Efficiency of gene silencing in Arabidopsis
... and homologous inverted repeat (hIR) vectors. hIR constructs carry self-complementary intron-spliced fragments of the target gene whereas transitive vectors have the target sequence fragment adjacent to an intron-spliced, inverted repeat of heterologous origin. Both transitive and hIR constructs fac ...
... and homologous inverted repeat (hIR) vectors. hIR constructs carry self-complementary intron-spliced fragments of the target gene whereas transitive vectors have the target sequence fragment adjacent to an intron-spliced, inverted repeat of heterologous origin. Both transitive and hIR constructs fac ...
Genome
... Right click on tracks NOT shown below and hide them. Right click on the RepeatMasker track and click full. It is dense by default. Adjust the zoom until you get a view you are comfortable with. ...
... Right click on tracks NOT shown below and hide them. Right click on the RepeatMasker track and click full. It is dense by default. Adjust the zoom until you get a view you are comfortable with. ...
Reference genome sequence of the model plant Setaria
... For full genome analysis, nuclear DNA was prepared from Yugu1 seedlings and subjected to Sanger sequence analysis on ABI3730xl capillary sequencing machines. Separate libraries with several insert sizes (3 kb, 6 kb, 37 kb, 121 kb) were end-sequenced using standard Sanger-based methods. A total of 5, ...
... For full genome analysis, nuclear DNA was prepared from Yugu1 seedlings and subjected to Sanger sequence analysis on ABI3730xl capillary sequencing machines. Separate libraries with several insert sizes (3 kb, 6 kb, 37 kb, 121 kb) were end-sequenced using standard Sanger-based methods. A total of 5, ...
The relationship between higher‑order chromatin structure and
... it sediments with bulk chromatin in non‑expressing cells [8,9,11]. However, can the β‑globin locus, whose regulation is known to be very complex in mammalian cells, be used as a paradigm for the other ∼25 000 genes in the genome? We would argue that it cannot. To understand the global relationships ...
... it sediments with bulk chromatin in non‑expressing cells [8,9,11]. However, can the β‑globin locus, whose regulation is known to be very complex in mammalian cells, be used as a paradigm for the other ∼25 000 genes in the genome? We would argue that it cannot. To understand the global relationships ...
Chromosome Aberrations
... • SINEs are nonautonomous – rely on other TEs (LINEs) for the enzymes required to mobilize • ~1 million copies ...
... • SINEs are nonautonomous – rely on other TEs (LINEs) for the enzymes required to mobilize • ~1 million copies ...
Document
... one in every 25 bases is edited on average, which leads to about 1 in every 8 codons being edited on average. In plant mitochondrial mRNAs, about 2% of the nucleotides are edited on average. In the remainder of this article, we briefly describe the editing events in these organisms. Then we focus fi ...
... one in every 25 bases is edited on average, which leads to about 1 in every 8 codons being edited on average. In plant mitochondrial mRNAs, about 2% of the nucleotides are edited on average. In the remainder of this article, we briefly describe the editing events in these organisms. Then we focus fi ...
Predicting tRNA and tmRNA genes Aragorn - SEA
... The phages that contain more than 1 tRNA within their genomes tend to localize the tRNAs to certain regions of the genomes (also called “tRNA clusters” in the phage tRNA literature.) It is highly unusual that a phage with multiple tRNAs will contain a sole tRNA distant genomically from all the other ...
... The phages that contain more than 1 tRNA within their genomes tend to localize the tRNAs to certain regions of the genomes (also called “tRNA clusters” in the phage tRNA literature.) It is highly unusual that a phage with multiple tRNAs will contain a sole tRNA distant genomically from all the other ...
Predicting_tRNA_and_tmRNA_genes_12-2-16
... The phages that contain more than 1 tRNA within their genomes tend to localize the tRNAs to certain regions of the genomes (also called “tRNA clusters” in the phage tRNA literature.) It is highly unusual that a phage with multiple tRNAs will contain a sole tRNA distant genomically from all the other ...
... The phages that contain more than 1 tRNA within their genomes tend to localize the tRNAs to certain regions of the genomes (also called “tRNA clusters” in the phage tRNA literature.) It is highly unusual that a phage with multiple tRNAs will contain a sole tRNA distant genomically from all the other ...
