The Art of Multiple Sequence Alignment in R
... aligned. This process is iterated to further refine the alignment. There are other functions that extend use of AlignSeqs for different purposes: 1. The first is AlignTranslation, which will align DNA/RNA sequences based on their amino acid translation and then reverse translate them back to DNA/RNA ...
... aligned. This process is iterated to further refine the alignment. There are other functions that extend use of AlignSeqs for different purposes: 1. The first is AlignTranslation, which will align DNA/RNA sequences based on their amino acid translation and then reverse translate them back to DNA/RNA ...
WHITE PANICLE1, a Val-tRNA Synthetase
... 2012). Thus, 70S ribosome biogenesis is essential for early chloroplast development in higher plants. Chloroplast differentiation is a process whereby chloroplasts develop from proplastids. During chloroplast differentiation, the proplastids first establish the plastidic genetic system. At this stage ...
... 2012). Thus, 70S ribosome biogenesis is essential for early chloroplast development in higher plants. Chloroplast differentiation is a process whereby chloroplasts develop from proplastids. During chloroplast differentiation, the proplastids first establish the plastidic genetic system. At this stage ...
Sequence Heterogeneities Among 16s
... content, the SSU rRNA sequences have become more widely used for estimating phylogenetic relationships among unicellular organisms (Fox, Wisotzkey, and Jurtshuk 1992). However, SSU rRNA sequences may not be adequate to analyze phylogenetic relationships between closely related species (not to speak ...
... content, the SSU rRNA sequences have become more widely used for estimating phylogenetic relationships among unicellular organisms (Fox, Wisotzkey, and Jurtshuk 1992). However, SSU rRNA sequences may not be adequate to analyze phylogenetic relationships between closely related species (not to speak ...
... pattern is consistent with results reported for brook trout [21] and gilthead sea bream [19]. In mammals, MSTN is expressed mainly in skeletal muscle [9]. In silver sea bream, MSTN2 mRNA were expressed at higher levels in muscle than in white muscle, consistent with the findings in gilthead sea brea ...
Adrenomedullin Gene Expression Is Developmentally Regulated and
... was used as the DNA template for PCR mutagenesis to produce mutated Adm promoter constructs, which lack one (pMutA or pMutB) or both of the potential HIF-1 binding sites (pMutAB). In pMutA, the core HIF-1 site (59-ACGT-39) at -1095 upstream of the transcription binding site was replaced with 59-AAAT ...
... was used as the DNA template for PCR mutagenesis to produce mutated Adm promoter constructs, which lack one (pMutA or pMutB) or both of the potential HIF-1 binding sites (pMutAB). In pMutA, the core HIF-1 site (59-ACGT-39) at -1095 upstream of the transcription binding site was replaced with 59-AAAT ...
Novel Blocked-Cleavable Primers for Quantitative Detection of
... Single nucleotide polymorphisms (SNPs) are common and often correlate with important biological traits. The ability to accurately discriminate between different alleles is critical for modern diagnostics. A mismatch at or near the RNA base has a large effect on the ability of RNase H2 to cleave a bl ...
... Single nucleotide polymorphisms (SNPs) are common and often correlate with important biological traits. The ability to accurately discriminate between different alleles is critical for modern diagnostics. A mismatch at or near the RNA base has a large effect on the ability of RNase H2 to cleave a bl ...
The Mobile Genetic Element Alu in the Human Genome
... not identical, and they are interspersed along the genome (not tandemly arrayed). Within this category are the trans po sons, elements that are able to move from one genomic location to another. This movement can be mediated by DNA or RNA. In RNA-mediated transposition, the transposon is transcribed ...
... not identical, and they are interspersed along the genome (not tandemly arrayed). Within this category are the trans po sons, elements that are able to move from one genomic location to another. This movement can be mediated by DNA or RNA. In RNA-mediated transposition, the transposon is transcribed ...
