Drought response in the spikes of barley: gene expression in the
... (block) and residuals (error) were random effects. The model was represented by the equation: yijk ¼ m þ stressi þ organj þ blockk þ stress organij þ error, where yijk was the normalized log2 expression level for stress i, organ j, and block k for each gene, µ was overall mean of log2 signal inten ...
... (block) and residuals (error) were random effects. The model was represented by the equation: yijk ¼ m þ stressi þ organj þ blockk þ stress organij þ error, where yijk was the normalized log2 expression level for stress i, organ j, and block k for each gene, µ was overall mean of log2 signal inten ...
and GvpD-mediated transcription regulation of the p
... the reason for these differences. The amino acid sequence of GvpD indicates a conserved p-loop motif near the N-terminus typical of ATP/GTP binding proteins and important for the repressor function of GvpD (Pfeifer et al., 2001). The GvpD and GvpE proteins of Hfx. mediterranei are able to interact i ...
... the reason for these differences. The amino acid sequence of GvpD indicates a conserved p-loop motif near the N-terminus typical of ATP/GTP binding proteins and important for the repressor function of GvpD (Pfeifer et al., 2001). The GvpD and GvpE proteins of Hfx. mediterranei are able to interact i ...
Whole-tree and tension wood-associated expression profiles of microRNAs in Eucalyptus Grant R. McNair
... derived from the procambium that, in turn, gives rise to the vascular cambium. Bi-directional differentiation of the vascular cambium results in the development of the phloem and xylem, with the xylem forming the wood of the tree. This developmental process has sequential steps that are strictly co- ...
... derived from the procambium that, in turn, gives rise to the vascular cambium. Bi-directional differentiation of the vascular cambium results in the development of the phloem and xylem, with the xylem forming the wood of the tree. This developmental process has sequential steps that are strictly co- ...
as a PDF
... In addition to the antiterminator and terminator structures, an RNA hairpin forms at the 5⬘ end of the trp leader transcript (5⬘ stem-loop) and participates in the transcription attenuation mechanism (Fig. 2). Disruption of this structure increases trp operon expression in vivo and transcriptional r ...
... In addition to the antiterminator and terminator structures, an RNA hairpin forms at the 5⬘ end of the trp leader transcript (5⬘ stem-loop) and participates in the transcription attenuation mechanism (Fig. 2). Disruption of this structure increases trp operon expression in vivo and transcriptional r ...
Differential Gene Expression in the Siphonophore
... workflows: SOLiD SAGE (Life Technologies), Illumina mRNASeq, and Helicos Digital Gene Expression (DGE). These workflows differ in sample preparation protocols (Figure S1), sequencing platform, and read mapping. All these differences have the potential to impact each workflow’s ability to measure dif ...
... workflows: SOLiD SAGE (Life Technologies), Illumina mRNASeq, and Helicos Digital Gene Expression (DGE). These workflows differ in sample preparation protocols (Figure S1), sequencing platform, and read mapping. All these differences have the potential to impact each workflow’s ability to measure dif ...
Price, DK, Zhang, F, Ashley, CT and Warren, ST: The chicken FMR1 gene is highly conserved containing a CTT 5\' untranslated repeat and encodes an RNA-binding protein. Genomics 31:3-12 (1996).
... cluding material representative of exons 11 and 12 were not present in detectable amounts in chicken brain FMR1 RNA. Indeed, while alternative splicing of exon 12 of the mammalian FMR1 gene has been documented in multiple tissues (Ashley et al., 1993a; Verkerk et al., 1993), alternative splicing eve ...
... cluding material representative of exons 11 and 12 were not present in detectable amounts in chicken brain FMR1 RNA. Indeed, while alternative splicing of exon 12 of the mammalian FMR1 gene has been documented in multiple tissues (Ashley et al., 1993a; Verkerk et al., 1993), alternative splicing eve ...
