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Has anyone ever worked with tagetitoxin, a selective transcription inhibitor of chloroplast with arabidopsis? I would like to know who sells tagetitoxin, and at which concentrations it is recommendable to work with on Arabidopsis. I would appriciate very much any info on this subject. Diana ,http://bgumail.bgu.ac.il/agent/[email protected], leicaj at bgumail.bgu.ac.il ...
The wheat bZip transcription factor TaABF1 mediates both abscisic acid (ABA)-induced and ABA-suppressed gene expression. As levels of TaABF1 protein do not change in response to ABA, and TaABF1 is in a phosphorylated state in vivo, we investigated whether TaABF1 could be regulated at the post-translational level. In bombarded aleurone cells, a TaABF1 protein carrying phosphomimetic mutations (serine to aspartate) at four sites (S36D, S37D, S113D, S115D) was three to five times more potent than wild-type TaABF1 in activating HVA1, an ABA-responsive gene. The phosphomimetic mutations also increased the ability of TaABF1 to downregulate the ABA-suppressed gene Amy32b. These findings strongly suggest that phosphorylation at these sites increases the transcriptional regulatory activity of TaABF1. In contrast to the activation observed by the quadruple serine to aspartate mutation, a single S113D mutation completely eliminated the ability of TaABF1 to upregulate HVA1 or downregulate Amy32b. Thus ...
Transcription begins with the binding of RNA polymerase, together with one or more general transcription factor, to a specific DNA sequence referred to as a "promoter" to form an RNA polymerase-promoter "closed complex". In the "closed complex" the promoter DNA is still fully double-stranded.[5]. RNA polymerase, assisted by one or more general transcription factors, then unwinds approximately 14 base pairs of DNA to form an RNA polymerase-promoter "open complex". In the "open complex" the promoter DNA is partly unwound and single-stranded. The exposed, single-stranded DNA is referred to as the "transcription bubble."[5]. RNA polymerase, assisted by one or more general transcription factors, then selects a transcription start site in the transcription bubble, binds to an initiating NTP and an extending NTP (or a short RNA primer and an extending NTP) complementary to the transcription start site sequence, and catalyzes bond formation to yield an initial RNA product.[5]. In bacteria, RNA ...
Transcription begins with the binding of RNA polymerase, together with one or more general transcription factor, to a specific DNA sequence referred to as a "promoter" to form an RNA polymerase-promoter "closed complex". In the "closed complex" the promoter DNA is still fully double-stranded.[5]. RNA polymerase, assisted by one or more general transcription factors, then unwinds approximately 14 base pairs of DNA to form an RNA polymerase-promoter "open complex". In the "open complex" the promoter DNA is partly unwound and single-stranded. The exposed, single-stranded DNA is referred to as the "transcription bubble."[5]. RNA polymerase, assisted by one or more general transcription factors, then selects a transcription start site in the transcription bubble, binds to an initiating NTP and an extending NTP (or a short RNA primer and an extending NTP) complementary to the transcription start site sequence, and catalyzes bond formation to yield an initial RNA product.[5]. In bacteria, RNA ...
Embryonic differentiation depends upon tissue-specific gene expression programs, created by temporally and spatially regulated transcription. Production of specific mRNAs can be stimulated or repressed via regulation of transcription initiation. Transcript production can also be controlled through a rate-limiting step of transcription elongation (Lis, 1998). For example, heat shock response genes, such as hsp70, are constitutively occupied by a RNA polymerase II (Pol II) complex that is paused proximal to the promoter after transcription initiation (Rougvie and Lis, 1988; Rasmussen and Lis, 1993). Transcription elongation is inhibited until heat shock stimulation occurs, at which time the paused Pol II becomes hyperphosphorylated and transcript synthesis proceeds. Several factors have been implicated in the stimulation or repression of transcription elongation (Conaway et al., 2000; Winston, 2001; Yamaguchi et al., 2001; Zorio and Bentley, 2001), but their precise regulatory roles during ...
In cells productively infected with adenovirus type 5, transcription is not terminated between the E1a gene and the adjacent downstream E1b gene. Insertion of the mouse beta(maj)-globin transcription termination sequence (GGT) into the E1a coding region dramatically reduces early, but not late, E1b expression (E. Falck-Pedersen, J. Logan, T. Shenk, and J. E. Darnell, Jr., Cell 40:897-905, 1985). In the study described herein, we showed that base substitution mutations in the globin DNA that specifically relieved transcription termination also restored early E1b promoter activity in cis, establishing that maximal early E1b expression requires readthrough transcription originating from the adjacent upstream gene. To identify potential targets of readthrough activation, a series of recombinant viruses with double mutations was constructed. Each double-mutant virus strain had the transcription termination sequences in the first exon of E1a and a deletion within the transcription control region of ...
Focused transcription typically initiates within the Inr, and the A nucleotide in the Inr consensus is usually designed as the "+ 1" position, whether or not transcription actually initiates at that particular nucleotide. This convention is useful because other core promoter motifs, such as the MTE and DPE, function with the Inr in a manner that exhibits a strict spacing dependence with the Inr consensus sequence (and hence, the A + 1 nucleotide) rather than the actual transcription start site (Burke and Kadonaga, 1997, Kutach and Kadonaga, 2000 and Lim et al., 2004)."[2]. "NC2 (negative cofactor 2; also known as Dr1-Drap1) [...] was identified as repressor of TATA-dependent transcription [...]."[2]. "Several core promoter elements have been previously identified in eukaryotes, but those cannot account for transcription from most RNA polymerase II-transcribed genes."[1]. ...
The major antiinflammatory effects of glucocorticoids appear to be due largely to interaction between the activated glucocorticoid receptor and transcription factors, notably nuclear factor-kappaB (NF-kappaB) and activator protein-1, that mediate the expression of inflammatory genes. NF-kappaB switc …
Faithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y, a ubiquitously expressed transcription factor, controls the fidelity of transcription initiation at gene promoters in mouse embryonic stem cells. We report that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription pre-initiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene
A retroviral vector-rescue system in which co-packaging of the two co-expressed vectors is required for transduction of one of the vectors has been established previously. By using this rescue system, two distinct packaging-cell populations have been generated. One cell population expressed retroviral RNA from co-localized transcription sites, resulting in local and overlapping accumulation of both RNA transcripts. In the other cell population, the two transcription cassettes were introduced separately, leading to distinct transcription sites of the two RNAs and no significant co-localization of the RNAs. Titre measurements from the two distinct cell populations showed large differences in rescue titre, which is an indirect measure of co-packaging efficiency. Thus, the cell populations with overlapping RNA accumulation gave rise to 15-80-fold-higher rescue titres than cell populations with non-overlapping RNA accumulation. These data show that the spatial position of proviral transcription sites affects
Transcription elongation elements in the NusG family members are ubiquitous from bacterias to human beings and play diverse assignments in the legislation of gene appearance. than facilitates transcript elongation by its cognate RNAP. Alternatively much like the regulators Tth NusG evidently binds close to the upstream end from the transcription bubble competes with σA Cdh13 and mementos forwards translocation by RNAP. Our data claim that the system of NusG recruitment to RNAP is normally universally conserved despite the fact that the regulatory final results among its homologs can happen distinct. Launch The transcription elongation aspect NusG continues to be identified in based on its requirement of phage λ N-dependent gene appearance and thus called N utilization product G (1). Following studies showed that (Eco) NusG impacts Rho-dependent termination (2) transcriptional arrest by HK022 Nun proteins (3) RNA string elongation (4) and translation (5) and can be an essential component from ...
Detects differential transcription between pairs of samples or between groups of replicates. FDM is based on a statistical method for performing a permutation test on ACT-Graphs that does not depend on annotations or an underlying transcripts inference. The application first align RNA-seq reads to a reference genome and determines the regions of differential RNA transcript expression between pairs of splice graphs for finally assess the significance of differential transcription.
Dehydroepiandrosterone (DHEA) is a peroxisome proliferating agent when administered in pharmacological dosages, but it has not been shown to function through the peroxisome proliferator-activated receptor in cell-based assays. Because members of the thyroid hormone/vitamins A and D nuclear receptor subfamily, including PPAR, are known to modulate each others function in gene expression by heterodimerization, we sought to establish whether DHEA and thyroid hormone interact to regulate several of the hepatic and renal enzymes associated with peroxisome proliferation, i.e., peroxisomal beta-oxidation and microsomal NADPH:cytochrome P450 oxidoreductase and the cytochromes P450 4A. In rats administered exogenous T3 to attain a hyperthyroid state, induction of the three isozymes of CYP4A (4A1, 4A2, and 4A3) by DHEA was suppressed , 60-80% at the mRNA level, with induction of CYP4A2 mRNA being completely inhibited. Nuclear run-on transcription assays indicated that this inhibitory effect was regulated ...
It recently has been established that adenine-containing cofactors, including nicotinamide adenine dinucleotide (NAD+), reduced nicotinamide adenine dinucleotide (NADH), and 3-desphospho-coenzyme A (dpCoA), can serve as non-canonical initiating nucleotides (NCINs) for transcription initiation by bacterial and eukaryotic cellular RNA polymerases (RNAPs) and that the efficiency of the reaction is determined by promoter sequence (Bird et al., 2016). Here we describe a protocol to quantify the relative efficiencies of transcription initiation using an NCIN vs. transcription initiation using a nucleoside triphosphate (NTP) for a given promoter sequence.
E7H and E9G lines, which exhibited ethylene insensitivity only when the inducer was utilized, were picked to avoid the unwanted effects of ethylene
Transcriptome Sequencing analyses provide information to detect novel transcribed regions, splice events and additional promoters and exons. Transcript annotation studies also help to analyze the impact of transcriptional complexity on current models of key signaling pathways. Next Generation Sequencing can also provide information on aberrant transcription events, like pseudogenes, fusion genes, and genome rearrangements. However, the greatest advantage is to decipher quantitative gene expression profile.. ...
Transcription has the capacity to mechanically modify DNA topology, DNA structure and nucleosome arrangement. Resulting from ongoing transcription, these modifications in turn may provide instant feedback to the transcription machinery. To substantiate the connection between transcription and DNA dy …
