Computers, Analog: Computers in which quantities are represented by physical variables; problem parameters are translated into equivalent mechanical or electrical circuits as an analog for the physical phenomenon being investigated. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Ribose: A pentose active in biological systems usually in its D-form.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.RNA Polymerase II: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Forensic Genetics: The application of genetic analyses and MOLECULAR DIAGNOSTIC TECHNIQUES to legal matters and crime analysis.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Genetic Vectors: DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.Carnitine Acyltransferases: Acyltransferases in the inner mitochondrial membrane that catalyze the reversible transfer of acyl groups from acyl-CoA to L-carnitine and thereby mediate the transport of activated fatty acids through that membrane. EC 2.3.1.Carnitine: A constituent of STRIATED MUSCLE and LIVER. It is an amino acid derivative and an essential cofactor for fatty acid metabolism.Palmitoylcarnitine: A long-chain fatty acid ester of carnitine which facilitates the transfer of long-chain fatty acids from cytoplasm into mitochondria during the oxidation of fatty acids.Mersalyl: A toxic thiol mercury salt formerly used as a diuretic. It inhibits various biochemical functions, especially in mitochondria, and is used to study those functions.Acetylcarnitine: An acetic acid ester of CARNITINE that facilitates movement of ACETYL COA into the matrices of mammalian MITOCHONDRIA during the oxidation of FATTY ACIDS.Fatty Acids: Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)Citric Acid: A key intermediate in metabolism. It is an acid compound found in citrus fruits. The salts of citric acid (citrates) can be used as anticoagulants due to their calcium chelating ability.Germ Cells: The reproductive cells in multicellular organisms at various stages during GAMETOGENESIS.Stem Cells: Relatively undifferentiated cells that retain the ability to divide and proliferate throughout postnatal life to provide progenitor cells that can differentiate into specialized cells.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.Silencer Elements, Transcriptional: Nucleic acid sequences that are involved in the negative regulation of GENETIC TRANSCRIPTION by chromatin silencing.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Sex Determination Processes: The mechanisms by which the SEX of an individual's GONADS are fixed.Sex Determination Analysis: Validation of the SEX of an individual by inspection of the GONADS and/or by genetic tests.Oryzias: The only genus in the family Oryziinae, order BELONIFORMES. Oryzias are egg-layers; other fish of the same order are livebearers. Oryzias are used extensively in testing carcinogens.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.SOX9 Transcription Factor: A SOXE transcription factor that plays a critical role in regulating CHONDROGENESIS; OSTEOGENESIS; and male sex determination. Loss of function of the SOX9 transcription factor due to genetic mutations is a cause of CAMPOMELIC DYSPLASIA.Gene Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Sex Differentiation: The process in developing sex- or gender-specific tissue, organ, or function after SEX DETERMINATION PROCESSES have set the sex of the GONADS. Major areas of sex differentiation occur in the reproductive tract (GENITALIA) and the brain.Double Outlet Right Ventricle: Incomplete transposition of the great vessels in which both the AORTA and the PULMONARY ARTERY arise from the RIGHT VENTRICLE. The only outlet of the LEFT VENTRICLE is a large ventricular septal defect (VENTRICULAR SEPTAL DEFECTS or VSD). The various subtypes are classified by the location of the septal defect, such as subaortic, subpulmonary, or noncommitted.Heart Defects, Congenital: Developmental abnormalities involving structures of the heart. These defects are present at birth but may be discovered later in life.Ebstein Anomaly: A congenital heart defect characterized by downward or apical displacement of the TRICUSPID VALVE, usually with the septal and posterior leaflets being attached to the wall of the RIGHT VENTRICLE. It is characterized by a huge RIGHT ATRIUM and a small and less effective right ventricle.Lutembacher Syndrome: A condition characterized by a combination of OSTIUM SECUNDUM ATRIAL SEPTAL DEFECT and an acquired MITRAL VALVE STENOSIS.Heart Septal Defects, Ventricular: Developmental abnormalities in any portion of the VENTRICULAR SEPTUM resulting in abnormal communications between the two lower chambers of the heart. Classification of ventricular septal defects is based on location of the communication, such as perimembranous, inlet, outlet (infundibular), central muscular, marginal muscular, or apical muscular defect.Tricuspid Valve: The valve consisting of three cusps situated between the right atrium and right ventricle of the heart.Heart: The hollow, muscular organ that maintains the circulation of the blood.WingSmad3 Protein: A receptor-regulated smad protein that undergoes PHOSPHORYLATION by ACTIVIN RECEPTORS, TYPE I. Activated Smad3 can bind directly to DNA, and it regulates TRANSFORMING GROWTH FACTOR BETA and ACTIVIN signaling.Smad4 Protein: A signal transducing adaptor protein and tumor suppressor protein. It forms a complex with activated RECEPTOR-REGULATED SMAD PROTEINS. The complex then translocates to the CELL NUCLEUS and regulates GENETIC TRANSCRIPTION of target GENES.Activin Receptors: Receptors for ACTIVINS are membrane protein kinases belonging to the family of PROTEIN-SERINE-THREONINE KINASES, thus also named activin receptor-like kinases (ALK's). Activin receptors also bind TRANSFORMING GROWTH FACTOR BETA. As those transmembrane receptors of the TGF-beta superfamily (RECEPTORS, TRANSFORMING GROWTH FACTOR BETA), ALK's consist of two different but related protein kinases, Type I and Type II. Activins initiate cellular signal transduction by first binding to the type II receptors (ACTIVIN RECEPTORS, TYPE II ) which then recruit and phosphorylate the type I receptors (ACTIVIN RECEPTORS, TYPE I ) with subsequent activation of the type I kinase activity.Smad7 Protein: An inhibitory smad protein that associates with TRANSFORMING GROWTH FACTOR BETA RECEPTORS and BONE MORPHOGENETIC PROTEIN RECEPTORS. It negatively regulates SIGNAL TRANSDUCTION PATHWAYS by inhibiting PHOSPHORYLATION of RECEPTOR-REGULATED SMAD PROTEINS.Papio: A genus of the subfamily CERCOPITHECINAE, family CERCOPITHECIDAE, consisting of five named species: PAPIO URSINUS (chacma baboon), PAPIO CYNOCEPHALUS (yellow baboon), PAPIO PAPIO (western baboon), PAPIO ANUBIS (or olive baboon), and PAPIO HAMADRYAS (hamadryas baboon). Members of the Papio genus inhabit open woodland, savannahs, grassland, and rocky hill country. Some authors consider MANDRILLUS a subgenus of Papio.

*Gene structure

Ogbourne, Steven; Antalis, Toni M. (1998). "Transcriptional control and the role of silencers in transcriptional regulation in ... Maston, G. A.; Evans, S. K.; Green, M. R. (2006). "Transcriptional Regulatory Elements in the Human Genome". Annual Review of ... Each element has a specific function in the multi-step process of gene expression. The sequences and lengths of these elements ... Maston, Glenn A.; Evans, Sara K.; Green, Michael R. (2006). "Transcriptional Regulatory Elements in the Human Genome". Annual ...

*Silencer (genetics)

"Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes" (PDF). Biochem. J. 331 (1): 1-14 ... silencer elements target the assembly of GTFs, necessary for transcription of the gene. These silencer elements are mostly ... which are the classical silencer element and the non-classical negative regulatory element (NRE). In classical silencers, the ... Among the many silencer elements and proteins, REST/NSRF is an important silencer factor that has a variety of impacts, not ...

*Regulation of gene expression

Transcriptional *Gene regulatory network. *cis-regulatory element. *lac operon. *Post-transcriptional *sequestration (P-bodies) ... Enhancers are much more common in eukaryotes than prokaryotes, where only a few examples exist (to date).[3] Silencers are ... Post-transcriptional regulation[edit]. Main article: Post-transcriptional regulation. After the DNA is transcribed and mRNA is ... Up-regulation and down-regulation[edit]. Up-regulation is a process that occurs within a cell triggered by a signal ( ...

*Regulation of gene expression

Transcriptional *Gene regulatory network. *cis-regulatory element. *lac operon. *Post-transcriptional *sequestration (P-bodies) ... Enhancers are much more common in eukaryotes than prokaryotes, where only a few examples exist (to date).[3] Silencers are ... Post-transcriptional regulation[edit]. Main article: Post-transcriptional regulation. After the DNA is transcribed and mRNA is ... Up-regulation and down-regulation[edit]. Up-regulation is a process that occurs within a cell triggered by a signal ( ...

*Silencer (genetics)

Ogbourne, Steven; Toni Antalis (1998). "Transcriptional control and the role of silencers in transcriptional regulation in ... silencer elements target the assembly of GTFs, necessary for transcription of the gene. These silencer elements are mostly ... which are the classical silencer element and the non-classical negative regulatory element (NRE). In classical silencers, the ... Among the many silencer elements and proteins, REST/NSRF is an important silencer factor that has a variety of impacts, not ...

*SNP annotation

Mutations in the untranslated region (UTR) affect many post-transcriptional regulation. Distinctive structural features are ... chromatin regulators and other distal transcriptional factors, which disturb the interaction between enhancer/silencer and its ... required for many RNA molecules and cis-acting regulatory elements to execute effective functions during gene regulation. SNVs ... Transcriptional gene regulation process depends on many spatial and temporal factors in the nucleus such as global or local ...

*RE1-silencing transcription factor

"Regulation of cholinergic gene expression by the neuron restrictive silencer factor/repressor element-1 silencing transcription ... Coulson JM (September 2005). "Transcriptional regulation: cancer, neurons and the REST". Current Biology. 15 (17): R665-8. doi: ... It represses transcription by binding a DNA sequence element called the neuron-restrictive silencer element (NRSE, also known ... Kemp DM, Lin JC, Habener JF (September 2003). "Regulation of Pax4 paired homeodomain gene by neuron-restrictive silencer factor ...

*Eukaryotic transcription

Eukaryotic transcriptional activators have separate DNA-binding and activating functions. Upon binding to its cis-element, an ... For example, the transcriptional activator Tat affects elongation rather than initiation during its regulation of HIV ... Well-characterized regulatory elements include enhancers, silencers, and insulators. These regulatory sequences can be spread ... These cis-acting control elements bind transcriptional activators or repressors to increase or decrease transcription from the ...

*Gene expression

CS1 maint: Multiple names: authors list (link) Plant Transcription Factor Database and Plant Transcriptional Regulation Data ... Among all regulatory motifs within the 3'-UTRs (e.g. including silencer regions), MREs make up about half of the motifs. As of ... The 3'-UTR often contains microRNA response elements (MREs). MREs are sequences to which miRNAs bind. These are prevalent ... see regulation of transcription in cancer). Transcriptional repression in cancer can also occur by other epigenetic mechanisms ...

