different rates down the DNA molecule in different regions a) Slow downs are referred to ...
Biol120 Mock Final Examination
... b) Cytosol, mitochondrial matrix, mitochondrial matrix. c) Mitochondrial matrix, mitochondrial matrix, cytosol. d) Cytosol, cytosol, mitochondrial matrix. 34. In Drosophila, two genes, one for body colour and one for eye colour, are carried on the same chromosome. The wild type grey body colour (G) ...
... b) Cytosol, mitochondrial matrix, mitochondrial matrix. c) Mitochondrial matrix, mitochondrial matrix, cytosol. d) Cytosol, cytosol, mitochondrial matrix. 34. In Drosophila, two genes, one for body colour and one for eye colour, are carried on the same chromosome. The wild type grey body colour (G) ...
Sequence, Transcription and Translation of a Late Gene of the
... infected cells at other times p.i. indicating that the appearance of this fragment is due to R N A protection (i.e. some transcripts cross the entire length of this 674 bp fragment). Aphidicolin, an inhibitor of both cellular and viral D N A polymerases, inhibited the synthesis of transcripts throug ...
... infected cells at other times p.i. indicating that the appearance of this fragment is due to R N A protection (i.e. some transcripts cross the entire length of this 674 bp fragment). Aphidicolin, an inhibitor of both cellular and viral D N A polymerases, inhibited the synthesis of transcripts throug ...
WormBase-Oct2004 - Gene Ontology Consortium
... which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc. ...
... which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc. ...
RNA polymerase I
... • The three-dimensional organization of chromatin within the cell nucleus plays a central role in transcriptional control. • There is increasing evidence that eukaryotic chromatin is organized as independent loops. • The formation of each loop is dependent on specific DNA sequence elements that are ...
... • The three-dimensional organization of chromatin within the cell nucleus plays a central role in transcriptional control. • There is increasing evidence that eukaryotic chromatin is organized as independent loops. • The formation of each loop is dependent on specific DNA sequence elements that are ...
Chapter 9 From DNA to Protein
... How is RNA Assembled? (cont’d.) • Transcription begins when an RNA polymerase and regulatory proteins attach to a DNA site called a promoter – RNA polymerase moves over a gene region and unwinds the double helix a bit so it can “read” the base sequence of the DNA strand – The polymerase joins free ...
... How is RNA Assembled? (cont’d.) • Transcription begins when an RNA polymerase and regulatory proteins attach to a DNA site called a promoter – RNA polymerase moves over a gene region and unwinds the double helix a bit so it can “read” the base sequence of the DNA strand – The polymerase joins free ...
SURVEY AND SUMMARY Origins of tmRNA: the
... as the elimination of the related incomplete proteins and mRNA. A particular RNA performs this process: tmRNA associated with Small protein B (SmpB). tmRNA is a hybrid molecule carrying out both transfer and messenger RNA activities, and its total length varies between about 260 and 430 nucleotides, ...
... as the elimination of the related incomplete proteins and mRNA. A particular RNA performs this process: tmRNA associated with Small protein B (SmpB). tmRNA is a hybrid molecule carrying out both transfer and messenger RNA activities, and its total length varies between about 260 and 430 nucleotides, ...
A mRNA localized to the vegetal cortex of Xenopus
... clear, however, that many of the early developmental decisions of the embryo depend on maternal information localized to the vegetal region during oogenesis. For example, the dorsal-ventral axis of the embryo, specified by a 30° rotation of the cortex before first cleavage, depends on a maternal com ...
... clear, however, that many of the early developmental decisions of the embryo depend on maternal information localized to the vegetal region during oogenesis. For example, the dorsal-ventral axis of the embryo, specified by a 30° rotation of the cortex before first cleavage, depends on a maternal com ...
Microarray experiment guidelines
... Capable of simultaneously measuring the expression levels for thousands of genes, microarrays provide a large quantity of information about an organism/cell/tissue – whether it be mutational studies (monitoring the effects of gene expression by knocking out/in a particular gene), conditional (monito ...
... Capable of simultaneously measuring the expression levels for thousands of genes, microarrays provide a large quantity of information about an organism/cell/tissue – whether it be mutational studies (monitoring the effects of gene expression by knocking out/in a particular gene), conditional (monito ...
CHANGES IN THE EXPRESSION OF THREE COLD
... spp., tobacco, peach and apple (Danyluk et al. 1994; Thomashow 1994; Stockinger et al. 1997; Gilmour et al. 1998; Liu et al. 1998; Ouellet at al. 1998; Medina et al. 1999; Wiśniewski et al 1999, 2006; Haake et al. 2002; Dubouzet et al. 2003; Miura & Furumoto 2013). Based on the model plant studies, ...