Renaud Dumas. Significance: In most biological processes, genes have to be activated and/or repressed. In plants, the TOPLESS protein is essential for gene repression through its action as a corepressor bridging transcription factor with chromatin remodeling complexes. Here we combine biochemical and structural studies to describe the structure of TOPLESS, how it tetramerizes, and how it interacts with its protein partners. We show that both the tetramerization interface and the binding site for protein partners have been conserved since algae, highlighting the ancestrality of TOPLESS function. Comparison of this plant protein with one of its animal counterparts also shows how corepressors can use a common domain differently to achieve similar properties, illustrating the tinkering of evolution in transcriptional repression.. Abstract: Transcriptional repression involves a class of proteins called corepressors that link transcription factors to chromatin remodeling complexes. In plants such as ...
Precise patterns of gene expression during development are regulated predominantly at the level of transcription. In transcription-driven gene regulation, transcriptional activators bind to enhancer elements and orchestrate the colocalization of proteins at the gene promoter to activate transcription. The transcriptional status of a particular gene in a cell or developing tissue is therefore determined primarily by the precise combination of transcription factors that can bind to the enhancer sequence in that specific cell.. There are, however, well-known exceptions to transcription-driven gene regulation. Most notably, in newly fertilized embryos of chicken, fish, frog, flies and worms, early cell divisions and fate specification are primarily controlled by proteins and RNAs deposited into the egg by the mother (Newport and Kirschner, 1982; Edgar and Schubiger, 1986; Powell-Coffman et al., 1996). Even in mammals, maternally contributed factors play an essential role early in preimplantation ...
One of the simplest ways to model GFP transcription is to use an ODE:. $\frac{d [GFP_{mRNA}]}{dt} = a - b{\cdot}[GFP_{mRNA}]$. where $a$ is GFP transcription rate and $b$ is GFP mRNA degradation rate (both constants). Normally, we assume $a,,b$.. Suppose we wish to account for plasmid concentration with the value of transcription rate $a$ - e.g. with higher plasmid concentration, the ratio $a/b$ should increase as the mRNA saturation levels are expected to be reached faster. In other words, suppose we transfect 2 individual constructs depicted above, 10 ng of one and 30 ng of the other - how should this difference in concentration impact the rate constants values, assuming the constructs are otherwise identical?. Assuming this, approximately how does gene transcription rate $a$ change as a function of the amount of transfected plasmid containing the above construct? Ideally, Id be interested in knowing this for HEK 293 cells, but any other decent estimation is acceptable. One simple option is ...
The recently determined three-dimensional (3D) structure of a bacterial class II transcription complex helps to reveal how it binds to specific DNA sequences, thus driving transcription of downstream genes. This X-ray-based structural analysis provides the first atomic structure for such an intact class II transcription activation complex, according to Richard H. Ebright at Rutgers University in Piscataway, N.J. He and his colleagues reported their findings on 10 June 2016 in Science (doi:10.1126/science.aaf4417).
Once transcription is initiated at the transcription start site (TSS), Pol II pauses at the site just downstream of TSS and requires elongation factors to allow it to proceed. Switching of the RNA Pol II complex from the initiation to the elongation complexes is important for functional transcription, which is mediated by P-TEFb kinase phosphorylating Ser2 position in CTD (Fig. 3A) (Jonkers and Lis, 2015). As assumed, most of the mRNA processing complexes are assembled during the elongation step of transcription (Perales and Bentley, 2009) So chromatin-associated and pol II-interacting mRNA processing proteins are likely to function in regulating transcription elongation (Allemand et al., 2008).. A direct role for SR proteins in transcriptional regulation has been shown for SRSF2. In contrast to shuttling SR proteins (such as SRSF1, SRSF3, and SRSF7), SRSF2 is a non-shuttling protein located in the nucleus. Interestingly, SRSF2 associates with DNA only, but not with cytoplasmic mRNA, suggesting ...
It has been shown that the overall transcription of ribosomal RNA genes can be stimulated by many signals (41); however, increased transcription is not due to an increased number of actively transcribed rDNA units but instead is due to changes in the rate of transcription, especially of elongation (42, 43). B-WICH is an ATP-dependent chromatin remodeling complex containing SNF2h, a human ISWI ATPase, and it was shown to associate with Pol I facilitating its transcription (30). The SIRT7 interaction with components of the B-WICH complex supports a hypothesis where SIRT7 regulates the rate of elongation of Pol I through the ATP-dependent remodeling activities of B-WICH.. SIRT7 knockdown is known to inhibit rDNA transcription (9, 10), and our results show for the first time that SIRT7 knockdown also leads to a reduction in the large subunit of Pol I at the protein level but not at the mRNA level. A question to be addressed in future studies is whether this regulation of Pol I protein level occurs ...
Cyclin-dependent kinase 7 (CDK7) is an important constituent of the cellular transcriptional machinery, where it phosphorylates the C-terminal domain (CTD) of RNAP polymerase II (RNAPII). Because many tumor types are critically dependent on transcription for maintenance of their oncogenic state, pharmacological modulation of CDK7 kinase activity is considered as an approach to treat cancer. Multiple series of CDK7 inhibitors were identified by iterative medicinal chemistry efforts and SAR based approach. Early compounds were optimized towards attaining good physicochemical properties, high potency, good selectivity and desirable pharmacokinetic profile to achieve anti-tumor activity. We have identified compounds from two distinct chemical series that are highly potent in inhibiting CDK7 in biochemical assays. These inhibitors demonstrate time-dependent inhibition of CDK7 indicating covalent nature of binding. The compounds showed potent anti-proliferative activity in cell lines derived from ...
Transcription. Molecular model of DNA (deoxyribonucleic acid, upper right) transcription. During transcription, a complementary messenger ribonucleic acid (mRNA) strand (bottom left) is synthesised. The enzyme RNA polymerase (not shown) recognises a start sign on the DNA strand and moves along the strand building the mRNA. mRNA is the intermediary between DNA and its protein product. - Stock Image C015/4455
Transcription and translation are fundamental molecular mechanisms of gene activity regulation with profound implications for human health. The ligand-dependent transcriptional regulation by nuclear receptors bound to DNA response elements involves the transient assembly of large co-regulator complexes. These trigger chromatin remodeling and facilitate the assembly of the general transcription machinery on the promoter of the target gene. Gene expression is also regulated at the level of protein synthesis, for example, by protein factors that bind to the ribosome during the translation initiation, elongation and termination phase. The initiation phase is strongly regulated by factors and also by the mRNA itself and well-characterized reaction intermediates of the initiating ribosomal nano-machinery are potential targets for antibiotics. Both transcription and translation complexes represent large, transient macromolecular assemblies that we investigate by using an integrative structural biology ...
In vitro analysis of transcription and the factors that play a role in transcription require preparation of an extract that faithfully reproduces in vivo transcription
Mice lacking the lymphocyte-specific transcription factor Bob1 (also called OBF-1 or OCA-B) fail to generate germinal centers and a robust Ig response. We show that peripheral B cells in Bob1−/− mice bear characteristics of chronically activated or anergic-like B cells and identify the immunosuppressive microRNA-146a, together with other microRNAs, as novel transcriptional targets of Bob1. The inability to restrict B cell signaling could contribute to the immunodeficient phenotype of these mice and is consistent with an important role for Bob1 in suppressing B cell activation in vivo. ...
Solving structures of complexes is inherently more difficult than solving those for individual proteins. As a result, significantly fewer structures of protein complexes than individual proteins have been determined experimentally [1]. In recent years, homology modeling [2, 3] proved to be successful when the target protein has a similar sequence to proteins with known structures. However, the lack of a sufficiently large database of reference complexes makes the method unsuitable for structural modeling of protein complexes. A conceptually simple and straightforwardly applicable approach for modeling structures of bio-molecular complexes is highly desirable. When proposing new protein complexes, the models developed should be checked against the following attributes: stereo-chemically sound, having sufficient interfacial Solvent Excluded Surface Areas [4] (SESAs) to provide adequate binding strengths, physically meaningful for transcription regulation and consistency with the known experimental ...
Although recent studies have revealed that the majority of human genes are subjected to regulation of alternative promoters (APs), the biological relevance of this phenomenon remains unclear. In order to understand biological significance of the presence of diverg .. [more]ent transcription initiation events in the respective cell types, it is indispensable to obtain bird-view of the transcriptome figures at every step of the gene expression; namely, i) how the genomic structure change to transcriptionally active form, ii) where the transcription initiation complex is recruited, iii) to what extent the transcription is activated, iv) what transcripts formed and sorted to what subcellular fractions. We have recently started multi-faceted use of the Illumina GA to answer these questions. Integrative analysis produced for respective aspects of the gene expression regulations revealed the comprehensive figures of the complex human gene transcriptome for the first time. [less] ...
Control transcription activation of target genes. Previously available from ARIAD as the ARGENT Regulated Transcription Plasmid Kit & AP21967.
Control transcription activation of target genes. Previously available from ARIAD as the ARGENT Regulated Transcription Plasmid Kit & AP21967.
First, 5-prime specificity. In bacteria, translation is co-transcriptional, which means that when mRNA is transcribed, it is translated immediately, before finishing off the transcription. There is even a physical link between the polymease and the ribosome via NusG. And when mRNA is translated, it is cleaved by RelE. Translation and transcription are starting from the 5-prime... and so is the RelE cleavage, one would guess. Moreover, if you cleave the mRNA once, translation downstream of the cleavage site stops - and the initial cleavage is likely to happen co-transcriptionally at the 5-prime and render cleavage at the 3-prime impossible. Is there any need to involve "a conformation or component of the translation complex that is unique to initiation or early elongation"? I think not ...
The image shows the cellular organization of chromosomes in the nucleus; you can observe that in the interchromatin space there is a transcription factory (in the picture: RNA transcripts) ,while around this region there are more than one active locus( of different chromosomes).Then,since the chromosomes are so close ,could happen that a traslocation appear between these active loci ...