*HHV Infected Cell Polypeptide 0

"Regulation of the cholinergic gene locus by the repressor element-1 silencing transcription factor/neuron restrictive silencer ... IE1 protein to modulate sumoylation of PML correlates with its functional activities in transcriptional regulation and ... Neuronal Restrictive Silencer Factor (NRSF) is also known as Repressor Element-1-Silencing Transcription factor (REST) and X2 ... Mori N, Schoenherr C, Vandenbergh DJ, Anderson DJ (July 1992). "A common silencer element in the SCG10 and type II Na+ channel ...

*Alternative splicing

Wang, Z; Burge, Cb (2008). "Splicing regulation: from a parts list of regulatory elements to an integrated splicing code" (Free ... Use of multiple promoters is properly described as a transcriptional regulation mechanism rather than alternative splicing; by ... Splicing silencers are sites to which splicing repressor proteins bind, reducing the probability that a nearby site will be ... For example, some cis-acting RNA sequence elements influence splicing only if multiple elements are present in the same region ...

*DNase I hypersensitive site

The number of distal cis-regulatory elements connected to a promoter is related to the quantitative average of the regulation ... Also, it was confirmed that only 5% of DHSs were found in TSS (Transcriptional Start Site) regions. The remaining 95% ... silencers and locus control regions. A high-throughput measure of these regions is available through DNase-Seq. The ENCODE ... ENCODE Project: Regulatory Elements DB Plant DHSs : PlantDHS Wang, YM; Zhou, P; Wang, LY; Li, ZH; Zhang, YN; Zhang, YX. " ...

*RNA-binding protein

... s' transcriptional and post-transcriptional regulation of RNA has a role in regulating the patterns of gene ... and intronic splicing silencers (ISSs) and depending on their location of binding, RBPs work as splicing silencers or enhancers ... Other than core splicesome complex, RBPs also bind to the sites of Cis-acting RNA elements that influence exons inclusion or ... Although RBPs have a crucial role in post-transcriptional regulation in gene expression, relatively few RBPs have been studied ...

*5' flanking region

... silencers, and promoters. The primary promoter element in eukaryotes is the TATA box. Other promoter elements found in ... flanking region change transcriptional regulation of the human cytochrome P450IIE1 gene". J Biochem. 110 (4): 559-65. PMID ... Prokaryotes only have three promoter elements: two elements are present -35 and -10 nucleotides upstream of the transcription ... Silencers are DNA sequences found in the 5' flanking region of eukaryotic genes, that aid in the silencing of a gene. They can ...

*TATA box

... polymerase II depends on the regulation of the core promoter by long-range regulatory elements such as enhancers and silencers. ... This cluster of RNA polymerase II and various transcription factors is known as the basal transcriptional complex (BTC). In ... Enhancers are long-range regulatory elements that increase promoter activity while silencers repress promoter activity. ... Initiator element. References[edit]. *^ a b c Lifton RP, Goldberg ML, Karp RW, Hogness DS (1978). "The organization of the ...

*DNA methyltransferase

Transcriptional regulation. prokaryotic. *Operon *lac operon. *trp operon. *gab operon. *ara operon ... Response element. *Enhancer *E-box. *Response element. *Insulator. *Silencer. *Internal control region ... Though DNMT3L appears incapable of methylation, it may participate in transcriptional repression. ...

*Promoter (genetics)

Promoters represent critical elements that can work in concert with other regulatory regions (enhancers, silencers, boundary ... Not listed here are the many kinds of cancers involving aberrant transcriptional regulation owing to creation of chimeric genes ... Some promoters contain one or more upstream promoter element (UP element) subsites[5] (consensus sequence 5'-AAAAAARNR-3' when ... The TATA element and BRE typically are located close to the transcriptional start site (typically within 30 to 40 base pairs). ...

*DNA methylation

Repression of transposable elements[edit]. DNA methylation is a powerful transcriptional repressor, at least in CpG dense ... are regarded as possible functional regions involved in gene transcriptional regulation. Although various human cell types may ... are regarded as possible functional regions involved in gene transcriptional regulation. The identification of DMRs among ... Lev Maor G, Yearim A, Ast G (May 2015). "The alternative role of DNA methylation in splicing regulation". Trends in Genetics. ...

*Histone acetyltransferase

HATs act as transcriptional co-activators or gene silencers and are most often found in large complexes made up of 10 to 20 ... Regulation of HAT activity[edit]. The catalytic activity of HATs is regulated by two types of mechanisms: (1) interaction with ... TIF-2 (transcriptional intermediary factor 2; also known as GRIP1) is another nuclear receptor coactivator with HAT activity, ... The level of packing of the DNA is important for gene transcription, since the transcriptional machinery must have access to ...

*Transcription (biology)

... see regulation of transcription in cancer). Transcriptional repression in cancer can also occur by other epigenetic mechanisms ... Response element. *Insulator. *Silencer. *Internal control region. Initiation (bacterial,. eukaryotic. *Transcription start ... Main article: Regulation of transcription in cancer. In vertebrates, the majority of gene promoters contain a CpG island with ... This new approach has revealed that transcription occurs in discontinuous bursts, or pulses (see Transcriptional bursting). ...

*Locus control region

Expression levels of genes can be modified by the LCR and gene-proximal elements, such as promoters, enhancers, and silencers. ... Once bound, the transcriptional apparatus increases gene expression. This hypothesis combines the looping and tracking models, ... These studies determined that the LCR was required for normal regulation of beta-globin gene expression. Evidence of the ... Even though all of the genes themselves and the other regulatory elements were intact, without this domain, none of the genes ...

*RNA silencing

Down-regulation of genes[edit]. For a detailed explanation of the down-regulation of genes, see RNAi:downregulation of genes ... Among all regulatory motifs within the 3'-UTRs (e.g. including silencer regions), MREs make up about half of the motifs. ... Hammond SM, Caudy AA, Hannon GJ (Feb 2001). "Post-transcriptional gene silencing by double-stranded RNA". Nature Reviews ... The 3'-UTR often contains microRNA response elements (MREs). MREs are sequences to which miRNAs bind. These are prevalent ...

*Behavioral epigenetics

Figure 4: Epigenetic basis of drug regulation of gene expression Nestler EJ (December 2012). "Transcriptional mechanisms of ... Gene expression can be controlled through the action of repressor proteins that attach to silencer regions of the DNA. DNA ... This includes the cAMP response element binding protein (CREB), the phosphorylation of which induces its association with the ... Epigenetic gene regulation involves changes other than to the sequence of DNA and includes changes to histones (proteins around ...

*DNA footprinting

... or silencers to drive or repress transcription are fundamental to understanding the unique regulation of individual genes ... Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin". Genome ... help elucidate which proteins bind to these associated regions of DNA and unravel the complexities of transcriptional control. ... The regulation of transcription has been studied extensively, and yet there is still much that is not known. Transcription ...

*Gene

Maston, G. A.; Evans, S. K.; Green, M. R. (2006). "Transcriptional Regulatory Elements in the Human Genome". Annual Review of ... The regulation of lactose metabolism genes in E. coli (lac operon) was the first such mechanism to be described in 1961. A ... conversely silencers bind repressor proteins and make the DNA less available for RNA polymerase. The transcribed pre-mRNA ... The structure of a gene consists of many elements of which the actual protein coding sequence is often only a small part. These ...

*Antisense RNA

As a regulatory element, asRNAs bear many advantages to be considered as a drug target. First of all, asRNAs regulate gene ... Therefore, asRNA dependent regulation is not limited to on/off mechanism; rather, it presents a fine tone control system. The ... One classic example in human is zinc-finger E-box binding homeobox 2 gene (ZEB2) which encodes E-cadherin, a transcriptional ... Besides cis-acting asRNAs that target mRNAs, there are cis-acting epigenetic silencers and activators. In terms of epigenetic ...