Molecular insights into RNA and DNA helicase evolution from the
... of helicases belonging to different SF1 and SF2 families (Fairman-Williams et al., 2010). Two other SF1 (Pif1-like and Upf1-like) and four other SF2 (Ski2-like; RecG-like; T1R; and Rad3/XPD) families have been identified (Fairman-Williams et al., 2010). Helicase core domains 1 and 2 are colored ligh ...
... of helicases belonging to different SF1 and SF2 families (Fairman-Williams et al., 2010). Two other SF1 (Pif1-like and Upf1-like) and four other SF2 (Ski2-like; RecG-like; T1R; and Rad3/XPD) families have been identified (Fairman-Williams et al., 2010). Helicase core domains 1 and 2 are colored ligh ...
D. melanogaster - GEP Community Server
... alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genet. 2012 Sep;8(9):e1002954. ...
... alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genet. 2012 Sep;8(9):e1002954. ...
Identification of functional domains in Arabidopsis thaliana mRNA
... identified by bioinformatics searches in over 360 species (14). Nudix enzymes catalyse the hydrolysis of a wide range of small nucleotide substrates composed of a nucleoside diphosphate linked to another moiety X, hence the name Nudix (14). All members of this superfamily share a conserved amino acid ...
... identified by bioinformatics searches in over 360 species (14). Nudix enzymes catalyse the hydrolysis of a wide range of small nucleotide substrates composed of a nucleoside diphosphate linked to another moiety X, hence the name Nudix (14). All members of this superfamily share a conserved amino acid ...
Genome Biology - Institute for Applied Ecology
... In birds, males are homogametic (ZZ) and females are heterogametic (ZW), in contrast to the mammalian pattern of female XX homogamety and male XY heterogamety. Like the mammalian X and Y chromosomes, the euchromatic Z is large (over 500 genes) and the heterochromatic W small (probably containing ten ...
... In birds, males are homogametic (ZZ) and females are heterogametic (ZW), in contrast to the mammalian pattern of female XX homogamety and male XY heterogamety. Like the mammalian X and Y chromosomes, the euchromatic Z is large (over 500 genes) and the heterochromatic W small (probably containing ten ...
Maternal mRNAs are regulated by diverse P body
... In embryos, the decapping enzyme subunits DCAP-1 and DCAP-2 colocalize with these other P body factors in P body–like particles (Lall et al., 2005; Squirrell et al., 2006). Germ granules (P granules) represent a distinct type of mRNP granule in C. elegans (Strome, 2005). Unlike the small cytoplasmic ...
... In embryos, the decapping enzyme subunits DCAP-1 and DCAP-2 colocalize with these other P body factors in P body–like particles (Lall et al., 2005; Squirrell et al., 2006). Germ granules (P granules) represent a distinct type of mRNP granule in C. elegans (Strome, 2005). Unlike the small cytoplasmic ...
1 Oviduct-embryo interactions in cattle
... the first mitotic cell divisions and transcriptionally it undergoes embryonic genome activation (at the 8- to 16-cell stage) [1]. The developing embryo then enters the uterus where it soon forms a blastocyst, hatches from the zona pellucida and forms an ovoid, then tubular structure before undergoin ...
... the first mitotic cell divisions and transcriptionally it undergoes embryonic genome activation (at the 8- to 16-cell stage) [1]. The developing embryo then enters the uterus where it soon forms a blastocyst, hatches from the zona pellucida and forms an ovoid, then tubular structure before undergoin ...
Presentation - people.vcu.edu
... Myelin-associated glycoprotein (MAG) Acts as a linker between the axon and the myelin sheath ...
... Myelin-associated glycoprotein (MAG) Acts as a linker between the axon and the myelin sheath ...
Bayesian Learning of MicroRNA Targets from Sequence
... In this section, we describe our Bayesian model for miRNA regulation. Our model takes into account the down-regulation of target mRNAs subject to the action of multiple miRNAs. Each miRNA can reduce the expression of its targets by some fixed amount: given high expression of one or many miRNAs, the ...
... In this section, we describe our Bayesian model for miRNA regulation. Our model takes into account the down-regulation of target mRNAs subject to the action of multiple miRNAs. Each miRNA can reduce the expression of its targets by some fixed amount: given high expression of one or many miRNAs, the ...