MIT initially used a unit of measurement called TIPS (Transcription Initiations per Second) for measure rates of transcription at the ends of its parts; however, this was insufficient because there are places on the DNA (e.g. terminators) where transcription initiations are not taking place. PoPS is a relatively new unit developed during construction of standardized "ends" of DNA pieces that measures the inputs and outputs of BioBrick™ parts. PoPS measure the rate at which RNA polymerase moves past a point in the DNA, similar to measuring the current flow across a specific point in a wire. Devices that have an input and output in PoPS are composable - that is, they can be arbitrarily joined together to create complex devices and systems. Creation of devices allows us to characterize devices and eventually more complex systems, thus PoPS is important as a common signal carrier. PoPS differs from transcription rate in that it can also be measured at terminator sites; upstream, they are ...
EMBL scientists show that close interaction of influenza and host cell transcription machineries is essential for the survival of the virus
A Possible Mechanism of DNA to DNA Transcription in Eukaryotic Cells: Endonuclease Dependent Transcript Cutout. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
BioAssay record AID 660672 submitted by ChEMBL: Inhibition of viral transcription in X4 tropic HIV1 pNL4.3-Luc transfected human MT2 cells at 20 uM dosed post transfection and measured 24 hrs post compound dose by luciferase reporter gene assay.
Ch/Bi 231. Advanced Topics in Biochemistry. 6 units (2-0-4); third term. Transcriptional regulation in eukaryotes. Topics: the subunit structure of eukaryotic RNA polymerases and their role in transcriptional reactions; the composition of eukaryotic promoters, including regulatory units; general and specific transcription factors; developmental regulatory circuits and factors; structural motifs involved in DNA binding and transcriptional initiation and control. Not offered 2016-17. ...
Researchers at the University of Tokyo and their collaborators have revealed genetic transcription systems from about 3 billion years ago
Many genetic variants associated with human disease have been found to be associated with alterations in mRNA expression. Although it is commonly a...
RT-PCR for fimA transcription. RT-PCR assays were used to monitor fimA and 16S rRNA transcription in the parental strain LB5010, ubiB mutant, and ubiB (pUbiB) s
MRNA is synthesized in transcription. During transcription, the DNA molecule unzips, and only one side serves as the template for the synthesis of the mRNA strand. Once synthesized, the mRNA molecule...
Unfortunately, much of the discussion surrounding the publication of ENCODE failed to focus on the usefulness of the catalogue and the techniques that built it. Instead, much of the debate centered on the failure to understand that transcription does not necessarily imply meaningful biological function. Cells are messy biological entities, with lots of gunk and goo floating around, so mistakes happen all the time. Many DNA sequences get translated into RNA, only to have the cell degrade that RNA. Much, perhaps most, of the DNA in our genomes-despite being occasionally transcribed, and thus recorded in ENCODE-is still functionless "junk DNA." That is actually not surprising; it is in fact expected from evolutionary theory. Thanks to ENCODE, though, we should eventually learn which sequences are the junk and which are the gems of cell activity. ...
Are All DNA Binding and Transcription Regulation by an Activator Physiologically Relevant?: Understanding how a regulatory protein occupies its sites in vivo is
Browse Transcription products on Labviva. Find relevant scientific protocols, papers and to help find the right product for your application.
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Signal amplification is an effective way to achieve sensitive analysis of biomarkers, exhibiting great promise in biomedical research and clinical diagnosis. Inspired by the transcription process, we here present a versatile strategy that enables to effectively amplify proteolysis into nucleic acid signal ou
(Phys.org)-An international team of researchers has found that gene transcription in an organism that has died continues for several days. In their paper published in the journal Royal Society Open Biology, the team describes ...
Learning Objectives Explain how RNA is synthesized using DNA as a template Distinguish between transcription in prokaryotes and eukaryotes Dur
Well first, the DNA strands unzip to allow the mRNA to copy a single gene. Then an enzyme builds the mRNA strand by bringing in nitrogen bases and matching
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Modulation of Prrxl1 transcriptional activity by phosphorylation. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Just read this Abstract from PLoS: Mammalian genes are highly heterogeneous with respect to their nucleotide composition, but the functional consequences of this heterogeneity are not clear. In the previous studies, weak positive or negative correlations have been found between the silent-site guanine and cytosine (GC) content and expression of mammalian genes. However, previous studies…. ...
Control system structure of a pseudo-integral or an ideal integral control problem. hTrsc(·) denotes the transcription process. gTrnl(·) denotes the rate of p
Braidwood Nuclear Generating Station Units 1 and 2 automatically shut down early this morning. Plant technical experts are working to determine the cause.
I ll try to make this short. After a PCT went wrong I ve been shut down for two years. These have been the worst years of my life and I tried
READ THIS Farewell Letter from a Blogger who was forced to shut down his site... Well as you know all good things must come to an end. Tod ...
I have had a rather back to front start to my day today, I dont know why but I found myself doing things in all the wrong order but for some reason, it felt right and did it really matter? I know I have said so many times that routine is so important, but I…
As I was installing new zone, My machine died. It had been running about 20 minutes and the thing just shut down. I think it is electrical as there is...
387448814 - EP 0851912 A4 2000-01-05 - NOVEL FACTORS WHICH MODIFY GENE TRANSCRIPTION AND METHODS OF USE THEREFOR - [origin: WO9708301A1] Eukaryotic RNA polymerase II holoenzymes that contain RNA polymerase II and one or more regulatory proteins are described. These holoenzymes selectively initiate transcription in vitro when supplemented with general transcription factors. The regulatory proteins act positively and negatively to regulate transcription initiation, at least in part, via functional interactions with RNA polymerase II.[origin: WO9708301A1] Eukaryotic RNA polymerase II holoenzymes that contain RNA polymerase II and one or more regulatory proteins are described. These holoenzymes selectively initiate transcription in vitro when supplemented with general transcription factors. The regulatory proteins act positively and negatively to regulate transcription initiation, at least in part, via functional interactions with RNA polymerase II.
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors.
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. May play a role as a target recruitment subunit in E3 ubiquitin-protein ligase complexes and thus in ubiquitination and subsequent proteasomal degradation of target proteins.
Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. May be part of a complex containing NF2/merlin that participates in cellular signaling to the actin cytoskeleton downstream of tyrosine kinase signaling pathways.
Yeast RNA polymerase II initiation factor b copurifies with three polypeptides of 85, 73, and 50 kilodaltons and with a protein kinase that phosphorylates the carboxyl-terminal repeat domain (CTD) of the largest polymerase subunit. The gene that encodes the 73-kilodalton polypeptide, designated TFB1, was cloned and found to be essential for cell growth. The deduced protein sequence exhibits no similarity to those of protein kinases. However, the sequence is similar to that of the 62-kilodalton subunit of the HeLa transcription factor BFT2, suggesting that this factor is the human counterpart of yeast factor b. Immunoprecipitation experiments using antibodies to the TFB1 gene product demonstrate that the transcriptional and CTD kinase activities of factor b are closely associated with an oligomer of the three polypeptides. Photoaffinity labeling with 3-O-(4-benzoyl)benzoyl-ATP (adenosine triphosphate) identified an ATP-binding site in the 85-kilodalton polypeptide, suggesting that the ...
Didier Picard, January 2015 Current list of HBD fusion proteins_ Protein X a HBD b regulated as c Refs. transcription factor in Arabidopsis transcription factor Arabidopsis transcription factor in tobacco coactivator transcription factor 1 2 3 transcription factor transcription factor, differentiation factor transcription factor putative transcription factor in arabidposis transcription factor oncoprotein transcription factor transcription factor oncoprotein oncoprotein oncoprotein transcription factor oncoprotein, transcription factor 6 7 transcription factor transcription factor in yeast, tissue culture cells and zebra fish transcriptional repressor transcription factor transcription factor in yeast, in tissue culture cells, transgenic mice, Xenopus, Drosophila and plants transcription factor, promoter of proliferation transcription factor transcription factor 19 20, 21, i Transcription factors APETALA3 ATF6α Athb-1 GR ER e GR Bob1/OBF1 ER e CCAT (from calcium ER e 4 5 channel cav1.2) C/EBP ...
In vitro studies using highly purified calf thymus RNA polymerase II and a fragment spanning the first intron of H3.3 as template DNA have demonstrated the existence of a strong transcription termination site consisting of thymidine stretches. In this study, nuclear run-on experiments have been performed to assess the extent to which transcription elongation is blocked in vivo using DNA probes corresponding to region 5 and 3 of the in vitro termination sites. These studies suggest that H3.3 expression is stimulated following the inhibition of DNA synthesis through the elimination of the transcription elongation block. Interestingly, both the in vivo and in vitro experiments have revealed that the transcriptional block/termination sites are positioned immediately downstream of a 73 bp region that has been over 90% conserved between the chicken and human H3.3 genes. The extreme conservation of this intronic region suggests a possible role in maintaining cis-acting function. Electrophoretic ...
We have used nuclear run-on, RT-PCR, and transient-transfection analyses to characterize transcription initiation and termination of LmjF chr3. Our data suggest that, like chr1 (19), specific Pol II transcription starts upstream of the most-5′ gene of the two long polycistronic clusters. We have also identified a region where Pol III transcription starts for a tRNA gene located at the convergence of these two gene clusters. Termination of Pol II transcription on both DNA strands, as well as Pol III transcription of the tRNA, seems to occur within this region. Thus, we have now characterized the transcriptional organization of two entire chromosomes and have identified sequences involved in both Pol II and Pol III transcription initiation and termination.. Identification and characterization of the Pol II promoters that drive the expression of protein-coding genes in trypanosomatids has proven to be an elusive goal, complicated by factors such as relatively low transcriptional activity and ...