*RNA interference

"RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing". Nat Genet. 36 (11): ... RNAi uptake and regulation is monitored by the kidneys. The human immune system is divided into two separate branches: the ... Among all regulatory motifs within the 3'-UTRs (e.g. including silencer regions), MREs make up about half of the motifs. As of ... The ancestral function of the RNAi system is generally agreed to have been immune defense against exogenous genetic elements ...
The usefulness of a digitally controlled analog computer in studying digital detection systems was examined. A program was developed for a computer equipped with parallel logic elements. Experience with the system shows it to be a very useful tool for such studies particularly because of the excellent man machine interaction and also because of a possible cost advantage. (Author)(*DEMODULATORS
This volume of Analog Circuit Design concentrates on three topics: Operational Amplifiers. A-to-D converters and Analog CAD. The book comprises six papers on each topic written by internationally recognised experts. These papers have a tutorial nature aimed at improving the design of analog circuits. The book is divided into three parts. Part I, Operational Amplifiers , presents new technologies for the design of Op-Amps in both bipolar and CMOS technologies. Two papers demonstrate techniques for improving frequency and gain behavior at high voltage. Low voltage bipolar Op-Amp design is treated in another paper. The realization high-speed and high gain VLSI building blocks in CMOS is demonstrated in two papers. The final paper shows how to provide output power with CMOS buffer amplifiers. Part II, Analog-to-Digital Conversion , presents papers which address very high conversion speeds and very high resolution implementations using sigma-delta modulation architectures. Analog to Digital ...
can the tft7020 samsung recieve both digital and analogue signals, from two computers at the same time, and switch between them?just curious...
Once transcription is complete, there are further controls that allow the network of enzymes and genes to control itself. Im not going to list all of them, but one that cannot be left out involves alternative splicing of RNA. This is a process in which the transcribed RNA is edited, usually removing a number of sections called introns, while creating the final mRNA. Which introns are removed, and sometimes where their boundaries are set, determines the sequence of the final mRNA, and thus the character of the protein. Alternative splicing can be affected by enzymes, but also by non-coding RNAs of various types and provenance, including those snipped out of the introns of other genes. A description of some of the ways in which alternative splicing can be regulated may be found in Regulation of Alternative Splicing: More than Just the ABC by Amy E. House and Kristen W. Lynch. It may turn out that the number of data connections that affect protein (enzyme) concentration via ...
A general purpose programmable neural computer which parallel processes analog data. The neural computer comprises neural elements for outputting an analog signal in response to at least one input signal, synaptic circuits interfaced with the neural elements for modifying gains of the neural elements, and switching circuits interfaced with the synaptic circuits and the neural circuits for routing signals between the synapse circuits and the neural circuits and for modifying the synaptic time constants, thereby changing connection architecture of the general purpose analog computer as desired. In this manner, the neural computer of the invention can be programmed to learn different confirurations as well as different synaptic values.
The kinetics of sodium, movement into human red blood cells has been studied in vivo with 24Na. When human serum albumin-131I is used to measure the percentage of plasma trapped in the packed red blood cells after centrifugation, approximately 30 % of red blood cell sodium is found to equilibrate immediately with plasma. It is concluded that this immediately exchangeable compartment of red blood cell sodium is an experimental artefact, associated with the use of labeled albumin for measuring plasma trapping. This immediately exchangeable fraction disappears when sucrose-14C is used to measure plasma trapping. The experimental results were examined by compartmental analysis, using an analogue computer. The results obtained, when plasma trapping was measured with sucrose-14C could be simulated by the use of models containing two compartments, arranged in series or in parallel. The errors of the techniques used and the possible physical basis for the results are discussed.. ...
DARPA future research includes fascinating new technology like simulating the brain, self-destructing computers, analog computers and more.
I]n a fundamental sense all computing is based on an analogy, that is, on a systematic relationship between the states and processes in the computer and those in the primary system. In a digital computer, the relationship is more abstract and complex than simple proportionality, but even so simple an analog computer as a slide rule goes beyond strict proportion (i.e., distance on the rule is proportional to the logarithm of the number). In both analog and digital computation-indeed in all computation-the relevant abstract mathematical structure of the problem is realized in the physical states and processes of the computer, but the realization may be more or less direct ([refs]). Therefore, despite the etymologies of the terms "analog" and "digital," in modern usage the principal distinction between digital and analog computation is that the former operates on discrete representations in discrete steps, while the later operated on continuous representations by means of continuous processes ...
The authors give the basic principles of an analog device for solving a system of differential equations describing the behavior of a nuclear reactor with respect to time. Systems of this type are difficult to solve, especially when the reactivity varies with time. The proposed device may be used for solving problems involving six groups of delayed neutrons, or may alternatively be programmed for a simplified equation with a single group of delayed neutrons. The proposed computer may be used in studying high-power reactors where the maximum neutron density in the core may reach 10 to the 15th power n/cu cm.*ANALOG COMPUTERS)
While the role of group I and group II intron-encoded proteins in homing has been well defined, the function of these proteins in intron dissemination to new sites remains the subject of intense study. These mobile introns, their intron-encoded proteins, and the mechanisms by which mobility occurs are the subject of this chapter. Although transition metals are not required for colicin DNase activity, it is likely that they play a stabilizing role related to the membrane translocation that must occur for colicins biological function. These data lend credence to the idea that the HNH domain, like the GIY-YIG domain, is an endonu clease cassette that can become associated with other protein domains to form multifunctional proteins. The open reading frames (ORFs) specifying group II intron-encoded proteins, when present, are located in the loop region of the structural domain IV, with most of the coding sequence outside the intron catalytic core. Of the three activities of the group II intron-encoded
Group II Self-Splicing Introns. -pre-rRNA of fungal and plant mitochondria -majority of chloroplast introns -several classes -require Mg 2+ -no cofactor. Domain Structure of a Group II Intron. A. 5 exon. 3 exon. Chemistry of Group II Self-Splicing. 1st step. 2nd step. lariat. Slideshow 3387240 by guang
Structure and Conformational Dynamics of the Domain 5 RNA Hairpin of a Bacterial Group II Intron Revealed by Solution Nuclear Magnetic Resonance and Molecular Dynamics ...
Exon shuffling was first introduced in 1978 when Walter Gilbert discovered that the existence of introns could play a major role in the evolution of proteins. It was noted that recombination within introns could help assort exons independently and that repetitive segments in the middle of introns could create hotspots for recombination to shuffle the exonic sequences. However, the presence of these introns in eukaryotes and absence in prokaryotes created a debate about the time in which these introns appeared. Two theories arose: the "introns early" theory and the "introns late" theory. Supporters of the "introns early theory" believed that introns and RNA splicing were the relics of the RNA world and therefore both prokaryotes and eukaryotes had introns in the beginning. However, prokaryotes eliminated their introns in order to obtain a higher efficiency, while eukaryotes retained the introns and the genetic plasticity of the ancestors. On the other hand, supporters of the "introns late" theory ...
DExD/H-box proteins are a diverse class of proteins that are implicated in RNA and RNP remodeling. They have sequence homology to DNA helicases and share conserved ATPase domains, suggesting that they use the energy of ATP binding and hydrolysis to mediate conformational rearrangements in RNAs. In the past, the action of DExD/H-box proteins has been characterized primarily on simple model substrates such as small RNA duplexes. It is not known how DExD/H-box proteins manipulate structured RNA, what determines target specificity and what molecular events follow their action. Here, using the well-characterized Tetrahymena group I intron ribozyme, I performed kinetic and thermodynamic studies to understand the mechanism of CYT-19 and related DExD/Hbox proteins. CYT-19 has been shown previously to facilitate the folding of several group I and group II introns. I demonstrated that CYT-19 acts as a chaperone, accelerating the re-folding of a long-lived misfolded species of the Tetrahymena group I ...
The objective of this study was primarily to determine the structure and biochemical characteristics of the NmeGp1Sd in order to gain a deeper insight into the evolution of metazoan Nme proteins and their functions.. Sponge Group I Nme genes are intron-rich and these introns are relatively short. The same has been found for introns in several other sponge genes [42, 43] and recently in A. queenslandica genome where median intron size is 80 bp [32]. The fourth intron (Figure 1) is likely the most ancient because it is also found in a choanoflagellate Group I Nme homolog. We conclude that the ancestral metazoan Group I Nme gene was intron-rich and probably had all four introns that are still present in most extant basal metazoan homologs. The ancestral gene structure is also well preserved in vertebrate homologs with three out of four introns present. D. melanogaster has only one of the ancestral introns and C. elegans lost all ancestral introns and gained two new ones which likely reflect ...
Introns may be lost or gained over evolutionary time, as shown by many comparative studies of orthologous genes. Subsequent analyses have identified thousands of examples of intron loss and gain events, and it has been proposed that the emergence of eukaryotes, or the initial stages of eukaryotic evolution, involved an intron invasion.[32] Two definitive mechanisms of intron loss, Reverse Transcriptase-Mediated Intron Loss (RTMIL) and genomic deletions, have been identified, and are known to occur.[33] The definitive mechanisms of intron gain, however, remain elusive and controversial. At least seven mechanisms of intron gain have been reported thus far: Intron Transposition, Transposon Insertion, Tandem Genomic Duplication, Intron Transfer, Intron Gain during Double-Strand Break Repair (DSBR), Insertion of a Group II Intron, and Intronization. In theory it should be easiest to deduce the origin of recently gained introns due to the lack of host-induced mutations, yet even introns gained ...
Many functional RNAs are required to fold into specific three-dimensional structures. A fundamental property of RNA is that its secondary structure and even some tertiary contacts are highly stable, which gives rise to independent modular RNA motifs and makes RNAs prone to adopting misfolded intermediates. Consequently, in addition to stabilizing the native structure relative to the unfolded species (defined here as stability), RNAs are faced with the challenge of stabilizing the native structure relative to alternative structures (defined as structural specificity). How RNAs have evolved to overcome these challenges is incompletely understood. Self-splicing group I introns have been used to study RNA structure and folding for decades. Among them, the Tetrahymena intron was the first discovered and has been studied extensively. In this work, we found that a version of the intron that was generated by in vitro selection for enhanced stability also displayed enhanced specificity against a stable ...
Nuclear DNA intron sequences are increasingly used to investigate evolutionary relationships among closely related organisms. The phylogenetic usefulness of intron sequences at higher taxonomic levels has, however, not been firmly established and very few studies have used these markers to address evolutionary questions above the family level. In addition, the mechanisms driving intron evolution are not well understood. We compared DNA sequence data derived from three presumably independently segregating introns (THY, PRKC I and MGF) across 158 mammalian species. All currently recognized extant eutherian mammalian orders were included with the exception of Cingulata, Dermoptera and Scandentia. The total aligned length of the data was 6366 base pairs (bp); after the exclusion of autapomorphic insertions, 1511 bp were analyzed. In many instances the Bayesian and parsimony analyses were complementary and gave significant posterior probability and bootstrap support (,80) for the monophyly of ...