Read the Nobel Lecture
... First we needed an assay – a way to detect if telomere elongation was happening. The first assay we tried explored whether a piece of DNA that included a telomere would incorporate DNA precursors more readily than a piece of DNA containing non-telomeric sequences. The idea was that if there was an ...
... First we needed an assay – a way to detect if telomere elongation was happening. The first assay we tried explored whether a piece of DNA that included a telomere would incorporate DNA precursors more readily than a piece of DNA containing non-telomeric sequences. The idea was that if there was an ...
p68/DDX5 DEAD-box RNA helicase gene encodes a novel miRNA
... of p68 protein levels (Barta and Iggo 1995), again suggesting that this intron is functionally important. However, in mammalian tissues, there is no obvious positive, or negative, correlation between levels of intron-containing p68 RNA and p68 protein (Stevenson et al. 1998). Therefore, the function ...
... of p68 protein levels (Barta and Iggo 1995), again suggesting that this intron is functionally important. However, in mammalian tissues, there is no obvious positive, or negative, correlation between levels of intron-containing p68 RNA and p68 protein (Stevenson et al. 1998). Therefore, the function ...
A Bifunctional tRNA for In Vitro Selection
... pressed in vivo; the cell membrane encapsulates corresponding protein and nucleic acid sequences during complex formation. Ribosome display [7] relies on the integrity of stalled translation complexes to maintain a link between an mRNA and its protein product. With mRNA display [8, 9], covalent prot ...
... pressed in vivo; the cell membrane encapsulates corresponding protein and nucleic acid sequences during complex formation. Ribosome display [7] relies on the integrity of stalled translation complexes to maintain a link between an mRNA and its protein product. With mRNA display [8, 9], covalent prot ...
In vivo evidence for the prokaryotic model of extended codon
... to nucleotides in the tRNAfMet anticodon loop are more prevalent immediately upstream of initiation codons than predicted by chance (Ganoza et al., 1985). In particular, a uridine at position ±1 was proposed to allow a fourth base pair with the adenine at position 37 of the tRNAfMet (immediately dow ...
... to nucleotides in the tRNAfMet anticodon loop are more prevalent immediately upstream of initiation codons than predicted by chance (Ganoza et al., 1985). In particular, a uridine at position ±1 was proposed to allow a fourth base pair with the adenine at position 37 of the tRNAfMet (immediately dow ...
Control of human β-globin mRNA stability and its impact on beta
... high quality prior to translation. Thus, cells have evolved surveillance mechanisms to guarantee a tight mRNA quality control, acting at several steps of mRNA biogenesis.44 Mammalian mRNA surveillance pathways include the nonstop decay pathway (NSD), the nonsense-mediated mRNA decay (NMD) and the ri ...
... high quality prior to translation. Thus, cells have evolved surveillance mechanisms to guarantee a tight mRNA quality control, acting at several steps of mRNA biogenesis.44 Mammalian mRNA surveillance pathways include the nonstop decay pathway (NSD), the nonsense-mediated mRNA decay (NMD) and the ri ...
manuscript pdf
... function with that of AP3. Our data show that DEF can complement the strong ap3-3 mutation. Because complementation depends on the appropriate spatial and temporal expression of the DEF gene, the interaction of the DEF protein with PI, and the activation of the appropriate target genes, our data str ...
... function with that of AP3. Our data show that DEF can complement the strong ap3-3 mutation. Because complementation depends on the appropriate spatial and temporal expression of the DEF gene, the interaction of the DEF protein with PI, and the activation of the appropriate target genes, our data str ...
Opposing Activities of DRM and MES
... somatic and germ cells, but dampening occurs by different mechanisms in the two cell types. In the hermaphrodite soma, a “dosage compensation complex” related to chromosome condensation factors binds the two X chromosomes and down-regulates their expression to equal that of the single X in males (Me ...