Localization and structural analysis of the ribosomal RNA operons of
... Isolation and subcloning of the rRNA operons In order to identify the rRNA genes, purified rRNA (10) was used to probe a lambda bank consisting of R. sphaeroides chromosomal DNA. One recombinant lambda phage was identified and appeared to contain a portion of an rRNA operon (P. Hallenbeck and S. Kap ...
... Isolation and subcloning of the rRNA operons In order to identify the rRNA genes, purified rRNA (10) was used to probe a lambda bank consisting of R. sphaeroides chromosomal DNA. One recombinant lambda phage was identified and appeared to contain a portion of an rRNA operon (P. Hallenbeck and S. Kap ...
Polyamines
... tertiary sulfonium compounds, the latter enzyme may be the same as BADH involved in glycinebetaine synthesis (Trossat et al, 1997). Putrescine serves as precursor of the nicotine and tropane alkaloids (Smith et al, 1979; Flores et al, 1989; Hashimoto and Yamada, 1994), which may play important roles ...
... tertiary sulfonium compounds, the latter enzyme may be the same as BADH involved in glycinebetaine synthesis (Trossat et al, 1997). Putrescine serves as precursor of the nicotine and tropane alkaloids (Smith et al, 1979; Flores et al, 1989; Hashimoto and Yamada, 1994), which may play important roles ...
Mitochondrial Transcript Processing and Restoration of Male Fertility
... this hypothesis; the 1.85 kb transcript is a primary (initiated) transcript and hence not the result of RNA processing ( Kennell and Pring 1989). Plants segregating for the Rf1, Rf8, or Rf* restorers accumulate novel T-urf13 transcripts. Genetic analyses of four rf1-m alleles established that rf1-m ...
... this hypothesis; the 1.85 kb transcript is a primary (initiated) transcript and hence not the result of RNA processing ( Kennell and Pring 1989). Plants segregating for the Rf1, Rf8, or Rf* restorers accumulate novel T-urf13 transcripts. Genetic analyses of four rf1-m alleles established that rf1-m ...
In situ hybridization
... Oligonucleotide gene probes have multiple advantages over RNA or cDNA probes when used for in situ hybridization. We can list them here for you. Stability, Availability, Faster and less expensive to use, Easier to work with, More specific, Better tissue penetration, Better reproducibility and a wide ...
... Oligonucleotide gene probes have multiple advantages over RNA or cDNA probes when used for in situ hybridization. We can list them here for you. Stability, Availability, Faster and less expensive to use, Easier to work with, More specific, Better tissue penetration, Better reproducibility and a wide ...
Strains to Theiler`s Virus Persistent Infection the Difference of
... The D10Pas4 deletion could have been responsible for the susceptibility of the SJL/J strain for two reasons. First, it is present in the only strain for which the H-2D haplotype does not correlate with susceptibility to persistent infection. Second, it is located 44 nt upstream of the TATA box, betw ...
... The D10Pas4 deletion could have been responsible for the susceptibility of the SJL/J strain for two reasons. First, it is present in the only strain for which the H-2D haplotype does not correlate with susceptibility to persistent infection. Second, it is located 44 nt upstream of the TATA box, betw ...
INO1 - of /home/sholmes/web
... positioning of these nucleosomes between short-term and long-term repressed INO1 •There was, however, a decrease in nucleosomal protection in short-term repressed INO1 •Decreased protection can indicate either an increased in the proportion of cells lacking nucleosomes, or a decrease in nucleosomal ...
... positioning of these nucleosomes between short-term and long-term repressed INO1 •There was, however, a decrease in nucleosomal protection in short-term repressed INO1 •Decreased protection can indicate either an increased in the proportion of cells lacking nucleosomes, or a decrease in nucleosomal ...
A nested deletion approach to generate Cre deleter mice with
... future, to the combination of various mutations. Murine Hox genes provide an interesting example of the interest of this system. Mammals have 39 Hox genes encoding transcription factors, whose function is to organize the body plan (see e.g. Krumlauf, 1994). These genes are grouped into four large ge ...