The large subunit of the mitochondrial ribosomal RNA genes (mtLSU) has previously been identified as a highly sensitive molecular marker for intraspecies diversity in the arbuscular mycorrhizal fungus Glomus intraradices. In this study, the respective region was analyzed in five species of Glomus (G. mosseae, G. geosporum, G. caledonium, G. clarum, G. coronatum) from the same major clade (Glomus group A), Glomus sp. ISCB 34 from the related Glomus group B and two species of Scutellospora. Results show low level of genetic polymorphism between related morphospecies. Introns homologous to those found in G. intraradices were detected as well as new ones, some of them containing putative ORFs for homing endonucleases (HEs). Introns without ORFs for HEs seem to have been inherited strictly vertically from the ancestors of Glomus groups A and B while other introns indicate occasional horizontal transfer and possibly maintenance, degeneration and loss together with their associated HE ORFs. Overall, we provide
Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (PF00078) followed by an RNA-binding maturase domain (PF08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029 ...
View Notes - Lecture8 from BIOC 100A at UCSC. 25 26 The hammerhead ribozyme (plant virus) Martick & Scott, Cell 2006 27 Group I intron ribozyme Golden et al, and cech Science (1998) 28 Acid-Base
A splice site mutation is a genetic mutation that inserts, deletes or changes a number of nucleotides in the specific site at which splicing takes place during the processing of precursor messenger RNA into mature messenger RNA. Splice site consensus sequences that drive exon recognition are located at the very termini of introns. The deletion of the splicing site results in one or more introns remaining in mature mRNA and may lead to the production of abnormal proteins. When a splice site mutation occurs, the mRNA transcript possesses information from these introns that normally should not be included. Introns are supposed to be removed, while the exons are expressed. The mutation must occur at the specific site at which intron splicing occurs: within non-coding sites in a gene, directly next to the location of the exon. The mutation can be an insertion, deletion, frame shift, etc. The splicing process itself is controlled by the given sequences, known as splice-donor and splice-acceptor ...
Group II introns are large metallo-ribozymes that use divalent metal ions in folding and catalysis. The 3-terminal domain 6 contains a conserved adenosine whose 2-OH acts as the nucleophile in the first splicing step. In the hierarchy of folding, D6 binds last into the active site. In order to investigate and understand the folding process to the catalytically active intron structure, it is important to know the individual binding affinities of Mg2+ ions to D6. We recently studied the solution structure of a 27 nucleotide long domain 6 (D6-27) from the mitochondrial yeast group II intron Sc.ai5, identifying also five Mg2+ binding sites including the one at the 5-terminal phosphate residues. Mg2+ coordination to the 5-terminal di- and triphosphate groups is strongest (e.g., log KA,TP = 4.55 ± 0.10) and could be evaluated here in detail for the first time. The other four binding sites within D6-27 are filled simultaneously (e.g., log KA,BR = 2.38 ± 0.06) and thus compete for the free Mg2+ ...
Although large scale informatics studies on introns can be useful in making broad inferences concerning patterns of intron gain and loss, more specific questions about intron evolution at a finer scale can be addressed using a gene family where structure and function are well known. Genome wide surveys of tetraspanins from a broad array of organisms with fully sequenced genomes are an excellent means to understand specifics of intron evolution. Our approach incorporated several new fully sequenced genomes that cover the major lineages of the animal kingdom as well as plants, protists and fungi. The analysis of exon/intron gene structure in such an evolutionary broad set of genomes allowed us to identify ancestral intron structure in tetraspanins throughout the eukaryotic tree of life. We performed a phylogenomic analysis of the intron/exon structure of the tetraspanin protein family. In addition, to the already characterized tetraspanin introns numbered 1 through 6 found in animals, three ...
Dinoflagellates are one of the last major lineages of eukaryotes for which little is known about genome structure and organization. We report here the sequence and gene structure of a clone isolated from a cosmid library which, to our knowledge, represents the largest contiguously sequenced dinoflagellate genomic tandem gene array. These data, combined with information from a large transcriptomic library, allowed a high level of confidence of every base pair call. This degree of confidence is not possible with PCR-based contigs. The sequence contains an intron-rich set of five highly-expressed gene repeats arranged in tandem. One of the tandem repeat gene members contains an intron 26,372 bp long. This study characterizes a splice-site consensus sequence for dinoflagellate introns. Two to nine base pairs around the 3 splice site are repeated by an identical two to nine base pairs around the 5 splice site. The 5 and 3 splice sites are in the same locations within each repeat so that the ...
Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ligation, have been structurally characterized. In this study, we report the cryo-electron microscopy structures of the human post-catalytic spliceosome (P complex) and intron lariat spliceosome (ILS) at average resolutions of 3.0 and 2.9 Å, respectively. In the P complex, the ligated exon remains anchored to loop I of U5 small nuclear RNA, and the 3-splice site is recognized by the junction between the 5-splice site and the branch point sequence. The ATPase/helicase Prp22, along with the ligated exon and eight other proteins, are dissociated in the P-to-ILS transition. Intriguingly, the ILS complex exists in two distinct conformations, one with the ATPase/helicase Prp43 and one without. Comparison of these three late-stage human spliceosomes reveals mechanistic insights into exon release and spliceosome ...
The exon/intron organisation of homologous nuclear genes was compared in several yeast species. CLUSTALX multiple alignments were performed to verify the degree of conservation of the homologues and to reconstruct a virtual (scaffold) gene, exhibiting the probable ancestral intron arrangement. Intron position was defined at the nucleotide level making it possible to determine whether the intron is at an identical position (same codon and same phase) or not in the homologues.. In the cases herein illustrated, some intron positions were found divergent in homologues sharing a high degree of sequence conservation, suggesting that these positions may result either from intron sliding or intron gain events [Bon et al., 2003]. Intron sliding is defined as the relocation of a pre-existing intron over short distances in the course of gene evolution [Rogozin et al., 2000, Trends Genet., 16, 430-432]. Although it is now admitted that intron sliding by one or two bases is a real phenomenon, it remains ...
Two types of spliceosomes catalyze splicing of pre-mRNAs. The major U2-type spliceosome is found in all eukaryotes and removes U2-type introns, which represent more than 99% of pre-mRNA introns. The minor U12-type spliceosome is found in some eukaryotes and removes U12-type introns, which are rare and have distinct splice consensus signals. The U12-type spliceosome consists of several small nuclear RNAs and associated proteins. This gene encodes a 65K protein that is a component of the U12-type spliceosome. This protein contains two RNA recognition motifs (RRMs), suggesting that it may contact one of the small nuclear RNAs of the minor spliceosome. [provided by RefSeq, Jul 2008 ...
The fission yeast genome, which contains numerous short introns, is an apt model for studies on fungal splicing mechanisms and splicing by intron definition. Here we perform a domain analysis of the evolutionarily conserved Schizosaccharomyces pombe pre-mRNA-processing factor, SpPrp18. Our mutational and biophysical analyses of the C-terminal alpha-helical bundle reveal critical roles for the conserved region as well as helix five. We generate a novel conditional missense mutant, spprp18-5. To assess the role of SpPrp18, we performed global splicing analyses on cells depleted of prp18(+) and the conditional spprp18-5 mutant, which show widespread but intron-specific defects. In the absence of functional SpPrp18, primer extension analyses on a tfIId(+) intron 1-containing minitranscript show accumulated pre-mRNA, whereas the lariat intron-exon 2 splicing intermediate was undetectable. These phenotypes also occurred in cells lacking both SpPrp18 and SpDbr1 (lariat debranching enzyme), a genetic ...
BackgroundThe genome of the pico-eukaryotic (bacterial-sized) prasinophyte green alga Ostreococcus lucimarinus has one of the highest gene densities known in eukaryotes, yet it contains many introns. Phylogenetic studies suggest this unusually compact genome (13.2 Mb) is an evolutionarily derived state among prasinophytes. The presence of introns in the highly reduced O. lucimarinus genome appears to be in opposition to simple explanations of genome evolution based on unidirectional tendencies, either neutral or selective. Therefore, patterns of intron retention in this species can potentially provide insights into the forces governing intron evolution.Methodology/Principal FindingsHere we studied intron features and levels of expression in O. lucimarinus using expressed sequence tags (ESTs) to annotate the current genome assembly. ESTs were assembled into unigene clusters that were mapped back to the O. lucimarinus Build 2.0 assembly using BLAST and the level of gene expression was inferred from the
FIG. 4. Bacterial mobile group II intron-mediated gene disruption of wsfP in P. alvei CCM 2051T. (A) Screening of Cm-resistant P. alvei CCM 2051T colonies for intron insertion by in situ PCR using primers KO_wsfP_control_for_1 (→) and KO_wsfP_control_rev_1 (←). A PCR product obtained from a wild-type colony (lane 1), a PCR fragment obtained from a wsfP mutant (lane 2), and PCR products obtained from a colony containing both wild-type and intron-inserted wsfP (lane 3) are shown. (B) Schematic drawing of the wsfP gene with (bottom) and without (top) intron insertion, indicating the positions of primers KO_wsfP_control_for_1 (→) and KO_wsfP_control_rev_1 (←). ...
Exon shuffling was first introduced in 1978 when Walter Gilbert discovered that the existence of introns could play a major role in the evolution of proteins. It was noted that recombination within introns could help assort exons independently and that repetitive segments in the middle of introns could create hotspots for recombination to shuffle the exonic sequences. However, the presence of these introns in eukaryotes and absence in prokaryotes created a debate about the time in which these introns appeared. Two theories arose: the "introns early" theory and the "introns late" theory. Supporters of the "introns early theory" believed that introns and RNA splicing were the relics of the RNA world and therefore both prokaryotes and eukaryotes had introns in the beginning. However, prokaryotes eliminated their introns in order to obtain a higher efficiency, while eukaryotes retained the introns and the genetic plasticity of the ancestors. On the other hand, supporters of the "introns late" theory ...
Genetic relationships of the 17 haplotypes (introns + HEG) obtained from PSA populations were accessed through network analyses. The network exhibit three main clusters suggesting a pattern of isolation by distance for the populations analyzed. The same grouping pattern was obtained for Fst analysis. Mantels test corroborated the hypothesis indicated by the two previous analyses. Therefore, isolation by distance appears to be the basic process accounting for structure in PSA populations, manifested in a cline of HEG degeneration. Populations sampled at the southernmost end of the distribution present the entire His-Cys box motif, while the population sampled at the northernmost end of the distribution, considering the start codon proposed by Haugen et al. [4], has only eight amino acids of the HE. Distributed between these two extremes, are the intermediate-sized alleles.. The neutrality tests results for the intron without HEG indicated a fast population growth from an ancestor population with ...
Likewise, the alpha-collagen has 50 exons that range from bases and the gene is about 40, bases. Clearly two genes of the same size can have different number of introns, and introns that vary in size.. Some species will have an intron in a gene, but another species may not have an intron in the same gene. We expect that these relationships can be used to predict the anticipated exon-intron structure and proteomic complexity in non-model species with large genomes, such as pines, that may remain unsequenced for a while. We applied our findings to loblolly pine Pinus taeda L.. The obtained knowledge is also essential for understanding the genetic control of the metabolomic complexity and functionality in the studied species and the evolutionary significance of AS in general. ...
DNA is made up of different units called nucleotides. There are a variety of four different nucleotides that make up the polymer that is DNA[1]. DNA consists of two different regions, one being exons and the other introns. The regions of exons in the DNA consist of fewer nucleotides than the regions of introns and are the regions that code for proteins[2]. It is also now thought that enhancer sequences for regulation of gene transcription is not just found in introns but also exons.[3]. Exons are the coding regions of a gene and are separated by regions of introns; they are copied during transcription (along with introns) to produce pre-mRNA[4] ...
HHT is a genetically heterogeneous disease with at least three causative genes [9-15]. 15% of clinically diagnosed HHT cases cannot be explained by mutations in the coding regions or exon/intron junctions of ACVRL1, ENG, or SMAD4[19, 20]). Yet in some families, linkage data suggests ACVRL1 or ENG to be the causative gene. Therefore, non-coding regions may play a role in the disease. However, previously described mutations in ENG were located only on the coding regions and exon-intron junctions of the gene [29, 30]. So far, no 5UTR mutations or deep intronic mutations have been described. ENG promoter activity was found to be within the upstream 400 bp region from the TIS, and an area near the transcription initiation site of ENG was determined to be essential for promoter function [21, 31]. We therefore chose this critical region to analyze in our unexplained HHT cases. We have identified a 5UTR mutation (c.-127C , T) in 3 unrelated probands, 2 of which had family members evaluated for ...