TY - JOUR. T1 - Phosphorylation of the carboxy-terminal repeat domain in RNA polymerase II by cyclin-dependent kinases is sufficient to inhibit transcription. AU - Gebara, Maha M.. AU - Sayre, Michael H.. AU - Corden, Jeffry L.. PY - 1997/3/1. Y1 - 1997/3/1. N2 - Cdc2 kinase triggers the entry of mammalian cells into mitosis, the only cell phase in which transcription is globally repressed. We show here that Cdc2 kinase phosphorylates components of the RNA polymerase II transcription machinery including the RNA polymerase II carboxy-terminal repeat domain (CTD). To test specifically the effect of CTD phosphorylation by Cdc2 kinase, we used a yeast in vitro transcription extract that is dependent on exogenous RNA polymerase II that contains a CTD. Phosphorylation was carried out using immobilized Cdc2 so that the kinase could be removed from the phosphorylated polymerase. ATPγS and Cdc2 kinase were used to produce an RNA polymerase 110 that was not detectably dephosphorylated in the ...
The DNA sequence that a transcription factor binds to is called a transcription factor-binding site or response element.[55]. Transcription factors interact with their binding sites using a combination of electrostatic (of which hydrogen bonds are a special case) and Van der Waals forces. Due to the nature of these chemical interactions, most transcription factors bind DNA in a sequence specific manner. However, not all bases in the transcription factor-binding site may actually interact with the transcription factor. In addition, some of these interactions may be weaker than others. Thus, transcription factors do not bind just one sequence but are capable of binding a subset of closely related sequences, each with a different strength of interaction. For example, although the consensus binding site for the TATA-binding protein (TBP) is TATAAAA, the TBP transcription factor can also bind similar sequences such as TATATAT or TATATAA. Because transcription factors can bind a set of related ...
Transcription steps are marked by different modifications of the C-terminal domain of RNA polymerase II (RNAPII). Phosphorylation of Ser5 and Ser7 by cyclin-dependent kinase 7 (CDK7) as part of TFIIH marks initiation, whereas phosphorylation of Ser2 by CDK9 marks elongation. These processes are thought to take place in localized transcription foci in the nucleus, known as transcription factories, but it has been argued that the observed clusters/foci are mere fixation or labeling artifacts. We show that transcription factories exist in living cells as distinct foci by live-imaging fluorescently labeled CDK9, a kinase known to associate with active RNAPII. These foci were observed in different cell types derived from CDK9-mCherry knock-in mice. We show that these foci are very stable while highly dynamic in exchanging CDK9. Chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) data show that the genome-wide binding sites of CDK9 and initiating RNAPII overlap on transcribed genes.
Transition from the closed to the open promoter complex happens by separation of the DNA strands to form an unwound DNA region. Once the transcription bubble forms the template single strand DNA gets positioned in the active center of Pol II. RNA synthesis then can initiate from the transcription start site. The initially transcribing complex (ITC) is unstable and releases short RNAs during abortive initiation (not shown in the movie). When the RNA reaches a certain length, initiation factors are released, and a stable elongation complex (EC) is formed. Elongation complex contains a DNA-RNA hybrid of eight to nine base pairs. During transcription elongation, the EC repeatedly performs the nucleotide addition cycle (NAC) to attach a nucleotide to the growing messenger RNA (mRNA) chain by catalyzing DNA template-directed formation of an RNA phosphodiester bond. Errors do occur during RNA transcription and must be corrected to prevent synthesis of mutated, nonfunctional proteins that possibly ...
Author Summary The transcription of eukaryotic genes involves a highly ordered series of events, including the recruitment of RNA polymerase to promoters, the production of the RNA transcript, and termination. These events are coordinated with changes in chromatin structure that allow regulatory proteins and RNA polymerase to access the DNA template. The recruitment of RNA polymerase II to promoters is rate-limiting for the expression of most eukaryotic genes. However, RNA polymerase often pauses or stalls a short distance downstream of promoters, providing an additional step at which transcription can be regulated. In this study, we present evidence suggesting that a chromatin-remodeling factor, KIS-L, activates transcription by counteracting promoter-proximal pausing in Drosophila. KIS-L also counteracts histone H3 lysine 27 methylation-a covalent modification of chromatin involved in hereditable gene silencing. Our findings provide a plausible explanation for the developmental abnormalities
On specific signals, segments of DNA corresponding to one or more cistrons become de-repressed and ready to transcribe. Each such DNA transcription segment has a promoter region, initiation site, coding region and a terminator region. Transcription begins at the initiation site and ends at the terminator region. A promoter region has RNA polymerase recognition site and RNA polymerase binding site.. Chain opening occurs in the region occupied by TATAATG nucleotides (TATA box) in most procaryotes. Enzymes required for chain separation are unwindases, gyrases and single stranded binding proteins. Terminator region has either poly A base sequence or palindromic sequence (iden-tical base sequence running in opposite directions in the two DNA chains).. RNA polymerase (common in procaryotes and specific in eucaryotes) binds itself to the promoter region. The two strands of DNA uncoil progressively from the site of polymerase binding. One of the two strands of DNA (3-» 5′) functions as a template ...
Transcription factors directly control when, where, and the extent to which genes are expressed. Signal transduction pathways are responsible for either activating or inhibiting many of them. Transcription factors are also regulated by cofactors, forming complexes that can activate or inhibit transcriptional activity. Many transcription factors, such as nuclear receptors, reside in the cytoplasm and enter the nucleus upon activation (e.g., ligand binding). Posttranslational modifications and coregulating proteins provide additional layers of regulation. Transcription factors are involved in a wide variety of processes, such as development, stress responses, and immunity. Activation or inhibition of transcription factors is often dysregulated during oncogenesis. Transcription factors can also be dysregulated during developmental processes, promoting or inhibiting cellular differentiation. Analyzing the expression, regulation, activity, and sequence of transcription factor genes can help determine ...
Antibodies for proteins involved in negative regulation of transcription elongation from RNA polymerase I promoter pathways, according to their Panther/Gene Ontology Classification
Transcriptional repression is a general mechanism for regulating transcriptional initiation in organisms ranging from yeast to humans. Accurate initiation of transcription from eukaryotic protein-encoding genes requires the assembly of a large multiprotein complex consisting of RNA polymerase II and general transcription factors such as TFIIA, TFIIB, and TFIID. DR1 is a repressor that interacts with the TATA-binding protein (TBP) of TFIID and prevents the formation of an active transcription complex by precluding the entry of TFIIA and/or TFIIB into the preinitiation complex. The protein encoded by this gene is a corepressor of transcription that interacts with DR1 to enhance DR1-mediated repression. The interaction between this corepressor and DR1 is required for corepressor function and appears to stabilize the TBP-DR1-DNA complex. [provided by RefSeq, Jul 2008 ...
The Arabidopsis genome contains a large number of gene pairs that encode sense and antisense transcripts with overlapping 3′ regions, indicative for a potential role of natural antisense transcription in regulating sense gene expression or transcript processing. When we mapped poly(A) transcripts of three plant gene pairs with long overlapping antisense transcripts, we identified an unusual transcript composition for two of the three gene pairs. Both genes pairs encoded a class of long sense transcripts and a class of short sense transcripts that terminate within the same polyadenylation region as the antisense transcripts encoded by the opposite strand. We find that the presence of the short sense transcript was not dependent on the expression of an antisense transcript. This argues against the assumption that the common termination region for sense and antisense poly(A) transcripts is the result of antisense-specific regulation. We speculate that for some genes evolution may have especially ...
Additional file 1: Figure S1. of Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers
Transcription is a crucial step in gene expression, orchestrated by RNA polymerase (RNAP), a molecular machine that transfers genetic information from DNA to RNA . Bacterial transcription provides a tractable model system which provides mechanistic insights on its more complex eukaryotic counterpart. Bacterial transcription is initiated after an RNAP holoenzyme (core RNAP bound to a σ initiation factor) melts the double-stranded DNA (dsDNA) around the transcription start to form a transcription bubble in the RNAP-promoter DNA open complex (RPo). Subsequently, RNAP performs cycles of RNA synthesis and dissociation (abortive initiation) and at a certain point, escapes from the promoter and enters elongation. RNAP has been studied extensively using genetic, biochemical and structural methods. Recent X-ray structures 3,4 vastly improved our understanding of transcription, leading to mechanistic proposals, and experiments that tested these proposals and further examined RNAP function. However, crystal
Cells are subjected to dramatic changes of gene expression upon environmental changes. Stresscauses a general down-regulation of gene expression together with the induction of a set of stress-responsivegenes. The p38-related stress-activated protein kinase Hog1 is an important regulator of transcription uponosmostress in yeast. Genome-wide localization studies of RNA polymerase II (RNA Pol II) and Hog1 showed that stress induced major changes in RNA Pol II localization, with a shift toward stress-responsive genes relative to housekeeping genes. RNA Pol II relocalization required Hog1, which was also localized to stress-responsive loci. In addition to RNA Pol II-bound genes, Hog1 also localized to RNA polymerase III-bound genes, pointing to a wider role for Hog1 in transcriptional control than initially expected. Interestingly, an increasing association of Hog1 with stressresponsive genes was strongly correlated with chromatin remodeling and increased gene expression. Remarkably, MNase-Seq ...
TY - JOUR. T1 - In vivo transcription analysis utilizing chromatin immunoprecipation reveals a role for trypanosome transcription factor PBP-1 in RNA polymerase III-dependent transcription. AU - Gilinger, Gwen. AU - Luo, Hua. AU - Bellofatto, Vivian. PY - 2004/1/1. Y1 - 2004/1/1. UR - http://www.scopus.com/inward/record.url?scp=1642431643&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=1642431643&partnerID=8YFLogxK. U2 - 10.1016/j.molbiopara.2003.10.020. DO - 10.1016/j.molbiopara.2003.10.020. M3 - Article. C2 - 14747156. AN - SCOPUS:1642431643. VL - 134. SP - 169. EP - 173. JO - Molecular and Biochemical Parasitology. JF - Molecular and Biochemical Parasitology. SN - 0166-6851. IS - 1. ER - ...
Injury-elicited differential transcriptional regulation of phospholipid growth factor receptors in the cornea.: The phospholipid growth factors (PLGFs), includi