... future, to the combination of various mutations. Murine Hox genes provide an interesting example of the interest of this system. Mammals have 39 Hox genes encoding transcription factors, whose function is to organize the body plan (see e.g. Krumlauf, 1994). These genes are grouped into four large ge ...
Contribution of IKBKE and IFIH1 gene variants to SLE susceptibility
... Figure 1. The IKBKE SNV rs12142086 affects the binding of SF1 with DNA. (a) The SNV rs12142086 is predicted to be located in the binding motif of SF1. Introns are represented by grey horizontal lines and exons by vertical bars with numbers. The position of rs12142086 is highlighted with a star. In t ...
... Figure 1. The IKBKE SNV rs12142086 affects the binding of SF1 with DNA. (a) The SNV rs12142086 is predicted to be located in the binding motif of SF1. Introns are represented by grey horizontal lines and exons by vertical bars with numbers. The position of rs12142086 is highlighted with a star. In t ...
Mechanisms of translational regulation in bacteria
... Consequently, the genetic code is degenerate: Except for tryptophan and methionine, the amino acids are encoded by two, four or six different so called synonymous codons. Hence an organism can tune the codon sequence according to its needs without changing the amino acid sequence of the expressed pr ...
... Consequently, the genetic code is degenerate: Except for tryptophan and methionine, the amino acids are encoded by two, four or six different so called synonymous codons. Hence an organism can tune the codon sequence according to its needs without changing the amino acid sequence of the expressed pr ...
- Philsci-Archive
... My strategy in what follows will be to introduce a very undemanding or minimalist notion of causation, based on the interventionist framework described in Woodward, 2003. I will then use this as a basis on which to explore the various other distinctions, having to do with stability, specificity and ...
... My strategy in what follows will be to introduce a very undemanding or minimalist notion of causation, based on the interventionist framework described in Woodward, 2003. I will then use this as a basis on which to explore the various other distinctions, having to do with stability, specificity and ...
Choosing the Right Centrifuge for Your - Laboratory
... g-forces of up to 802,000 × g and volumes up to 250 mL; and microultracentrifuges, which support g-forces of above 1,000,000 × g and microvolume samples up to 13.5 mL. Common ultracentrifuge applications include the separation of virus particles; DNA, protein, or RNA fractionation; as well as lipopr ...
... g-forces of up to 802,000 × g and volumes up to 250 mL; and microultracentrifuges, which support g-forces of above 1,000,000 × g and microvolume samples up to 13.5 mL. Common ultracentrifuge applications include the separation of virus particles; DNA, protein, or RNA fractionation; as well as lipopr ...
PowerCut™ Dicer
... eGFP and phi6 as substrates. The reactions were assembled and incubated according to the standard protocol, and unpurified aliquots were run on a 2 % agarose gel. No uncut substrate is seen in the reactions demonstrating 100 % cleaving efficiency. M denotes a 27-bp RNA marker. ...
... eGFP and phi6 as substrates. The reactions were assembled and incubated according to the standard protocol, and unpurified aliquots were run on a 2 % agarose gel. No uncut substrate is seen in the reactions demonstrating 100 % cleaving efficiency. M denotes a 27-bp RNA marker. ...
Temperature-dependent expression of virulence genes in fish
... 2010; Steinmann and Dersch, 2013). In addition, bacteria also have response mechanisms to drastic changes in temperature. The paradigms of this adaptation are the cold and heat shock response systems under which the bacteria induce a fast response to sudden and extreme temperature shift (Guisbert et ...
... 2010; Steinmann and Dersch, 2013). In addition, bacteria also have response mechanisms to drastic changes in temperature. The paradigms of this adaptation are the cold and heat shock response systems under which the bacteria induce a fast response to sudden and extreme temperature shift (Guisbert et ...
The Comparison of Transcriptomes Undergoing Waterlogging at the
... under waterlogging stress. It is interesting to note that 3.1% of differentially expressed transcripts encode products that are involved in pathways related to cell-wall loosening enzymes. An additional 6.7% of the differentially expressed transcripts were predicted to encode enzymes related to prot ...