The wide, but scattered distribution of group I introns in nature is a result of two processes; the vertical inheritance of introns with or without losses, and the occasional transfer of introns across species barriers. Reversal of the group I intron
TY - JOUR. T1 - Tissue-specific splicing regulator Fox-1 induces exon skipping by interfering E complex formation on the downstream intron of human F1γ gene. AU - Fukumura, Kazuhiro. AU - Kato, Ayako. AU - Jin, Yui. AU - Ideue, Takashi. AU - Hirose, Tetsuro. AU - Kataoka, Naoyuki. AU - Fujiwara, Toshinobu. AU - Sakamoto, Hiroshi. AU - Inoue, Kunio. PY - 2007/8/1. Y1 - 2007/8/1. N2 - Fox-1 is a regulator of tissue-specific splicing, via binding to the element (U)GCAUG in mRNA precursors, in muscles and neuronal cells. Fox-1 can regulate splicing positively or negatively, most likely depending on where it binds relative to the regulated exon. In cases where the (U)GCAUG element lies in an intron upstream of the alternative exon, Fox-1 protein functions as a splicing repressor to induce exon skipping. Here we report the mechanism of exon skipping regulated by Fox-1, using the hF1γ gene as a model system. We found that Fox-1 induces exon 9 skipping by repressing splicing of the downstream intron 9 ...
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The interactions established at the 5-splice site during spliceosome assembly are likely to be important for both precise recognition of the upstream intron boundary and for positioning this site in the active center of the spliceosome. Definition of the RNA-RNA and the RNA-protein interactions at the 5 splice site would be facilitated by the use of a small substrate amenable to modification during chemical synthesis. We describe a trans-splicing reaction performed in Saccharomyces cerevisiae extracts in which the 5 splice site and the 3 splice site are on separate molecules. The RNA contributing the 5 splice site is only 20 nucleotides long and was synthesized chemically. The trans-splicing reaction is accurate and has the same sequence, ATP, and Mg^2+ requirements as cis-splicing. We also report how deoxy substitutions around the 5-splice site affect trans-splicing efficiency. ...
The classification of human gene sequences into exons and introns is a difficult problem in DNA sequence analysis. In this paper, we define a set of features, called the simple Z (SZ) features, which is derived from the Z-curve features for the recognition of human exons and introns. The classification results show that SZ features, while fewer in numbers ~three in total!, can preserve the high recognition rate of the original nine Z-curve features. Since the size of SZ features is one-third of the Z-curve features, the dimensionality of the feature space is much smaller, and better recognition efficiency is achieved. If the stop codon feature is used together with the three SZ features, a recognition rate of up to 92% for short sequences of length ,140 bp can be obtained ...
In contrast to bacteria which have no introns, eukaryotes (cells with a nucleus) have introns which are intervening sequences within genes which get spliced out when genes are transcribed and are not expressed in the protein. In contrast, exons are the sequences within a gene which do get expressed and translated into protein. Intergenic DNA, as the name suggests, is DNA between genes which does not code for proteins. Hope this helps gabriel vargas md/phd References Genes VII by Benjamin Lewin ...
The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA with those of protein-coding genes for which a large body of functional information is available. A prominent feature of mammalian protein-coding genes is the high evolutionary conservation of the exon-intron structure. Comparative analysis of putative intron positions in lincRNA genes from various mammalian genomes suggests that some lincRNA introns have been conserved for over 100 million years, thus the primary and/or secondary structure of these molecules is likely to be functionally important.
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Comparative analysis of exon/intron organization of genes and their resulting protein structures is important for understanding evolutionary relationships between species, rules of protein organization, and protein functionality. We present SEDB, the Structural Exon Database, with a web interface, an application which allows users to retrieve the exon/intron organization of genes and map the location of the exon boundaries and intron phase onto a multiple structural alignment. SEDB is linked with Friend, an integrated analytical multiple sequence/structure viewer, which allows simultaneous visualization of exon boundaries on structure and sequence alignments. With SEDB researchers can study the correlations of gene structure with the properties of the encoded three-dimensional protein structures across eukaryotic organisms ...
Many introns in Drosophila and other invertebrates are less than 80 nucleotides in length, too small to be recognized by the vertebrate splicing machinery. Comparison of nuclear splicing extracts from human HeLa and Drosophila Kc cells has revealed species-specificity, consistent with the observed size differences. Here we present additional results with the 68 nucleotide fifth intron of the Drosophila myosin heavy chain gene. As observed with the 74 nucleotide second intron of the Drosophila white gene, the wild-type myosin intron is accurately spliced in a homologous extract, and increasing the size by 16 nucleotides both eliminates splicing in the Drosophila extract and allows accurate splicing in the human extract. In contrast to previous results, however, an upstream cryptic 5 splice site is activated when the wild-type myosin intron is tested in a human HeLa cell nuclear extract, resulting in the removal of a 98 nucleotide intron. The size dependence of splicing in Drosophila extracts is ...
Wragg, M., Hutton, M., Talbot, C., Busfield, F., Han, S., Lendon, C., ... Goate, A. (1996). Genetic association between intronic polymorphism in presenilin-1 gene and late-onset Alzheimers disease. Lancet, 347(9000), 509 - 512 ...
Pre-mRNA splicing and cell cycle control have independent functions for eukaryotic cells. However, these processes might be linked, because yeast proteins have been identified through genetic criteria as splicing factors and independently as essential for cell cycle progression (10). The conserved Myb-related CDC5/Cef1p proteins carry essential functions in both processes, because their genetic depletion in the fission (30) and budding (11) yeasts causes accumulation of pre-mRNAs and cell cycle arrest at G2/M. Through characterization of a novel temperature-sensitive allele of S. cerevisiae CEF1, cef1-13, we have demonstrated that G2/M cell cycle arrest results from inefficient splicing of the TUB1 pre-mRNA that encodes the major yeast α-tubulin. TUB1 intron deletion also partially suppresses the G2/M arrest observed in mutants of the splicing proteins Prp17p and Prp22p.. cef1-13 cells arrest homogeneously in G2/M prior to the first encountered anaphase when released to the restrictive ...
TY - JOUR. T1 - Genes within genes. T2 - independent expression of phage T4 intron open reading frames and the genes in which they reside.. AU - Gott, J. M.. AU - Zeeh, A.. AU - Bell-Pedersen, D.. AU - Ehrenman, Karen. AU - Belfort, M.. AU - Shub, D. A.. PY - 1988/1/1. Y1 - 1988/1/1. N2 - The td, nrdB, and sunY introns of bacteriophage T4 each contain a long open reading frame (ORF). These ORFs are preceded by functional T4 late promoters and, in the case of the nrdB intron ORF, a functional middle promoter. Expression of phage-encoded intron ORF-lacZ fusions indicates that these T4 genes are highly regulated. The lack of translation of these ORFs from early pre-mRNAs can be accounted for by the presence of secondary structures that are absent from the late RNAs. Because translation of the intron ORFs could disrupt core structural elements required for pre-mRNA splicing, such regulation may be necessary to allow expression of the genes in which they reside.. AB - The td, ...
Fig. S1. Predicted secondary structures of the tmRNA and associated group I intron in the chromosome of B. pseudofirmus OF4. The structures were predicted by alignment with the homologous sequences in C. botulinum (Williams, 2002) followed by manual rearrangements. Nucleotides that are conserved in both sequence and structural position in B. pseudofirmus and C. botulinum are coloured in red. The various subdomains of the tmRNA (P1-P12) and group I intron (P1-P9) are indicated. In addition, for the tmRNA, the regions forming pseudoknots are labelled (Ψ1 and Ψ4) the nucleotides encoding the proteolysis tag are underlined; for the intron, flanking exon sequences are in lower case letters.. Fig. S2. Schematic representation of the 4.5 kb group II twintron in the pBpOF4-01 plasmid of B. pseudofirmus OF4. The twintron consists of two nested group II intron retroelements, where the innermost intron (in grey) encoding the reverse transcriptase (RT) BpOF4_20224 is inserted at the catalytic site of ...
Saitta B., Wang Y.-M., Renkart L., Zhang R.-Z., Pan T.-C., Timpl R., Chu M.-L.. The alpha 1(VI) and alpha 2(VI) chains, two of the three constituent chains of type VI collagen, are highly similar in size and domain structure. They are encoded by single-copy genes residing in close proximity on human chromosome 21. To study the evolution of the type VI collagen genes, we have isolated and characterized genomic clones coding for the triple-helical domains of the human alpha 1(VI) and alpha 2(VI) chains, which consist of 336 and 335 amino acid residues, respectively. Nucleotide sequencing indicates that, in both genes, the exons are multiples of 9 bp in length (including 27, 36, 45, 54, 63, and 90 bp) except for those encoding for regions with triple-helical interruptions. In addition, the introns are positioned between complete codons. The most predominant exon size is 63 bp, instead of 54 bp as seen in the fibrillar collagen genes. Of particular interest is the finding that the exon structures of ...
Lucero Rogel. PREP Program. Lab Group: Alan Zahler. PREP Research: The Zahler lab works to investigate the mechanism of RNA splicing by utilizing C. elegans as a model organism. Accurate splicing of pre-mRNA is a critical step in the gene expression pathway in eukaryotes carried out by a large ribonucleoprotein complex known as the spliceosome. The spliceosome consists of 5 RNAs (U1, U2, U4, U5, and U6) that assemble onto the pre-mRNA by recognizing conserved sequence elements that define the beginning and ends of introns, known as 5 and 3 splice sites. To facilitate the interactions between the pre-mRNA and the 5 RNAs, over 150 proteins are employed to aid in the process. Currently in the lab, I am working on elucidating the role of spliceosomal protein SNRP-27 in 5 splice site selection by uncovering differential interactions that a mutant and wild type form of this factor have with the splicing machinery.. Undergraduate Major: Biochemistry and Molecular Biology. Undergraduate Institution: ...
This study documents the effect of body mass on the size and strength of draglines produced by the orb-weaving spider Araneus diadematus and the jumping spider Salticus scenicus. Silk samples obtained from individuals spanning the range from first-instar juveniles to gravid adults were tested to determine both the properties of the silk material and the strength and static safety factor of the draglines produced by each individual spider. Analysis of material properties indicates that the tensile strength and extensibility of the silks employed by each species are identical over the entire size range of the species. Analysis of the breaking forces for individual draglines, however, indicates that the draglines scale allometrically with the spiders body mass. For Araneus, breaking force (N) scales with body mass (kg) as Fmax=11.2M0.786, and the static safety factor (SBW=Fmax/Mg) scales as SBW=1.14M-0.214. For Salticus, Fmax=0.363M0.66 and SBW=0.037M-0.34. Thus, static safety factors decrease as ...
Somatically acquired mutations in components of the RNA processing pathway in CLL. Presented is an overview illustrating the individual components of the RNA-processing pathway, with those components identified as being somatically mutated highlighted (*) and the mutated protein listed in red. Initially, nascent pre-mRNA transcripts undergo 5′ capping and binding of the cap-binding complex (CBC), followed by the formation of the major spliceosome, the machinery responsible for the removal of pre-mRNA introns via a stepwise mechanism. Initial assembly steps include formation of pre-spliceosome complex A (top left nuclear complex) involving recognition of the 5′ splice site by U1 snRNP (an interaction stabilized by members of the serine-arginine-rich (SR) protein family) and recognition of the 3′ SS region by the U2 Auxiliary factor U2AF and by U2snRNP. U2AF binds to the intronic polypyrimidine tract and 3′SS, and facilitates binding of U2 snRNP to the branch-point sequence. Stable U2 ...
By studying a mutation that causes specific defects in lymphocyte cytotoxicity, we have delineated a critical role for STAT4 in regulating Munc13-4 expression upon cytotoxic lymphocyte differentiation and identified a novel, evolutionarily conserved promoter within intron 1 of UNC13D. The intronic c.118-308C,T mutation causative of FHL3 abolished an ELF1-binding site that is necessary for the recruitment of STAT4 and BRG1 as well as the acquisition of histone marks permissive for transcription. TCR stimulation of naive CD8+ T cells led to robust induction of Munc13-4, STAT4, and BRG1, and knockdown of STAT4 abrogated induction of Munc13-4 expression. Our data show that the UNC13D intronic sequence can act both as an alternative promoter and as a general enhancer, promoting Munc13-4 expression upon cytotoxic lymphocyte differentiation.. A surprising finding from our analysis of lymphocyte subsets was that Munc13-4 expression levels are selectively up-regulated upon cytotoxic lymphocyte ...