There are three major forms of life on Earth, bacteria, archaea and eukaryotes (Figure 3). RNA polymerase in bacteria is less complex than RNA polymerase in eukaryotes. Some of the increased complexity of RNA polymerase in eukaryotes reflects differences between DNA in eukaryotes and DNA in bacteria. Two important differences are that eukaryotes organize their DNA into nucleosomes and have more complex mechanisms for regulation of gene transcription.[5] Nucleosomes are a complex of DNA and histone proteins (Figure 4). In order for transcription to occur, DNA must be released from being tightly coiled in nucleosomes. Bacteria do not have nucleosomes. Another complication of eukaryotic gene expression regulation is that gene sequences controlling transcription are often distant from the DNA site where transcription starts. The RNA polymerase of bacteria is relatively small with a core of five protein subunits and one additional protein that recognizes the start points for transcription[6]. In ...
A promoter is a region of DNA that facilitates the transcription of a particular gene. "Promoters can be about 100-1000 [nucleotides] long.[1]. A promoter is on the template strand for the gene and near the gene in numbers of nucleotides (nts) along the DNA template strand. Usually, the promoter lies within the string of nucleotides between genes. Some promoters are called constitutive as they are active in all circumstances in the cell, while others are regulated becoming active in response to specific stimuli. These specific stimuli for a gene find a receptive portion within that genes promoter. In the case of genes that are used to produce proteins, the RNA polymerase II holoenzyme that actually performs the transcription from the template strand needs to find chemical cues for attachment to the DNA and where to begin transcription. Preceding this are chemical cues for which DNA strand is the template strand and in what direction transcription is to be performed. A promoter contains cues for ...
Recent work suggests a role for multiple host factors in facilitating HIV-1 reverse transcription. Previously, we identified a cellular activity which increases the efficiency of HIV-1 reverse transcription in vitro. Here, we describe aspects of the activity which shed light on its function. The cellular factor did not affect synthesis of strong-stop DNA but did improve downstream DNA synthesis. The stimulatory activity was isolated by gel filtration in a single fraction of the exclusion volume. Velocity-gradient purified HIV-1, which was free of detectable RNase activity, showed poor reverse transcription efficiency but was strongly stimulated by partially purified cell proteins. Hence, the cell factor(s) did not inactivate an RNase activity that might degrade the viral genomic RNA and block completion of reverse transcription. Instead, the cell factor(s) enhanced first strand transfer and synthesis of late reverse transcription suggesting it stabilized the reverse transcription complex. The ...
How does RNA polymerase II coordinate the synthesis of messenger RNA, resulting in proper cellular regulation and organismic development? The sessions will cover new findings in transcriptional initiation, elongation and termination and the role of RNA polymerase II, its C-terminal domain and the associated factors in this process. New findings on the roles of chromatin, their interacting proteins and post-translational modifications, their numerous transcriptional properties and their role in development also will be addressed. The plenary lecture will be presented by Ramin Shiekhattar, who will describe his work on the functions of long noncoding RNAs in transcriptional regulation, development and disease pathogenesis. This years meeting represents the 10th anniversary of this important and influential conference. ...
During RNA Polymerase II transcription, the C-terminal domain (CTD) of Rpb1 has been proposed to act as a scaffold to coordinate transcription initiation, elongation, termination, histone modification, and mRNA processing events. These events have been shown to correlate with distinct changes in the pattern of CTD phosphorylation across open reading frames. The major focus of our research is to study the role of the CTD phosphatase Rtr1 during the transcription cycle and to understand how alterations in the phosphorylation state of the CTD influence gene expression and mRNA processing.. ...
Free CAK and rCAK complexes show a stronger preference for the cdk2 substrate versus the ctd oligopeptide. CAK is thus most likely involved in regulation of the cell cycle through cdk phosphorylation (Morgan, 1995). Although free CAK is able to use the ctd oligopeptide as a substrate, it cannot phosphorylate the CTD of RNA pol II alone or when added to an in vitro transcription system lacking TFIIH. On the contrary, TFIIH which contains CAK, is able to phosphorylate the CTD of RNA pol II, in addition to TBP and TFIIEα, two polypeptides absolutely required for basal transcription of protein‐coding genes.. Free CAK and rCAK are not able to substitute for TFIIH in transcription. TFIIH lacking CAK complex allows RNA synthesis when added to an in vitro transcription system that contains all the components of the basal transcription machinery. However, when a CAK subcomplex (free CAK or rCAK) is added, the level of RNA synthesis is significantly increased. TFIIH may thus incorporate CAK to become ...
Transcription factors are frequently the chief determinants of the composition and stability of large transcription complexes. Transcriptional regulation is mediated through the interactions of transcription factors with specific binding sites. Transcription factors help to recruit RNA polymerases to active genes for the production of RNA transcripts. Detect Transcription factors using Mercks antibodies.
The second session will delve into fundamental mechanisms in gene regulation. Joan Conaway (Stowers Institute for Medical Research) will focus on the Mediator complex, which bridges interactions between transcription activators and RNA polymerase II, helping to recruit polymerase to a genes promoter. New results from the Conaway lab reveal that Mediator also can enhance transcription elongation through stimulating the release of paused Pol II.. Dylan Taatjes (University of Colorado at Boulder) will provide additional insights into Mediator and its interactions with the transcription machinery. Structural analyses of Mediator in complex with various transcription activators shed light on how Mediator translates activator binding to Pol II and the general transcription factors to influence transcription. In addition to protein factors, RNA species are emerging as important regulators of gene expression. Ramin Shiekhettar (Wistar Institute) will present his recent findings on the roles of long ...
A central, yet unresolved question related to cytokine‐regulated gene transcription is the mechanism by which STATs are connected to activation of basal transcription machinery. Here, we show that the TAD of STAT6 is interacting with p100. p100 was found to enhance the STAT6‐mediated transcription, and to bind to the large subunit of RNA pol II, thus providing a link between STAT6 and the general transcription apparatus.. p100 is a ubiquitously expressed protein that was initially identified as a protein interacting with the acidic TAD of EBNA2 (Tong et al., 1995). p100 enhanced transcriptional activity of EBNA2, but did not affect the function of another acidic TAD of VP16. Thus, p100 is not a general coactivator of transcription but its function requires specific protein interactions with transcription factors. Based on hydrophobic cluster analysis, the p100 protein is predicted to consist of four similar domains with homology to the SN domain, followed by a C‐terminal TD (Callebaut and ...
DNA transcription control. Computer model showing a molecule of the FP50 homodimer (green) from NF-kB (nuclear factor kappa-light-chain-enhancer of activated B cells) bound to the DNA interferon regulatory factor (IRF) recognition sequence on a strand of DNA (deoxyribonucleic acid, orange). NF-kB is a protein complex that controls the transcription of DNA. IRFs are proteins that regulate the transcription of interferons, which are released in response to the presence of pathogens. - Stock Image C010/4990
Transcription is a process finely regulated by different transcription factors (TFs) which bind regulatory sequences present in gene promoters and allow the precise execution of gene expression programs. Misregulation of such process can lead to different pathologies, including development/differentiation defects, uncontrolled cell growth and cancer. For these reasons it is important to understand the molecular details of the interplay that occurs between different TFs to modulate gene expression. NF-Y, the heterotrimeric complex composed by NF-YA, NF-YB and NF-YC subunits, all required for DNA binding, recognizes the consensus sequence CCAAT, present in about 30% of eukaryotic promoters, at -60/-100 bp from the Transcription Start Site (TSS). One of the most important roles of NF-Y in transcription is to interact synergistically with other TFs to activate, or to repress, gene expression. In this study we focused on the relationship occurring between NF-Y and the TFs MAX, Myc and USF1, which ...
Nutrients regulate gene transcription by the dynamic cycling of O-linked N-acetylglucosamine (O-GlcNAc) on proteins that constitute the transcriptional machinery. A study shows that O-GlcNAcylation of the nuclear factor κB (NF-κB) subunit c-Rel is required for its binding to the promoters of some, but not all, key T cell receptor-dependent genes; however, O-GlcNAcylation is dispensable for the binding of c-Rel to the promoters of tumor necrosis factor-α-dependent genes. This study not only illustrates how specific stimuli that act on the same transcription factor can elicit the expression of particular sets of genes, it also suggests a possible mechanism for autoimmunity in diabetes.. ...
Buy our Recombinant Human RNA Polymerase II p14.5 protein. Ab81852 is a full length protein produced in Escherichia coli and has been validated in SDS-PAGE…
article{2983518, abstract = {Tyrosine phosphorylation is a hallmark for activation of STAT proteins, but their transcriptional activity also depends on other secondary modifications. Type I IFNs can activate both the ISGF3 (STAT1:STAT2:IRF9) complex and STAT3, but with cell-specific, selective triggering of only the ISGF3 transcriptional program. Following a genome-wide RNAi screen, we identified the SIN3 transcription regulator homolog A (Sin3a) as an important mediator of this STAT3-targeted transcriptional repression. Sin3a directly interacts with STAT3 and promotes its deacetylation. SIN3A silencing results in a prolonged nuclear retention of activated STAT3 and enhances its recruitment to the SOCS3 promoter, concomitant with histone hyperacetylation and enhanced STAT3-dependent transcription. Conversely, Sin3a is required for ISGF3-dependent gene transcription and for an efficient IFN-mediated antiviral protection against influenza A and hepatitis C viruses. The Sin3a complex therefore acts ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Author Summary The regulation of mRNA levels in the cell is important to ensure, for instance, timely cellular responses to changes in the environment. mRNA transcription and mRNA degradation directly affect mRNA levels and it would make sense to have a system in place that would coordinate these opposing processes. Previous studies suggested that regulation of transcription in the nucleus may be linked to regulation of mRNA degradation in the cytoplasm, yet the details of this connection are poorly understood. In this study, we took an evolutionary approach to address this question by comparing both transcription and mRNA degradation between two yeast species. We found that evolution of these distinct processes is coordinated, as genes that diverged in mRNA degradation tend to also diverge in transcription. Interestingly, the coordination is counterproductive, as increased transcription is linked to increased mRNA degradation. We analyzed a hybrid between the two yeast species to classify evolutionary
Reactome is pathway database which provides intuitive bioinformatics tools for the visualisation, interpretation and analysis of pathway knowledge.