... spp., tobacco, peach and apple (Danyluk et al. 1994; Thomashow 1994; Stockinger et al. 1997; Gilmour et al. 1998; Liu et al. 1998; Ouellet at al. 1998; Medina et al. 1999; Wiśniewski et al 1999, 2006; Haake et al. 2002; Dubouzet et al. 2003; Miura & Furumoto 2013). Based on the model plant studies, ...
The WD40-Repeat Proteins NFC101 and NFC102
... MA tissues of V3/V4 wild-type and transgenic seedlings (Figure 1A). These tissues contain SAM and leaf primordia and were sampled at a developmental stage preceding floral transition, which in the B73 temperate line occurs at stage V5 (Meng et al., 2011; Figure 2F). Therefore, a putative maize FLC ho ...
... MA tissues of V3/V4 wild-type and transgenic seedlings (Figure 1A). These tissues contain SAM and leaf primordia and were sampled at a developmental stage preceding floral transition, which in the B73 temperate line occurs at stage V5 (Meng et al., 2011; Figure 2F). Therefore, a putative maize FLC ho ...
A tale of two functions: enzymatic activity and
... assay with a CT b-enhanced yellow fluorescent protein (eYFP) fusion protein as the donor and the RNA binding dye Sytox Orange (Molecular Probes) as the acceptor. The gene for eYFP was amplified with primers eYFP5 and eYFP3, digested with XhoI and PacI, and cloned into equivalently digested pGDM9 and p ...
... assay with a CT b-enhanced yellow fluorescent protein (eYFP) fusion protein as the donor and the RNA binding dye Sytox Orange (Molecular Probes) as the acceptor. The gene for eYFP was amplified with primers eYFP5 and eYFP3, digested with XhoI and PacI, and cloned into equivalently digested pGDM9 and p ...
D melanogaster - GEP Community Server
... sequence, as there are few markers to help order subclones; hence centromeric regions of the chromosomes are usually left unsequenced. 2. Other repetitious DNA, derived from transposable elements, also causes difficulties; because one finds nearly identical sequences located in different regions of ...
... sequence, as there are few markers to help order subclones; hence centromeric regions of the chromosomes are usually left unsequenced. 2. Other repetitious DNA, derived from transposable elements, also causes difficulties; because one finds nearly identical sequences located in different regions of ...
changes in the expression of three cold
... proteins which are associated with tolerance to low temperature but are not cold-inducible during plant acclimation (Takahashi et al. 2006). The cultivars ‘Elsanta’ and ‘Selvik’ were also different in terms of the activity of three candidate cold-regulated genes. The CBF, belonging to the group of t ...
... proteins which are associated with tolerance to low temperature but are not cold-inducible during plant acclimation (Takahashi et al. 2006). The cultivars ‘Elsanta’ and ‘Selvik’ were also different in terms of the activity of three candidate cold-regulated genes. The CBF, belonging to the group of t ...
NON-CANONICAL TRANSCRIPTION INITIATION: THE EXPANDING
... genes (Turnbough and Switzer, 2008). Regulation of transcription initiation by the concentration of the iNTP was described also for eukaryotes (Kuehner and Brow, 2008). Non-canonical substrates of RNAP (i): NanoRNAs Besides the four NTPs, non-canonical substrates called nanoRNAs (2-4 nt long oligori ...
... genes (Turnbough and Switzer, 2008). Regulation of transcription initiation by the concentration of the iNTP was described also for eukaryotes (Kuehner and Brow, 2008). Non-canonical substrates of RNAP (i): NanoRNAs Besides the four NTPs, non-canonical substrates called nanoRNAs (2-4 nt long oligori ...
Chapter 17 (Oct 23, 27, 28)
... (a) An mRNA molecule is generally translated simultaneously by several ribosomes in clusters called polyribosomes. ...
... (a) An mRNA molecule is generally translated simultaneously by several ribosomes in clusters called polyribosomes. ...
Nature Biotechnology, 21(4) - Weizmann Institute of Science
... several years in a variety of eukaryotic organisms2–5. Antisense transcripts often code for proteins involved in diverse biological functions. Noncoding antisense transcripts have also been identified. Their role appears to be mainly regulatory6 and their transcription is often associated with genom ...
... several years in a variety of eukaryotic organisms2–5. Antisense transcripts often code for proteins involved in diverse biological functions. Noncoding antisense transcripts have also been identified. Their role appears to be mainly regulatory6 and their transcription is often associated with genom ...
PART I
... of RNAs containing the appropriate 3' dinucleotide adjacent to the poly A tail.The product is then PCR amplified in the presence of 33P-dATP and a known primer. Of these first-strand cDNAs, only a fraction serve as appropriate templates for separate PCR reactions containing a known arbitrary primer. ...
... of RNAs containing the appropriate 3' dinucleotide adjacent to the poly A tail.The product is then PCR amplified in the presence of 33P-dATP and a known primer. Of these first-strand cDNAs, only a fraction serve as appropriate templates for separate PCR reactions containing a known arbitrary primer. ...
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.