Pre-mRNA splicing or the removal of introns from precursor messenger RNAs depends on the accurate recognition of intron sequences by the plant splicing machinery. The major components of this machinery are small nuclear ribonucleoprotein protein particles (snRNPs) which consist of snRNAs and snRNP proteins. We have analysed various aspects of intron sequence and structure in relation to splice site selection and splicing efficiency and we have cloned snRNA genes and a gene encoding the snRNP protein, U2B". In the absence of an in vitro splicing system for plants, transient expression in protoplasts and stable plant transform ations have been used to analyse splicing of intron constructs. We aim to address the function of the UsnRNP-specific protein, U2B", via the production of transgenic plants expressing antisense U2B" transcripts and epitope-tagged U2B" protein. In addition, we have cloned genes encoding other proteins which potentially interact with RNA, such as RNA helicases, and strategies ...
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Prot_map - a fast tool to align proteins with genome and reconstruct exon- intron structure has been developed recently and available to run at: http://sun1.softberry.ru/berry.phtml? topic=prot_map&group=programs&subgroup=xmap Prot_map program maps a set of protein sequences onto genomic sequence producing gene structures and the corresponding alignments of coding exons with the similar or identical protein queries. Prot_map uses a genomic sequence and a set of protein sequences as its input parameters. Prot_map reconstructs the gene structure on the base of identical or similar protein instead of a set of unordered alignment fragments that generated the Blast program. The program is very fast, and the produces gene structure similar with the accuracy of slow Genewise program (that practically required knowing the protein genomic location) (Table 1). You can further significantly improve the accuracy of gene reconstruction with Fgenesh+ program by using the results of Prot_map (i.e.a fragment of ...
In the current study, we applied cDNA cloning and RNA-Seq methods to identify two alternative CYP3A4 mRNA transcripts, one of which contained partial intron-6 retention and the other with a shorter 3′-UTR.. The CYP3A4 mRNA transcript with partial intron-6 retention can potentially be translated into a novel protein with a shortened amino acid sequence as a result of a translational stop codon in intron 6. However, the absence of a heme-binding signature in the encoded polypeptide precludes a catalytically active protein. Proportion of this transcript in all examined samples is less than 2% of total CYP3A4 mRNA. Therefore, its influence on CYP3A4 function is considered to be limited; as a result, we did not investigate function of this transcript in the current study. Although RNA-Seq also showed faint peaks in intron 11, Cufflinks did not assemble a transcript with intron-11 retention. Thus, the possible existence of intron-11 retention cannot be excluded based on the current evidence, and ...
Monogenic diseases make excellent models for the study of gene functions and basal cellular mechanisms in humans. The aim of this thesis was to elucidate how genetic mutations affect the basal cellular mechanisms in the monogenic diseases Nerve growth factor (NGF) dependent pain insensitivity and Iron-Sulphur cluster assembly protein U (ISCU) myopathy.. NGF dependent pain insensitivity is a rare genetic disorder with clinical manifestations that include insensitivity to deep pain, development of Charcot joints, and impaired temperature sensation but with no effect on mental abilities. The disease is caused by a missense mutation in the NGFβ gene causing a drastic amino acid substitution (R221W) in a well-conserved region of the protein. NGF is secreted in limited amounts by its target tissues and is important for the development and maintenance of the cholinergic forebrain neurons as well as the sensory and sympathetic neurons. To reveal the underlying mechanisms of disease we performed ...
Andolfatto took a different approach toward identifying functional non-coding sequences. He looked at coding and non-coding sequences from twelve D. melanogaster individuals and one D. simulans individual from the X-chromosome. He divided the non-coding sequences into 5 classes: 5 UTRs, 3 UTRs, introns, intergenic sequences within 2kb of a gene, and intergenic sequences more than 4kb from a gene. He then calculated a variety of population genetics statistics based on these sequences to determine if any of the non-coding DNA displays signatures of natural selection. I would expect that the UTRs (sequences that are transcribed, but not translated) are under more functional constraint than the intergenic regions and probably also display more signatures of positive selection. I also would expect that the introns would be constrained and have more evidence of positive selection (due to regulatory elements located within), and that the intergenic sequences located closer to genes are under more ...
Five small nuclear RNAs (snRNAs) (U1, U2, U4, U5, U6) found in the nucleus of eukaryotic cells mediate the excision of introns from pre-mRNAs. The structure and expression of the snRNA components have been well documented in animal and yeast systems but little information has existed on the structure and expression of the splicesomal snRNAs involved in plant intron excision. To further define the snRNA components involved in intron excision, a clone library has been constructed from anti-m$\sb3$G immunoprecipitated snRNAs expressed in pea seedlings. cDNA clones representing U1, U2, U4, and U5 snRNAs expressed in seedling tissue have been isolated and sequenced. Comparison of the pea snRNA variants with other organisms suggest that functionally important primary sequences are conserved phylogenetically even though the overall sequences have diverged substantially. Structural variations occur in regions required for U1-specific protein binding suggesting that alternate U1 snRNP particles may exist ...
RNA is a fundamental molecule that codes for protein and controls gene expression, playing a part in regulating many cell responses and vital processes. The genetic information contained in premature messenger RNA (mRNA), before being converted to proteins, needs to be processed and cleared of its non-coding sections, known as introns. In several simpler organisms, this key process is carried out by group II introns, enzymes entirely made up of RNA (different from the true protein enzymes) called ribozymes that are able to self-cleave by removing themselves from the mRNA filament and thereby promoting RNA maturation. A SISSA/CNR-IOM Democritos study carried out in collaboration with the École Polytechnique Fédérale de Lausanne (EPFL) gives a detailed account of the cleavage reaction, so far totally unknown. The mechanism is thought to be similar to that of the human spliceosome whose malfunctioning can lead to several diseases among which neurodegeneration and cancer. The study has been ...
Inflammation involves timed gene expression, suggesting that the fine-tuned onset, amplitude, and termination of expression of hundreds of genes is of critical importance to organismal homeostasis. Recent study of post-transcriptional regulation of inflammatory gene expression led to the suggestion of a regulatory role for pre-mRNA splicing. Here, using a hybrid capture approach to purify incompletely spliced, chromatin-associated pre-mRNAs, we use deep sequencing to study pre-mRNA splicing of the NF-kB transcriptome. By freezing transcription and examining subsequent splicing of complete transcripts, we find many introns splice tens to hundreds of times slower than average. In many cases, this is attributable to poor splice donor sequences that are evolutionarily conserved. When these introns were altered by ~2 base pairs to yield stronger splice donors, gene expression levels increased markedly for several genes in the context of a reporter system. We ...
The large majority of genes encoded by humans and other metazoans contain introns. In general, mRNAs containing introns give rise to a higher level of the encoded protein than do the equivalent intronless, cDNA-derived mRNAs. The mechanisms underlying this difference are complex because splicing can strongly influence not only the efficiency of mRNA 3′ end formation but also mRNA stability and even translation (Ryu and Mertz, 1989; Niwa et al., 1990; Matsumoto et al., 1998). Nevertheless, for most human genes, splicing is not essential for detectable mRNA and protein synthesis. In fact, a recent survey of 15 genes showed that the presence of an excisable intron enhanced gene expression in human cells by an average of 6.3±4.7 fold with a range of from 1.5- to over 20-fold (S. Lu and B. R. Cullen, unpublished).. The first evidence suggesting that splicing also enhances the efficiency of mRNA export came from the demonstration that several intron-containing mRNAs are exported more efficiently ...
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Here we present a collection markers based on single nucleotide polymorphisms (SNPs) mined from expressed sequence tags (EST) available at The SOL Genomics Network,SGN(Unigene set version 200607). These markers are designed to detect inter-specific SNPs among three tomato species: Solanum lycopersicum, Solanum habrochaites and Solanum pennellii. Indels have not been included in the database but are available on the downloads page.. For each SNP we designed a set of primers that take into account predicted intron positions and provide restriction endonucleases that can be used to detect the polymorphism. Please note that for certain SNPs that are close to introns or to the end of the sequences our pipeline fails to design primers. In those cases we recommend manual development of primers based on the given estimated allele sequences and intron positions.. If you plan to use any of the molecular markers made available through this website please cite our publication. More information at How to ...
When using the safety factor approach, confidence intervals are not given and the degree of protection is usually unknown. Because of the somewhat arbitrary nature of safety factors, their application must be appropriate to the particular purpose and documentation describing the logic used in selecting a particular number should always be provided. The use of the same safety factor (e.g., 10) in all cases has been discouraged by several regulatory and scientific bodies in favor of case-specific values. In particular, the scale, frequency, severity, and potential for long-term consequences of the environmental insult must be taken into account. Providing protection against an acute spill that is easily remediated may require less precaution (and therefore smaller safety factors) than the permitted continual release of a pollutant discharge. The decision to use a safety factor approach, and the eventual selection of the appropriate number, is more a management decision than a scientific ...
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Step 2 will create the upstream sequence, intronic sequences and the downstream sequence, as well as exon lengths tables in html and text format, in which the exon start and end positions (in c. and g. numbering) and exon and intron lengths are provided. These are all saved in the refseq directory. Step 2 will also create the input for step 3 for you. Optionally, you can also have it create a file in GenBank format. You will then have to fill in the appropriate transcript_id, protein_id and db_xref numbers. The created file will meet the minimum requirements for uploading in Mutalyzer ...
This chapter reviews what is known about the mechanism of precursor tRNA splicing: (i) the tRNA substrates for the splicing reaction, (ii) the enzymes involved in removing the introns to form the mature tRNA, (iii) interactions between these enzymes and their tRNA substrates and cofactors, (iv) the organization of tRNA splicing in the nucleus, (v) the identity of splicing mutants that affect the enzymatic machinery, (vi) current knowledge about the differences and similarities of tRNA splicing in systems of various organisms, and (vii) the possible function of tRNA introns.
The current South African Code of Practice for structural use of masonry uses four partial safety factors gm, for materials depending on construction control and quality control. With the boom in the construction industry, new entrants in the industry lack skills and the construction quality, particularly of masonry structures, is compromised. This has been proven by a number of structural failures and poor workmanship in the home building industry. However, the values of gm are based on the British Standards with some slight modifications to take into account local conditions. In this paper, focus is on establishing the reliability level as prescribed in the current code. The parametric calibration is based on current stochastic models and on statistical data collated by the National Home Building Registration Council (NHBRC) using a well researched quality assessment tool (Building Quality Index for Houses). Highlights are also made on the current work-in-progress in testing masonry walls so ...
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Toxicity can be measured by the effects on the target (organism, organ, tissue or cell). Because individuals typically have different levels of response to the same dose of a toxin, a population-level measure of toxicity is often used which relates the probabilities of an outcome for a given individual in a population. One such measure is the LD50. When such data does not exist, estimates are made by comparison to known similar toxic things, or to similar exposures in similar organisms. Then "safety factors" are added to account for uncertainties in data and evaluation processes. For example, if a dose of toxin is safe for a laboratory rat, one might assume that one tenth that dose would be safe for a human, allowing a safety factor of 10 to allow for interspecies differences between two mammals; if the data are from fish, one might use a factor of 100 to account for the greater difference between two chordate classes (fish and mammals). Similarly, an extra protection factor may be used for ...
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AKs Rambling Thoughts: How Smart is the Cell? Part II: The Gene Activation network as an Analog ComputerAK's Rambling Thoughts: How Smart is the Cell? Part II: The Gene Activation network as an Analog Computer