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University of North Texas

# Find the limit.$\lim_{t\to 0} \left(e^{-3t} i + \frac{t^2}{\sin^2 t}\ j + \cos 2t\ k \right)$

## $(i+j+k)$

Vector Functions

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##### Lily A.

Johns Hopkins University

##### Catherine R.

Missouri State University

##### Samuel H.

University of Nottingham

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### Video Transcript

So if we want to find this limit here, we can go ahead and apply pretty much all the same limit rules that we've learned for the one dimensional case. We could first distribute this across the pluses and pull out any constant. So this I, j and K or assuming are constants. So we converse. Rewrite this as the limit as T approaches zero of e to the negative three t times, and I'll just write I out here and I'll write. This is I hat, um, plus the limit as he approaches zero of tea and I'm actually going to rewrite this as t over sign T uh, squared. And then on the outside we have this multiplied by J hat and then, uh, co sign or the limit as T approaches zero of co sign of two t times K hat so we could just go ahead and apply the limit directly here, my plug in and zero. So that would just be one times I hat Plus, now, this limit might look a little bit familiar to you if we were to kind of rewrite this as the limit. As fate approaches zero of sine of t over T. We know this is equal toe one. And we know if we were to actually reciprocate this, um, we would end up getting the same thick. So this also implies that the limit s fate approaches. Zero of tea over sine of T is equal to one as well. So that means we can pull this inside. And this limit is just going to be one. So it would be one squared J hat plus and then we just apply the limit. Here's would be co sign of zero and co sign of zero is one B k hat. So this just ends up being I had plus jihad plus k hot. And then this here is going to be our limit.

University of North Texas

#### Topics

Vector Functions

##### Lily A.

Johns Hopkins University

##### Catherine R.

Missouri State University

##### Samuel H.

University of Nottingham

Lectures

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# CLEAR Calculus

## Lab 3: The physics of rotation

“δῶς μοι πᾶ στῶ καὶ τὰν γᾶν κινάσω”
“Give me a place to stand, and I shall move the world.”
- Archimedes

1. The angular velocity $$\pmb{\omega}$$ of rotation of a rigid body has direction equal to the axis of rotation and magnitude equal to the rate of spinning measured in radians per second. The sense of $$\pmb{\omega}$$ is determined by the right-hand rule: if your right hand fingers curl in the direction of rotation, your thumb gives the direction of $$\pmb{\omega}$$ as shown in the figure below.

Let $$\bf r$$ be a vector from a point $$O$$ on the axis to a point $$P$$ on the rigid body.
1. What is the radius of the circular path traveled by $$P$$?
2. Show that the quantity $$\bf v=\pmb{\omega}\times\bf r$$ is the velocity of $$P$$.
Hint: You need to check both the length and the direction.

2. A door knob is located as far as possible from the hinge line for a good reason. If you want to open a heavy door, Where you apply a force and in what direction you push are important. Consider a vector force $$\bf F$$ acting on a body that is free to rotate about a point $$O$$. The force is applied at a point $$P$$ whose position determines the vector $$\bf r$$. The directions of $$\bf F$$ and $$\bf r$$ make an angle of $$\varphi$$ with each other as in the figure below.
1. Decompose the force into a radial component $${\bf F}_r$$ (in the direction of $$\bf r$$ ) and the tangential component $${\bf F}_t$$ (in the direction of motion). That is, write the vectors  $${\bf F}_r$$ and  $${\bf F}_t$$ in terms of the other vectors and quantities provided. Which of these components acts to move the body? What happens to the other component of $$\bf F$$?
2. Define torque as the vector $$\pmb{\tau}= \bf r\times \bf F$$. Derive a formula for $$||\pmb{\tau}||$$ in terms of $$||\bf F_t||$$ and $$||\bf r||$$.
3. What happens to $$||\pmb{\tau}||$$ if $$||\bf r||$$ is doubled? What does this correspond to with a door?
4. What happens to $$||\pmb{\tau}||$$ if $$||\bf F_t||$$ is doubled? What does this correspond to with a door?
5. What happens to $$||\pmb{\tau}||$$ if $$||\bf F_r||$$ is doubled? What does this correspond to with a door?
6. Sometimes torque is described as "force times lever arm." What does this mean?