... somatic and germ cells, but dampening occurs by different mechanisms in the two cell types. In the hermaphrodite soma, a “dosage compensation complex” related to chromosome condensation factors binds the two X chromosomes and down-regulates their expression to equal that of the single X in males (Me ...
Transgene inheritance in plants
... The nature of the recipient genome may influence the stability of the introduced transgenes as well as their expression. REGISTER et al. (1994) observed that the transgenes, pat and nptII genes, were not stably inherited in 6 maize transformants. The authors inferred that this might be caused by the ...
... The nature of the recipient genome may influence the stability of the introduced transgenes as well as their expression. REGISTER et al. (1994) observed that the transgenes, pat and nptII genes, were not stably inherited in 6 maize transformants. The authors inferred that this might be caused by the ...
Fig. 1 - Repositorio Académico
... MA) for production of transgenic flies. For each transgene, at least three independent insertions were isolated and analyzed. 2.8. Mad-binding sites prediction In a series of previously known regulatory regions of Dpp target genes (training set), we identified overrepresented motifs using the software ...
... MA) for production of transgenic flies. For each transgene, at least three independent insertions were isolated and analyzed. 2.8. Mad-binding sites prediction In a series of previously known regulatory regions of Dpp target genes (training set), we identified overrepresented motifs using the software ...
Results - BioMed Central
... little thick after 15 days, at this point, the inoculated tissue surface was covered with ...
... little thick after 15 days, at this point, the inoculated tissue surface was covered with ...
pdf - University of Pennsylvania
... Smibert et al., 1996; Gavis et al., 1996a). TCE function requires formation of a bipartite secondary structure consisting of two stem-loops (Crucs et al., 2000). Smaug (Smg) protein interacts with one stem-loop and is required for repression of nos translation in the early embryo (Smibert et al., 19 ...
... Smibert et al., 1996; Gavis et al., 1996a). TCE function requires formation of a bipartite secondary structure consisting of two stem-loops (Crucs et al., 2000). Smaug (Smg) protein interacts with one stem-loop and is required for repression of nos translation in the early embryo (Smibert et al., 19 ...
RNA interference
RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecules. Historically, it was known by other names, including co-suppression, post-transcriptional gene silencing (PTGS), and quelling. Only after these apparently unrelated processes were fully understood did it become clear that they all described the RNAi phenomenon. Andrew Fire and Craig C. Mello shared the 2006 Nobel Prize in Physiology or Medicine for their work on RNA interference in the nematode worm Caenorhabditis elegans, which they published in 1998.Two types of small ribonucleic acid (RNA) molecules – microRNA (miRNA) and small interfering RNA (siRNA) – are central to RNA interference. RNAs are the direct products of genes, and these small RNAs can bind to other specific messenger RNA (mRNA) molecules and either increase or decrease their activity, for example by preventing an mRNA from producing a protein. RNA interference has an important role in defending cells against parasitic nucleotide sequences – viruses and transposons. It also influences development.The RNAi pathway is found in many eukaryotes, including animals, and is initiated by the enzyme Dicer, which cleaves long double-stranded RNA (dsRNA) molecules into short double-stranded fragments of ~20 nucleotide siRNAs. Each siRNA is unwound into two single-stranded RNAs (ssRNAs), the passenger strand and the guide strand. The passenger strand is degraded and the guide strand is incorporated into the RNA-induced silencing complex (RISC). The most well-studied outcome is post-transcriptional gene silencing, which occurs when the guide strand pairs with a complementary sequence in a messenger RNA molecule and induces cleavage by Argonaute, the catalytic component of the RISC complex. In some organisms, this process spreads systemically, despite the initially limited molar concentrations of siRNA.RNAi is a valuable research tool, both in cell culture and in living organisms, because synthetic dsRNA introduced into cells can selectively and robustly induce suppression of specific genes of interest. RNAi may be used for large-scale screens that systematically shut down each gene in the cell, which can help to identify the components necessary for a particular cellular process or an event such as cell division. The pathway is also used as a practical tool in biotechnology, medicine and insecticides.