Figure 15.6 Nonreplicative transposition allows a transposon to
... 15.2 Insertion sequences are simple transposition modules Direct repeats are identical (or related) sequences present in two or more copies in the same orientation in the same molecule of DNA; they are not necessarily adjacent. Inverted terminal repeats are the short related or identical sequences ...
... 15.2 Insertion sequences are simple transposition modules Direct repeats are identical (or related) sequences present in two or more copies in the same orientation in the same molecule of DNA; they are not necessarily adjacent. Inverted terminal repeats are the short related or identical sequences ...
15.13 Spm elements influence gene expression
... 15.2 Insertion sequences are simple transposition modules Direct repeats are identical (or related) sequences present in two or more copies in the same orientation in the same molecule of DNA; they are not necessarily adjacent. Inverted terminal repeats are the short related or identical sequences ...
... 15.2 Insertion sequences are simple transposition modules Direct repeats are identical (or related) sequences present in two or more copies in the same orientation in the same molecule of DNA; they are not necessarily adjacent. Inverted terminal repeats are the short related or identical sequences ...
Bacteroides mobilizable and conjugative genetic elements
... expression. This was somewhat surprising because RteA and RteB are both essential for CTn excision and transfer functions and resemble components of a two-component regulatory system. RteA, the putative sensor protein, is a sensing something other than tetracycline15,16. TetQ was not required for te ...
... expression. This was somewhat surprising because RteA and RteB are both essential for CTn excision and transfer functions and resemble components of a two-component regulatory system. RteA, the putative sensor protein, is a sensing something other than tetracycline15,16. TetQ was not required for te ...
Document
... Elements (SINEs), specifically of the ALU family, in the well-known VHL tumor suppressor gene. The goal of this exercise is to gain experience using BLAST, particularly blastN, and the UCSC genome browser to answer biologically relevant questions. Jian Ma | Sequence Comparison and Genome Alignment ...
... Elements (SINEs), specifically of the ALU family, in the well-known VHL tumor suppressor gene. The goal of this exercise is to gain experience using BLAST, particularly blastN, and the UCSC genome browser to answer biologically relevant questions. Jian Ma | Sequence Comparison and Genome Alignment ...
An Introduction to RNA Interference (RNAi)
... Prize in Physiology or Medicine, even though they did not show or expect the RNAi mechanism to work in mammalian systems when their early work was performed. Short double-stranded RNAs (dsRNAs) mediate RNAi in human cells Shortly after Fire and Mello’s discovery, dsRNAs were found to induce similar ...
... Prize in Physiology or Medicine, even though they did not show or expect the RNAi mechanism to work in mammalian systems when their early work was performed. Short double-stranded RNAs (dsRNAs) mediate RNAi in human cells Shortly after Fire and Mello’s discovery, dsRNAs were found to induce similar ...
Applications of Bioinformatics and Genomics/Proteomics
... 4. How to work with Human genome (FASTQ, SAM, BAM, VCF, BET files and IGV program). (Alexei Fedorov) 1/20/2017 5. Complex hierarchy of non-randomness in the human genome GMRI. (Alexei Fedorov) ...
... 4. How to work with Human genome (FASTQ, SAM, BAM, VCF, BET files and IGV program). (Alexei Fedorov) 1/20/2017 5. Complex hierarchy of non-randomness in the human genome GMRI. (Alexei Fedorov) ...
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 ...
Genomic Organization of Evolutionarily Correlated Genes in
... widen the scope of co-function by analyzing a benchmark data set consisting of 2254 proteincoding genes contributing to 22,500 gene pairs. 7 These pairs had been identified by comparing 105 bacterial genomes on the basis of two types of evolutionary correlations: 7 a tendency to be located close toge ...
... widen the scope of co-function by analyzing a benchmark data set consisting of 2254 proteincoding genes contributing to 22,500 gene pairs. 7 These pairs had been identified by comparing 105 bacterial genomes on the basis of two types of evolutionary correlations: 7 a tendency to be located close toge ...
Fig 16.12a - McGraw Hill Higher Education
... When Myc is present, Myc/Max heterodimers form and activate transcription • Myc - Max affinity is higher than Max - Max affinity ...