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# Different types of deuterium?

1. Nov 14, 2012

### nukeman

I know you can order deuterium oxide (d2o), but can anyone tell me how I can get different permutations of heavy water? Semi heavy water? And so on....?

Thanks

2. Nov 14, 2012

### Enthalpy

You can't, because hydrogen jumps between the molecules. You know, the H30+ and OH- story.

So all you can specify is what proportion of deuterium you want - usually sold quite pure, you might dilute it if you really wanted.

3. Nov 14, 2012

### nukeman

Dilute it?

So, if I buy a certain concentration of Deuterium oxide, lets say just for our example its 90% pure d20. This will have a certain molecular vibration (slower than normal water of course since deuterium is heavier)

NOW....if I dilute it: Will that sample then have a different molecular vibration as the 90% pure d20?

Basically what I am wanting to get is 2 different samples of a solution containing Deuterium, but with different vibrational frequencies of each sample.

4. Nov 15, 2012

### Enthalpy

Sellers use to offer heavy water D2O of 99%+ purity.

If you want to have different frequencies in one single batch, mix it with normal water and wait a little; add an acid or heat would save time. You will obtain a mix of D2O, H2O and HDO.

5. Nov 15, 2012

### nukeman

What I want is Sample A(Which is D20), Sample B(Which is H20) and Sample C(Which is HDO)

I can do this by diluting it?

Each of the 3 samples will have different vibration states. Correct?

6. Nov 15, 2012

### K^2

Even mix of H20 and D20 will have vibration states corresponding to H20, D20, and HDO. You cannot have a pure HDO sample because of water dissociation.

7. Nov 15, 2012

### nukeman

So is there no way to have different samples of water and heavy water with different vibrational states?

8. Nov 15, 2012

### K^2

Depends. What's the application? If you are looking at $\gamma$ for water vapor, for example, it will average out, so you can control it by mixing different proportions of H2O and D2O. If you are looking at actual resonant frequencies, however, you'll have all three with different proportions from any mix that isn't 100% one or the other. (Not counting various H3O+ resonances you'll get.)

9. Nov 15, 2012

### nukeman

Ok let me try and explain. Please let me know ok? Thanks for great info so far!

Ok, lets say I want to test Deuterium on a biological system (like a insect)

My GOAL is to give Sample A to a insect, which I hope to be Deuterium Oxide (d20)

Then...Give Sample B to another insect, and I want sample B to contain deuterium, but have a different vibration frequency as sample A. So, I was thinking if I had a sample of anything containing deuterium, but different structure.

Plus sample C would be simply Water (h2o)

Make any sense?

10. Nov 16, 2012

### K^2

What does vibration frequency have to do with anything? It will make a tiny contribution to a heat capacity, which is a bulk quantity, so heat capacity of different mixes of D2O and H2O will be different.

The biggest impact on organism is going to be the diffusion rates of water and hydrogen ions. That will also be averaged over a bunch of molecules/ions. So again, you'll get a smooth variation.

11. Nov 16, 2012

### nukeman

K^2, tried PM'ing you but ur inbox is full ;)

Instead of constant bumping of the thread, I thought I would try and PM you, because I really appreciate the info I am getting from you.

I really hope you can reply to this PM (Promise, I'll stop asking questions lol )

Let me start from square one. Please correct me if I am wrong in any sense!

Here is what I plan on doing, and you please tell me your thoughts and any info you can give me to help.

The plan is:

We have a couple groups of flies. Now, it has been proven that Deuterium slows down the flies circadian clock! So, I think that different vibrations in the substance given to the fly will react differently with the fly.

This is why I am trying to figure out how to give the fly some type of deuterium, that has a different vibration.

Maybe the frequency of the vibration will interact with the cell membrane/receptors. So, possibly the flies receptors act as a key hole, and the substance that has a certain vibrational frequency will fit that key hole better than other substances that have different frequencies.

But, it has to include some type of Deuterium.

Does any of that make sense. I know very little about Biology (as you can tell).

Do you have any suggestions possibly?

Personally, I think the reason it affects the flies is because Deuterium is simply heavier, so whatever biological mechanism that governs the flies circadian clock will be affect by a slower moving molecule like Deuterium.

Thanks in advance. Really appreciate it!

(Please, if I am wrong in any sense, please correct me. I want to learn)

12. Nov 16, 2012

### K^2

Resonant frequencies of water are extremely high. This page has them listed by wave number, k, given in cm-1. To get wavelength use, $\lambda=\frac{2 \pi}{k}$.

Note that the lowest frequencies are in THz ranges. This is not going to affect any part of biological clock.

What's going to affect biology is diffusion rates. That's really the only thing that affects timing on scales comparable to timing of various processes. And yes, diffusion rates are related to molecule's or ion's mass.

13. Nov 16, 2012

### Staff: Mentor

And kinetic isotope effect.

14. Nov 16, 2012

### jetwaterluffy

In which case, sample A would probably mix with the water in the insects body anyway, leading to some form of HDO automatically.

15. Nov 16, 2012

### Staff: Mentor

@nukeman: Answers won't change even if you open 10 threads with the same question. They might use different words, but D2O simply has one frequency spectrum for each oxygen isotope. HDO has one frequency spectrum for each oxygen isotope, and H2O, too.
And you need water vapor to see this at all, as liquid water will blur everything.


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• Nand Lal

Articles written in Journal of Earth System Science

• New age constraints on the cooling and unroofing history of the Trans-Himalayan Ladakh Batholith (Kargil area), N. W. India

Thermotectonic history of the Trans-Himalayan Ladakh Batholith in the Kargil area, N. W. India, is inferred from new age data obtained here in conjunction with previously published ages. Fission-track (FT) ages on apatite fall around 20±2 Ma recording cooling through temperatures of ∼100°C and indicating an unroofing of 4 km of the Ladakh Range since the Early Miocene. Coexisting apatite and zircon FT ages from two samples in Kargil show the rocks to have cooled at an average rate of 5–6°C/Ma in the past 40 Ma. Zircon FT ages together with mica K−Ar cooling ages from the Ladakh Batholith cluster around 40–50 Ma, probably indicating an Eocene phase of uplift and erosion that affected the bulk of the batholith after the continental collision of India with the Ladakh arc at 55 Ma. Components of the granitoids in Upper Eocene-Lower Oligocene sediments of the Indus Molasse in Ladakh supports this idea. Three hornblende K−Ar ages of 90 Ma, 55 Ma, and 35 Ma are also reported; these distinctly different ages probably reflect cooling through 500–550°C of three phases of I-type plutonism in Ladakh also evidenced by other available radiometric data: 102 Ma (mid-Cretaceous), 60 Ma (Palaeocene), and 40 Ma (Late Eocene); the last phase being localised sheet injections. The geodynamic implications of the age data for the India-Asia collision are discussed.

• Cooling age record of domal uplift in the core of the Higher Himalayan Crystallines (HHC), southwest Zanskar, India

The cooling and tectonic history of the Higher Himalayan Crystallines (HHC) in southwest Zanskar (along the Kishtwar-Padam traverse) is constrained by K-Ar biotite and fission-track (FT) apatite and zircon ages. A total of nine biotite samples yields ages in the range of 14–24 Ma, indicating the post-metamorphic cooling of these rocks through ∼ 300°C in the Miocene. Overall, the ages become younger away from the Zanskar Shear Zone (ZSZ), which marks the basement-cover detachment fault between the HHC and the Tethyan sedimentary zone, towards the core of the HHC. The same pattern is also observed for the FT apatite ages, which record the cooling of the rocks through ∼ 120°C. The apatite ages range from 11 Ma in the vicinity of the ZSZ to 4 Ma at the granitic core of the HHC. This pattern of discordant cooling ages across the HHC in southwest Zanskar reveals an inversion of isotherms due to fast uplift-denudation (hence cooling) of the HHC core, which is, in turn, related to domal uplift within the HHC. The Chisoti granite gneiss is the exposed domal structure along the studied traverse. Cooling history of two granite gneisses at the core of the HHC is also quantified with the help of the biotite, zircon and apatite ages; the time-temperatures thus obtained indicate a rapid pulse of cooling at ∼ 6 Ma, related to accelerated uplift-denudation of the HHC core at this time. Long-term denudation rates of 0.5–0.7 mm/yr are estimated for the high-grade rocks of the Higher Himalaya in southwest Zanskar over the past 4.0–5.5 m.yr.