The classic description of Transcriptional regulation involves a laundry list of elements such as promoters, enhancers, ... silencers, insulators, or locus control regions (LCR). (A good description based on these terms is given in Transcriptional ... A few example consensus sequences are found in table 2 from The Evolution of Transcriptional Regulation in Eukaryotes. This ... The Evolution of Transcriptional Regulation in Eukaryotes Energy-dependent fitness: A quantitative model for the evolution of ...
more infohttp://artksthoughts.blogspot.com/2009/04/how-smart-is-cell-part-ii-gene.html

Currículo do Sistema de Currículos Lattes (Antonio Cechelli de Mattos Paiva)Currículo do Sistema de Currículos Lattes (Antonio Cechelli de Mattos Paiva)

Transcriptional regulation of the rat bradykinin B2 receptor gene: Identification of a silencer element. Molecular Pharmacology ... PESQUERO, J. B. ; LINDSEY, C. J. ; PAIVA, A. C. M. ; GANTEN, D. ; BADER, M. . Transcriptional Regulatory Elements In The Rat ... BAPTISTA, H. A. ; AVELLAR, M. C. ; PAIVA, A. C. M. ; BADER, M. ; PESQUERO, J. B. . Transcriptional regulation of rat bradykinin ... Molecular structure and transcriptional regulation by nuclear factor-kappaB of the mouse kinin B1 receptor gene. Biological ...
more infohttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?metodo=apresentar&id=K4721347H4

Currículo do Sistema de Currículos Lattes (Ronaldo de Carvalho Araújo)Currículo do Sistema de Currículos Lattes (Ronaldo de Carvalho Araújo)

Transcriptional Regulation of the Rat Bradykinin B2 Receptor Gene: Identification of a Silencer Element. MOLECULAR PHARMACOLOGY ... ARA JO, R. C.; BAPTISTA, H. A. ; BADER, M. ; PESQUERO, J. B. . Mechanisms in the transcriptional regulation of rat bradykinin ... Molecular structure and transcriptional regulation by nuclear factor-κB of the mouse kinin B1 receptor gene. Biological ... Molecular structure and transcriptional regulation of mouse kinin B1 receptor gene. In: FESBE, 2001, Caxambu. Programa e ...
more infohttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4797070P5

Silencer (genetics) - WikipediaSilencer (genetics) - Wikipedia

Ogbourne, Steven; Toni Antalis (1998). "Transcriptional control and the role of silencers in transcriptional regulation in ... silencer elements target the assembly of GTFs, necessary for transcription of the gene. These silencer elements are mostly ... which are the classical silencer element and the non-classical negative regulatory element (NRE). In classical silencers, the ... Among the many silencer elements and proteins, REST/NSRF is an important silencer factor that has a variety of impacts, not ...
more infohttps://en.wikipedia.org/wiki/Silencer_(genetics)

Eukaryotic and prokaryotic gene..."Eukaryotic and prokaryotic gene...

Ogbourne, Steven; Antalis, Toni M. (1998). "Transcriptional control and the role of silencers in transcriptional regulation in ... Maston, G. A.; Evans, S. K.; Green, M. R. (2006). "Transcriptional Regulatory Elements in the Human Genome". Annual Review of ... Wray, G. A. (2003). "The Evolution of Transcriptional Regulation in Eukaryotes". Molecular Biology and Evolution 20 (9): 1377- ... Common gene structural elements are colour-coded by their function in regulation, transcription, or translation. ...
more infohttps://en.wikiversity.org/wiki/WikiJournal_of_Medicine/Eukaryotic_and_prokaryotic_gene_structure

Gene structure - WikipediaGene structure - Wikipedia

Ogbourne, Steven; Antalis, Toni M. (1998). "Transcriptional control and the role of silencers in transcriptional regulation in ... Maston, G. A.; Evans, S. K.; Green, M. R. (2006). "Transcriptional Regulatory Elements in the Human Genome". Annual Review of ... Each element has a specific function in the multi-step process of gene expression. The sequences and lengths of these elements ... Maston, Glenn A.; Evans, Sara K.; Green, Michael R. (2006). "Transcriptional Regulatory Elements in the Human Genome". Annual ...
more infohttps://en.wikipedia.org/wiki/Gene_structure

Laboratory ScientistsLaboratory Scientists

Mechanisms of positive and negative transcriptional regulation, Enhancer and silencer elements that modulate gene expression, ... Epigenetic mechanisms of transcription regulation, Cancer-specific transcription factor signatures, Molecular biology, Cancer ...
more infohttps://www.hopkinsmedicine.org/kimmel_cancer_center/experts/Laboratory_Scientists/

Transcriptional Regulation of the Human Mimecan Gene  | IOVS | ARVO JournalsTranscriptional Regulation of the Human Mimecan Gene | IOVS | ARVO Journals

The first intron of human mimecan contains enhancer and silencer elements. Reporter gene transfections demonstrated that ... Transcriptional Regulation of the Human Mimecan Gene You will receive an email whenever this article is corrected, updated, or ... ES Tasheva; Transcriptional Regulation of the Human Mimecan Gene . Invest. Ophthalmol. Vis. Sci. 2002;43(13):3194. ... the human mimecan promoter region and identify the cis-elements and transcription factors that play a role in the regulation of ...
more infohttps://iovs.arvojournals.org/article.aspx?articleid=2420437

A discrete transcriptional silencer in the bam gene determines asymmetric division of the Drosophila germline stem cell |...A discrete transcriptional silencer in the bam gene determines asymmetric division of the Drosophila germline stem cell |...

Regulation of elements controlling bam transcription. The transcriptional silencer in the bam 5′-UTR is active in the cells in ... We find that one transcriptional control element in the 5′-UTR acts as a silencer in the GSC and bam transcriptional silencing ... Defining the limits of the silencer element. In order to delineate the silencer element more precisely, we tested the ability ... We confirmed the transcriptional role of the silencer element by constructing a [bamP-SErev-GFP] transgene that carried an ...
more infohttps://dev.biologists.org/content/130/6/1159?ijkey=14ca00feee553d0c529cc1f9e267a6777a8d54e5&keytype2=tf_ipsecsha

Silencer (genetics) - WikipediaSilencer (genetics) - Wikipedia

"Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes" (PDF). Biochem. J. 331 (1): 1-14 ... silencer elements target the assembly of GTFs, necessary for transcription of the gene. These silencer elements are mostly ... which are the classical silencer element and the non-classical negative regulatory element (NRE). In classical silencers, the ... Among the many silencer elements and proteins, REST/NSRF is an important silencer factor that has a variety of impacts, not ...
more infohttps://en.wikipedia.org/wiki/Silencer_%28DNA%29

Plus itPlus it

Ko JL, Liu HC, Minnerath SR, and Loh HH (1998) Transcriptional regulation of mouse μ-opioid receptor gene. J Biol Chem 273: ... cAMP response element-binding protein (Lee and Lee, 2003), and neurorestrictive suppressor element (Andria and Simon, 2001). ... Kim CS, Hwang CK, Choi HS, Song KY, Law PY, Wei LN, and Loh HH (2004) Neuron-restrictive silencer factor (NRSF) functions as a ... Lee PW and Lee YM (2003) Transcriptional regulation of μ opioid receptor gene by cAMP pathway. Mol Pharmacol 64: 1410-1418. ...
more infohttp://molpharm.aspetjournals.org/content/68/2/279

Characterization of the promoter of the gene encoding human tripeptidyl-peptidase II and identification of upstream silencer...Characterization of the promoter of the gene encoding human tripeptidyl-peptidase II and identification of upstream silencer...

The CCAAT-boxes appear to be most important for the transcriptional activation. Furthermore, several silencer element were ... transcriptional regulation, NF-Y, USF-1, Oct-1, EMSA, pGL3 National Category Medical and Health Sciences Identifiers. URN: urn: ... Several silencer elements were identified and we also showed that Oct-1 binds to one of these elements. Thus, this ... 1. Tripeptidyl-Peptidase II: Structure, Function and Gene Regulation. Open this publication in new window or tab ,,Tripeptidyl- ...
more infohttp://uu.diva-portal.org/smash/record.jsf?pid=diva2:169309

Gene Regulation Flashcards by Anna  Myrmoe | BrainscapeGene Regulation Flashcards by Anna Myrmoe | Brainscape

Regulation at the transcriptional level is upstream or downstream from the +1 site? ... Each gene has a specific set of regulatory elements that are bound by specific regulatory proteins. -More efficient because no ... Proximal elements---close. -Distal elements---far. 1. Enhancers. 2. Silencers 13 Regulatory Elements ... Study Gene Regulation flashcards from Anna Myrmoe ... Cis regulating element. -When bound, increase transcription of ...
more infohttps://www.brainscape.com/flashcards/gene-regulation-2781539/packs/4629025

Regulation of gene expression - WikipediaRegulation of gene expression - Wikipedia

Transcriptional *Gene regulatory network. *cis-regulatory element. *lac operon. *Post-transcriptional *sequestration (P-bodies) ... Enhancers are much more common in eukaryotes than prokaryotes, where only a few examples exist (to date).[3] Silencers are ... Post-transcriptional regulation[edit]. Main article: Post-transcriptional regulation. After the DNA is transcribed and mRNA is ... Up-regulation and down-regulation[edit]. Up-regulation is a process that occurs within a cell triggered by a signal ( ...
more infohttps://en.wikipedia.org/wiki/Gene_regulation

Plus itPlus it

2011) Transcriptional and epigenetic regulation of opioid receptor genes: present and future. Annu Rev Pharmacol Toxicol 51:75- ... cAMP response-element binding protein (CREB)] and negative regulatory factors [e.g., neuron-restrictive silencer factor, ... 2010) Up-regulation of the mu-opioid receptor gene is mediated through chromatin remodeling and transcriptional factors in ... 2003) Mouse mu opioid receptor distal promoter transcriptional regulation by SOX proteins. J Biol Chem 278:3742-3750. ...
more infohttp://molpharm.aspetjournals.org/content/91/4/357

KAKEN - Research Projects | Transcriptional regulation of the human ABO histo-blood group genes is dependent on the negative...KAKEN - Research Projects | Transcriptional regulation of the human ABO histo-blood group genes is dependent on the negative...