... When Myc is present, Myc/Max heterodimers form and activate transcription • Myc - Max affinity is higher than Max - Max affinity ...
Mary Ann Osley*, Alastair Fleming, and Cheng
... histones - levels that are in part accounted for by the dynamic nature of histone ubiquitylation. The ubiquitin mark turns over continually throughout mitotic cell growth, and during mitosis the core histones are globally deubiquitylated at metaphase and reubiquitylated as cells enter anaphase{Seale ...
... histones - levels that are in part accounted for by the dynamic nature of histone ubiquitylation. The ubiquitin mark turns over continually throughout mitotic cell growth, and during mitosis the core histones are globally deubiquitylated at metaphase and reubiquitylated as cells enter anaphase{Seale ...
Transgenic Plastids in Basic Research and Plant Biotechnology
... to effective inhibition of plastid protein biosynthesis by spectinomycin (an aminoglycoside antibiotic speci®cally blocking translation on prokaryotic-type 70 S ribosomes). A successfully transformed chloroplast expresses the spectinomycin-resistance gene, aadA, thus allowing for continued cell and ...
... to effective inhibition of plastid protein biosynthesis by spectinomycin (an aminoglycoside antibiotic speci®cally blocking translation on prokaryotic-type 70 S ribosomes). A successfully transformed chloroplast expresses the spectinomycin-resistance gene, aadA, thus allowing for continued cell and ...
Table S1.
... Only genes are taken into account that overlap by at least one base pair with window. Attributes are then calculated at exon level for each exon that fulfils the patch overlap definition (overlap >25% of exon length or >10% of window size): _elen = total length of exonic DNA with window, standardize ...
... Only genes are taken into account that overlap by at least one base pair with window. Attributes are then calculated at exon level for each exon that fulfils the patch overlap definition (overlap >25% of exon length or >10% of window size): _elen = total length of exonic DNA with window, standardize ...
MiRNA_GO_Meeting_August2015
... Direct curation of the roles of miRNAs is expected to improve miRNA functional analysis that has so far relied on indirect analysis of the gene targets’ functions “We show that the most commonly used functional enrichment test is inappropriate for the analysis of sets of genes targeted by miRNAs.” B ...
... Direct curation of the roles of miRNAs is expected to improve miRNA functional analysis that has so far relied on indirect analysis of the gene targets’ functions “We show that the most commonly used functional enrichment test is inappropriate for the analysis of sets of genes targeted by miRNAs.” B ...
Widespread expression of the bovine Agouti gene results from at
... Agouti coding sequences. These results show that the Agouti gene is expressed in all examined bovine tissues including skin regardless of their coat colour. Northern hybridizations on bovine tissues were conducted to detect more accurately Agouti transcripts. A probe corresponding to the entire codi ...
... Agouti coding sequences. These results show that the Agouti gene is expressed in all examined bovine tissues including skin regardless of their coat colour. Northern hybridizations on bovine tissues were conducted to detect more accurately Agouti transcripts. A probe corresponding to the entire codi ...
Conspiracy of silence among repeated transgenes
... conjecture might be correct. When vertebrates are transformed with exogenous DNA, chromosomal insertions almost always consist of long tandem arrays of the transfected transgene-containing DNA.(5) Sometimes transgene arrays can comprise hundreds or even thousands of copies. In a cytologic study of o ...
... conjecture might be correct. When vertebrates are transformed with exogenous DNA, chromosomal insertions almost always consist of long tandem arrays of the transfected transgene-containing DNA.(5) Sometimes transgene arrays can comprise hundreds or even thousands of copies. In a cytologic study of o ...
Dissecting Gene Expression Changes Accompanying a Ploidy
... the particular pattern of chromosome (and hence gene) copy number change. With sufficiently strong selective pressure, the benefits of the specific effects can sometimes outweigh the general costs of aneuploidy, giving aneuploids a selective advantage (PAVELKA et al. 2010; SHELTZER AND AMON 2011). I ...
... the particular pattern of chromosome (and hence gene) copy number change. With sufficiently strong selective pressure, the benefits of the specific effects can sometimes outweigh the general costs of aneuploidy, giving aneuploids a selective advantage (PAVELKA et al. 2010; SHELTZER AND AMON 2011). I ...