• Seasonal variability in aerosol optical and physical characteristics estimated using the application of the Ängström formula over Mohal in the northwestern Himalaya, India

Investigations of aerosol optical and physical characteristics using the application of Ängström formula and second order polynomial fit were carried out from April 2006 to March 2009 at Mohal in the Kullu valley. The measurements of spectral aerosol optical depths (AODs) were conducted using multiwavelength radiometer (MWR). The AOD at 0.5 𝜇 m wavelength on daily basis (mean ± standard deviation) for the entire three-year study period is obtained as 0.24 ± 0.08. Seasonal variations show the highest AOD at 0.5 𝜇 m wavelength with ∼0.34 ± 0.08 during pre-monsoon (April–July), followed by ∼0.26 ± 0.08 during monsoon (August–September), ∼0.21 ± 0.05 during post-monsoon (October–November) and ∼0.20 ± 0.07 during winter (December–March). The seasonal values indicate that the AOD at 0.5 𝜇 m wavelength is decreasing from pre-monsoon to winter with a notable reduction around 41%. The Ängström parameters using least square method is not found appropriate for size distribution particularly when coarse mode aerosols dominate. The coefficients of second order polynomial fit are more appropriate for the discrimination of aerosol size or irrespective to the dominance of either of the aerosols size. The difference in coefficient of polynomial fit is used to get confirmation on the dominant mode during different seasons. Study reveals that about 93%, 72% and 59% of AOD spectra are dominated by a wide range of fine mode fractions or mixture of modes during post-monsoon, winter and monsoon, respectively. On the other hand, during pre-monsoon, 72% of AOD spectra are found to be dominated by coarse mode aerosols.

• Apatite and zircon fission-track thermochronology constraining the interplay between tectonics, topography and exhumation, Arunachal Himalaya

Thirty-eight new apatite and zircon fission-track ages from 26 bedrock samples vary from 2.0 $\pm$ 0.3 to 12.1 $\pm$ 1.2 Ma, and 3.3 $\pm$ 0.3 and 13.2 $\pm$ 0.7 Ma, respectively, along three transects of the Kurung, Subansiri, and Siyom Rivers, which flow across the major structures of the Arunachal Himalaya. These cooling ages reveal marked variations in millennial-scale ( >10$^{5}$ yr) exhumation rates from 0.6 to 3.0 mm/yr. A distinct positive correlation is visible between local topographic relief, hill slopes, channel steepness, and exhumation rates. The cooling ages are younger in the northern antiformal domains and older within the synformal nappe along the mountain front. Thermal modelling and time–temperature paths suggest that zones of rapid exhumation are controlled by structural windows within the Lesser Himalaya that were developed between 8 and 6 Ma over blind Main Himalayan Thrust (MHT). This time of rapid rock uplift and major topographic change led to a two-fold increase in the exhumation rates in the northern antiformal domains than the southern front of Arunachal Himalaya. Variation in cooling ages does not correlate with the present-day precipitation pattern. Tectonics appears to be the leading factor in driving the exhumation rates and landscape evolution in the Arunachal Himalaya.

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 Izv. Akad. Nauk SSSR Ser. Mat., 1977, Volume 41, Issue 4, Pages 937–958 (Mi izv1874)

On $(H,k)$-summability of multiple trigonometric Fourier series

Abstract: A theorem is proved from which, in particular, it follows that if $f\in L(\ln^+L)^{N-1}$ on $T^N\equiv[-\pi,\pi]^N$, then the multiple trigonometric Fourier series of $f$ and all conjugate series are $(H,k)$-summable almost everywhere on $T^N$ for every $k>0$.
In the case where $f\in L(\ln^+L)^{N+1}$ this result was obtained by Marcinkiewicz (Collected papers, PWN, Warsaw, 1964).
That it is unimprovable, in a certain sense, follows from a result of Saks (On the strong derivatives of functions of intervals, Fund. Math. 25 (1935), 235–252).
Bibliography: 15 titles.

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English version:
Mathematics of the USSR-Izvestiya, 1977, 11:4, 889–908

Bibliographic databases:

UDC: 517.5
MSC: 42A24, 42A92, 42A40, 40G05

Citation: L. D. Gogoladze, “On $(H,k)$-summability of multiple trigonometric Fourier series”, Izv. Akad. Nauk SSSR Ser. Mat., 41:4 (1977), 937–958; Math. USSR-Izv., 11:4 (1977), 889–908

Citation in format AMSBIB
\Bibitem{Gog77} \by L.~D.~Gogoladze \paper On $(H,k)$-summability of multiple trigonometric Fourier series \jour Izv. Akad. Nauk SSSR Ser. Mat. \yr 1977 \vol 41 \issue 4 \pages 937--958 \mathnet{http://mi.mathnet.ru/izv1874} \mathscinet{http://www.ams.org/mathscinet-getitem?mr=473711} \zmath{https://zbmath.org/?q=an:0362.42003} \transl \jour Math. USSR-Izv. \yr 1977 \vol 11 \issue 4 \pages 889--908 \crossref{https://doi.org/10.1070/IM1977v011n04ABEH001750}

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This publication is cited in the following articles:
1. L. D. Gogoladze, “On strong summability almost everywhere”, Math. USSR-Sb., 63:1 (1989), 153–164
2. M. I. Dyachenko, “Some problems in the theory of multiple trigonometric series”, Russian Math. Surveys, 47:5 (1992), 103–171
3. V. A. Rodin, “The tensor BMO-property of the sequence of partial sums of a multiple Fourier series”, Russian Acad. Sci. Sb. Math., 80:1 (1995), 211–224
4. Weisz F., “Convergence and Summability of Fourier Transforms and Hardy Spaces”, Convergence and Summability of Fourier Transforms and Hardy Spaces, Applied and Numerical Harmonic Analysis, Birkhauser Boston, 2017, 1–435
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My Math Forum A limit

 Calculus Calculus Math Forum

 August 27th, 2019, 07:27 AM #1 Senior Member   Joined: Dec 2015 From: somewhere Posts: 642 Thanks: 91 A limit Evaluate $\displaystyle \lim_{n\rightarrow \infty }n^{-1} \underbrace{\ln \ln...\ln}_{n}(n)$. Last edited by skipjack; August 27th, 2019 at 07:54 AM.
 August 27th, 2019, 07:53 AM #2 Global Moderator   Joined: Dec 2006 Posts: 20,972 Thanks: 2222 Did you invent this problem?
 August 27th, 2019, 12:26 PM #3 Math Team   Joined: Dec 2013 From: Colombia Posts: 7,683 Thanks: 2664 Math Focus: Mainly analysis and algebra Mmm... since $\ln x \to -\infty$ as $x \to 0$ at an exponential rate, I'm going to guess that this blows up. But I'm far from certain.
August 27th, 2019, 12:35 PM   #4
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Quote:
 Originally Posted by v8archie Mmm... since $\ln x \to -\infty$ as $x \to 0$ at an exponential rate, I'm going to guess that this blows up. But I'm far from certain.
The limit is to infinity. $\log x$ goes to infinity as does any number of iterations of $\log$. It's an old joke that $\log \log x$ is constant for all practical purposes, the point being that it goes to infinity very slowly. But to infinity it goes nonetheless. So I don't follow your intuition. The intuition would have to be that the iterated log goes to infinity so slowly that the n in the denominator pulls it to zero.

It looks like you could prove it by using L'Hospital perhaps.

August 27th, 2019, 01:25 PM   #5
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*sigh* Mathematicians...

It sure looks like it's going towards zero to me.
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August 27th, 2019, 02:37 PM   #6
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In fact, the magnitude is shrinking as 1/n.
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 August 27th, 2019, 03:32 PM #7 Senior Member   Joined: Sep 2016 From: USA Posts: 645 Thanks: 408 Math Focus: Dynamical systems, analytic function theory, numerics The limit is 0. You can easily see this by noticing that $\log^{(k)}(n) \leq \log n$ for all $k \geq 1$ where the notation on the left means iteration. Combine this with the fact that $n^{-1} \log n \to 0$.
August 27th, 2019, 03:49 PM   #8
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Quote:
 Originally Posted by SDK $\log^{(k)}(n) \leq \log n$ for all $k \geq 1$
I thought of this, but the iterated logs quickly become negative (and thus complex). If $| \log^{(k)}(n) | \leq |\log n|$, then it still works, but I wasn't sure how to determine that. Plotting was easier.

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If $A = \begin{pmatrix} 1 & 0 & 0 & 1 \\ 0 & -1 & 0 & -1 \\ 0 & 0 & i & i \\ 0 & 0 & 0 & -i \end{pmatrix}$ the matrix $A^4$, calculated by the use of Cayley-Hamilton theorem or otherwise, is ____
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+2

This might help ....

Let λ be eighen value

Characteristic polynomial is

(1-λ)(-1-λ)(i-λ)(-i-λ)

=(λ2-1)(λ2+1)

4-1

Characteristic equation is λ4-1=0

According to Cayley Hamilton theorem every matrix matrix satisfies its own characteristic equation

So A4=I

selected
0
Cayley Hamilton theorem is very useful to find (1) Inverse of given matrix

(2) Higher power of given matrix


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