... suggesting that transcription from the ABO proximal promoter is in part controlled by silencer elements just upstream of the ... Transcriptional regulation of the human ABO histo-blood group genes is dependent on the negative regulation through the N box ... Journal Article] Transcriptional regulation of the human ABO histo-blood group genes in dependent on the N box upstream of the ... Journal Article] Transcriptional regulation of the human ABO histo-blood group genes is dependent on the N box upstream of the ...
more infohttps://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-15590575/

Mechanisms of Breast Cancer in Shift Workers: DNA Methylation in Five Core Circadian Genes in Nurses Working Night ShiftsMechanisms of Breast Cancer in Shift Workers: DNA Methylation in Five Core Circadian Genes in Nurses Working Night Shifts

Transcriptional regulation is a complex process, limited not only to cis-acting elements but also to trans-acting elements such ... as enhancers, silencers, insulators and locus specific regions, and may involve several regions and CpG islands [48] not only ... Transcriptional regulatory elements in the human genome. Ann Rev Genom Hum Genet. 2006;7:29-59 ... CLOCK is a substrate of SUMO and sumoylation of CLOCK upregulates the transcriptional activity of estrogen receptor-alpha. ...
more infohttp://www.jcancer.org/v08p2876.htm

The αIIbβ3 integrin and GPIb-V-IX complex identify distinct stages in the maturation of CD34+cord blood cells to megakaryocytes...The αIIbβ3 integrin and GPIb-V-IX complex identify distinct stages in the maturation of CD34+cord blood cells to megakaryocytes...

The tissue-specific transcriptional regulation of the megakaryocytic glycoprotein IIb gene is controlled by interactions ... Detailed analysis of the GPIIb gene promoter has revealed the importance of Ets and GATA elements for transcription in the ... 34point to a similar role of GATA and Ets in the transcription of these proteins and the presence on the GPV gene of a silencer ... The time course of cell surface markers was typical for MK differentiation with down-regulation of CD34 and up-regulation of ...
more infohttp://www.bloodjournal.org/content/96/13/4169?ijkey=ca4889ed9599acd488c1aedf422c8548646fac56&keytype2=tf_ipsecsha&sso-checked=true

A core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes | PNASA core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes | PNAS

Transcriptional Regulation of the Albumin Gene Depends on the Removal of Histone Methylation Marks by the FAD-Dependent ... of neuron-specific genes through the cis-regulatory element known as the repressor element 1 or neural restrictive silencer ( ... The Repressor Element Silencing Transcription Factor (REST)-mediated Transcriptional Repression Requires the Inhibition of Sp1 ... The basic helix loop helix domain of maize R links transcriptional regulation and histone modifications by recruitment of an ...
more infohttp://www.pnas.org/content/99/11/7420

Transcriptional regulation in helper versus cytotoxic-lineage decision. - Semantic ScholarTranscriptional regulation in helper versus cytotoxic-lineage decision. - Semantic Scholar

CD4-CD8 lineage commitment is regulated by a silencer element at the ThPOK transcription-factor locus.. *Xi He. , Kyewon Park. ... Transcriptional regulation in helper versus cytotoxic-lineage decision.. *. Ichiro Taniuchi. *. Published. 2009. in Current ... Cascading suppression of transcriptional silencers by ThPOK seals helper T cell fate. *Sawako Muroi. , Yoshinori Naoe. , +5 ... article{Taniuchi2009TranscriptionalRI, title={Transcriptional regulation in helper versus cytotoxic-lineage decision.}, author ...
more infohttps://www.semanticscholar.org/paper/Transcriptional-regulation-in-helper-versus-cytoto-Taniuchi/64359d00ab8cee23a95898aa25d6ce2bca7ccb2c

DiVA - Search resultDiVA - Search result

Transcriptional regulation of the human type X collagen gene expression.1996In: Annals of the New York Academy of Sciences, ... Localization of silencer and enhancer elements in the human type X collagen gene.1997In: Journal of Cellular Biochemistry, ISSN ... Regulatory elements of the human type X collagen gene are located upstream of the region where the repetitive element is ... to the heat shock element of the hsp70 gene or formation of nuclear HSF1 granules, revealing a lack of transcriptional ...
more infohttp://umu.diva-portal.org/smash/resultList.jsf?af=%5B%5D&aq=%5B%5B%7B%22personId%22%3A%22authority-person%3A62693+OR+0000-0002-6181-9904%22%7D%5D%5D&aqe=%5B%5D&aq2=%5B%5B%5D%5D&language=en&query=

Repressor element-1 silencing transcription factor/neuronal restrictive silencer factor (REST/NRSF) can regulate HSV-1...Repressor element-1 silencing transcription factor/neuronal restrictive silencer factor (REST/NRSF) can regulate HSV-1...

... the HSV-1 DNA sequence for potential regulatory elements identified a Repressor Element-1/Neuronal Restrictive Silencer Element ... We predicted that the Repressor Element Silencing Transcription Factor/Neuronal Restrictive Silencer Factor (REST/NRSF) ... Coulson JM: Transcriptional regulation: cancer, neurons and the REST. Curr Biol 2005,15(17):R665-668. 10.1016/j.cub.2005.08.032 ... Regulation of the cholinergic gene locus by the repressor element-1 silencing transcription factor/neuron restrictive silencer ...
more infohttps://virologyj.biomedcentral.com/articles/10.1186/1743-422X-4-56

Gene Report for G00002407 - Genes2Cognition Neuroscience Research ProgrammeGene Report for G00002407 - Genes2Cognition Neuroscience Research Programme

The transcriptional start site was mapped to a G residue 74 base pairs 5 of the ATG initiation codon. A TATA box-like element ... Using deletion fragments of the human 5-flanking region we have shown the presence of putative silencer elements in the -220 ... These findings indicate that complex mechanisms control the transcriptional regulation of TN gene. ... This region contains an atypical nucleotide recognition element for the Smad family of transcriptional regulators. A DNA ...
more infohttp://www.genes2cognition.org/db/Gene/G00002407

Histone deacetylase inhibition-mediated neuronal differentiation of multipotent adult neural progenitor cells | PNASHistone deacetylase inhibition-mediated neuronal differentiation of multipotent adult neural progenitor cells | PNAS

The protein NRSF/REST binds to the neuron-restrictive silencer element sequence to mediate transcriptional repression of target ... It is becoming increasingly apparent that chromatin accessibility plays a key role in the transcriptional regulation of cell- ... Transcriptional coactivators, such as CREB (cAMP-responsive element-binding protein)-binding protein/p300 and its associated ... Recent work examined the role of HDAC-dependent repression of neuron-restrictive silencer element-containing, neuron-specific ...
more infohttp://www.pnas.org/content/101/47/16659

Adult Stage γ-Globin Silencing Is Mediated by a Promoter Direct Repeat Element | Molecular and Cellular BiologyAdult Stage γ-Globin Silencing Is Mediated by a Promoter Direct Repeat Element | Molecular and Cellular Biology

We also examined the role of the CCTTG repeat motifs in Aγ-globin transcriptional regulation. These analyses showed that γ- ... These results therefore demonstrate that the DR sequence is a potent definitive stage-specific γ-globin gene silencer element ... Synergistic regulation of human beta-globin gene switching by locus control region elements HS3 and HS4. Genes Dev. 9:3083-3096 ... To evaluate the contribution of these hypothetical silencers to γ-globin regulation, we generated point mutations that ...
more infohttps://mcb.asm.org/content/25/9/3443?ijkey=9a7c2f281d03fb3388cb846606e8c6a0628cc48d&keytype2=tf_ipsecsha
  • Some of these modifications that regulate gene expression are inheritable and are referred to as epigenetic regulation . (wikipedia.org)
  • In this study, we demonstrate that MOR epigenetic regulation requires multiple coordinated signals converging at the MOR promoter, involving mitogen-activated protein kinase (MAPK) activation and mitogen- and stress-activated protein kinase 1 (MSK1)-ranges of intracellular signaling pathways similar to those activated by opioid agonists. (aspetjournals.org)
  • In summary, our data suggest that epigenetic regulation of CLOCK , BMAL1, CRY1 and PER1 may contribute to breast cancer in shift workers. (jcancer.org)
  • However, the epigenetic regulation of CD4 gene in chicken and its relationship with any virus infection are still unclear. (biomedcentral.com)
  • Features of DNA methylation in plants, including CG, CHG and CHH (H being A, T or C) methylation, are discussed in the review "Epigenetic Regulation of Gene Expression in Insects and Plants," Genomic DNA is packaged in higher structures (see page 8, Figure 2). (epigenie.com)
  • PESQUERO, J B . Molecular structure and transcriptional regulation by nuclear factor-kappaB of the mouse kinin B1 receptor gene. (cnpq.br)
  • Using molecular, biochemical and genetic analysis I am currently studying the promoter elements of Dpp terget genes and searching for coactivators and corepressors involved in their regulation. (nyu.edu)
  • This review focuses on some of the many applications of molecular cut-and-paste tools for the manipulation of promoters and transcription factors leading to the understanding of crucial aspects of transcriptional regulation. (mdpi.com)
  • However, tight molecular regulation allows for rapid COX-2 expression and increased prostaglandin synthesis when necessary. (rupress.org)
  • Both processes (going from no expression to basal expression, and going from basal to activated expression) are part of transcriptional activation , which is currently an area of intense investigation in molecular genetics. (psu.edu)
  • This process results from the activity of many transcriptional regulators, expressed as the result of cell-autonomous and intercellular interactions. (jneurosci.org)
  • mRNAs involved in the definition of different macrophage activation phenotypes share elements of RBP recognition rendering them amenable to ribonomic regulation. (wiley.com)
  • Nova‐1 regulates alternative splicing of pre‐mRNAs encoding the inhibitory neurotransmitter receptor subunits GABA A Rγ2 and GlyRα2 by directly binding intronic elements, resulting in enhancement of exon inclusion. (embopress.org)
  • The 'antagonistic' model of an inflammatory post‐transcriptional regulon in macrophages predicts that RNPs can be assembled by RNA activators (i.e. (wiley.com)
  • For instance, for some genes the former could require that the strong negative effect of silencing chromatin be removed, whereas the latter could involve covalent modification of particular transcriptional activators. (psu.edu)
  • Changes in chromatin structure and roles for transcriptional activators have been proposed in both processes, so in fact there may be more similarity than one would have supposed initially. (psu.edu)
  • It controls the cell fates along the dorsal-ventral axis of the embryo and anterior-posterior patterning of the adult appendages in a concentration dependent manner by eliciting differential transcriptional response from its target genes. (nyu.edu)
  • We are also investigating the mechanism of negative regulation of Dpp target genes by the gene brinker with a goal to uncover the general principles governing gene response to the embryonic morphogens. (nyu.edu)
  • The ER subtypes have different tissue distribution ( 22 ) and exert, as homodimers or heterodimers, transcriptional regulation of different target genes through their binding to estrogen response elements (ERE) ( 10 ). (physiology.org)
  • These results demonstrate a role for core-BRAF35-containing complex in the regulation of neuron-specific genes through modulation of the chromatin structure. (pnas.org)
  • These common elements largely result from the shared ancestry of cellular life in organisms over 2 billion years ago. (wikiversity.org)
  • To exert their diverse functions, these pathways are used reiteratively, mainly by regulating different transcriptional programs depending on the cellular context. (biomedcentral.com)