... under waterlogging stress. It is interesting to note that 3.1% of differentially expressed transcripts encode products that are involved in pathways related to cell-wall loosening enzymes. An additional 6.7% of the differentially expressed transcripts were predicted to encode enzymes related to prot ...
Regulation of Bacterial Conjugation in Microaerobiosis by
... (Camacho and Casadesus 2002, 2005). Post-transcriptional control of tra operon expression has been shown to involve the RNA chaperone Hfq (Will and Frost 2006), the GroEL heat-shock chaperone (Zahrl et al. 2007), and the extracytoplasmic stress CpxAR system (Gubbins et al. 2002; Zahrl et al. 2006; L ...
... (Camacho and Casadesus 2002, 2005). Post-transcriptional control of tra operon expression has been shown to involve the RNA chaperone Hfq (Will and Frost 2006), the GroEL heat-shock chaperone (Zahrl et al. 2007), and the extracytoplasmic stress CpxAR system (Gubbins et al. 2002; Zahrl et al. 2006; L ...
Counting Small RNA in Pathogenic Bacteria
... novel Yersinia sRNAs involved in pathogenesis. (Manuscript in preparation, Hu, Stubben, and Chain). From this sequencing work, we selected a novel sRNA, termed sRNA-8 (YSP8), for single molecule analysis in Y. pestis. smFISH Probe Sets. Probe sets were purchased from Biosearch Technologies, utilizin ...
... novel Yersinia sRNAs involved in pathogenesis. (Manuscript in preparation, Hu, Stubben, and Chain). From this sequencing work, we selected a novel sRNA, termed sRNA-8 (YSP8), for single molecule analysis in Y. pestis. smFISH Probe Sets. Probe sets were purchased from Biosearch Technologies, utilizin ...
A long-term demasculinization of X
... Recent studies have revealed key roles of noncoding RNAs in sex-related pathways, but little is known about the evolutionary forces acting on these noncoding RNAs. Profiling the transcriptome of Drosophila melanogaster with whole-genome tiling arrays found that 15% of male-biased transcribed fragmen ...
... Recent studies have revealed key roles of noncoding RNAs in sex-related pathways, but little is known about the evolutionary forces acting on these noncoding RNAs. Profiling the transcriptome of Drosophila melanogaster with whole-genome tiling arrays found that 15% of male-biased transcribed fragmen ...
DNA Sequence Changes of Mutations Altering
... When double mutants were prepared with his01242 and either the ochre (his09654) or the UGA (his09675) mutations, both of which block leader peptide gene translation, or with one of the mutations altering the BC stem (h&09663), one class of recombinant5 yielded only rough transductants in the backcro ...
... When double mutants were prepared with his01242 and either the ochre (his09654) or the UGA (his09675) mutations, both of which block leader peptide gene translation, or with one of the mutations altering the BC stem (h&09663), one class of recombinant5 yielded only rough transductants in the backcro ...
Non-coding RNA
A non-coding RNA (ncRNA) is an RNA molecule that is not translated into a protein. Less-frequently used synonyms are non-protein-coding RNA (npcRNA), non-messenger RNA (nmRNA) and functional RNA (fRNA). The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene.Non-coding RNA genes include highly abundant and functionally important RNAs such as transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as RNAs such as snoRNAs, microRNAs, siRNAs, snRNAs, exRNAs, and piRNAs and the long ncRNAs that include examples such as Xist and HOTAIR (see here for a more complete list of ncRNAs). The number of ncRNAs encoded within the human genome is unknown; however, recent transcriptomic and bioinformatic studies suggest the existence of thousands of ncRNAs., but see Since many of the newly identified ncRNAs have not been validated for their function, it is possible that many are non-functional. It is also likely that many ncRNAs are non functional (sometimes referred to as Junk RNA), and are the product of spurious transcription.