In-class assignment: Fukuda et al. (2016) paper
... Roles of the pluripotency factor Oct 4 6. What can you directly conclude from Figure 5a? siRNA against Oct4 is sufficient to decrease the expression of Xist and Tsix in XmXm morulae. Unaltered Oct4 levels are necessary for ‘normal’ levels of Xist and Tsix in the XmXm morulae (i.e. the levels observe ...
... Roles of the pluripotency factor Oct 4 6. What can you directly conclude from Figure 5a? siRNA against Oct4 is sufficient to decrease the expression of Xist and Tsix in XmXm morulae. Unaltered Oct4 levels are necessary for ‘normal’ levels of Xist and Tsix in the XmXm morulae (i.e. the levels observe ...
No Slide Title
... • Imprinted genes are expressed differently depending on whether they are inherited through the maternal or paternal parent. ...
... • Imprinted genes are expressed differently depending on whether they are inherited through the maternal or paternal parent. ...
Comparative Analysis Using DNA Microarrays: Sensitivity
... Application within strategy of recurrence (first approximation) Let p denote probability that SLRMEASURE for a given gene will exceed a threshold l on a single comparison Then the probability that SLRMEASURE will exceed l on all 2n-1 independent measurements will be ~ p2n–1 ...
... Application within strategy of recurrence (first approximation) Let p denote probability that SLRMEASURE for a given gene will exceed a threshold l on a single comparison Then the probability that SLRMEASURE will exceed l on all 2n-1 independent measurements will be ~ p2n–1 ...
Two Waves of Nuclear Factor κB Recruitment to Target Promoters
... for the NF-B dependency of MnSOD expression (29); also in this case p65/RelA is recruited quickly and persistently, and transcriptional induction occurs shortly after initial NF-B binding (Fig. 2 a). Thus, NF-B persists on both MnSOD enhancer and MIP-2 promoter long after IB resynthesis has bee ...
... for the NF-B dependency of MnSOD expression (29); also in this case p65/RelA is recruited quickly and persistently, and transcriptional induction occurs shortly after initial NF-B binding (Fig. 2 a). Thus, NF-B persists on both MnSOD enhancer and MIP-2 promoter long after IB resynthesis has bee ...
Codon usage bias from tRNA`s point of view
... species. Surprisingly, despite the wide G+C variation of bacterial genomes these anticodons are the same in most genomes. This suggests an optimization of the translation machinery to use a small subset of optimal codons and anticodons in fast-growing bacteria and in highly expressed genes. As a res ...
... species. Surprisingly, despite the wide G+C variation of bacterial genomes these anticodons are the same in most genomes. This suggests an optimization of the translation machinery to use a small subset of optimal codons and anticodons in fast-growing bacteria and in highly expressed genes. As a res ...
Quantitative expression of cholera toxin mRNA in Vibrio cholerae
... from each sample as template for RT-PCR. cDNA synthesis and PCR amplification were performed using a QuantiTect reverse transcription kit (Qiagen). RT-PCR was performed in the presence of random primers at 42 uC for 10 min. Amplification of recA was used as the internal control. The amplified produc ...
... from each sample as template for RT-PCR. cDNA synthesis and PCR amplification were performed using a QuantiTect reverse transcription kit (Qiagen). RT-PCR was performed in the presence of random primers at 42 uC for 10 min. Amplification of recA was used as the internal control. The amplified produc ...
Potato Genome Sequencing Consortium: Final
... really start in earnest until 2008, due to delays in securing funding. The genome of the potato, in common with other organisms, is comprised of a series of ‘bases’ often referred to by the letters A, C, T and G that are linked together in ‘strings’ called chromosomes. One copy of the potato genome ...
... really start in earnest until 2008, due to delays in securing funding. The genome of the potato, in common with other organisms, is comprised of a series of ‘bases’ often referred to by the letters A, C, T and G that are linked together in ‘strings’ called chromosomes. One copy of the potato genome ...
Increased transcription rates correlate with increased reversion rates
... In the leu operon and arg regulon, reversions of mutants would not be expected to occur during growth in the presence of their end product, when transcription rates are low. During starvation, when transcription is activated by deattenuation or derepression, reversion rates should increase. In contr ...
... In the leu operon and arg regulon, reversions of mutants would not be expected to occur during growth in the presence of their end product, when transcription rates are low. During starvation, when transcription is activated by deattenuation or derepression, reversion rates should increase. In contr ...
Document
... adding to this area of essential knowledge by studying how the plant hormone cytokinin is involved in controlling leaf development and expansion. Both cytokinin mode of action and leaf development are important areas that are poised to be experimentally explored. Plant hormones are vital compounds t ...
... adding to this area of essential knowledge by studying how the plant hormone cytokinin is involved in controlling leaf development and expansion. Both cytokinin mode of action and leaf development are important areas that are poised to be experimentally explored. Plant hormones are vital compounds t ...
T-box-mediated control of the anabolic proline biosynthetic genes of
... Bacillus subtilis possesses interlinked routes for the synthesis of proline. The ProJ–ProA–ProH route is responsible for the production of proline as an osmoprotectant, and the ProB–ProA–ProI route provides proline for protein synthesis. We show here that the transcription of the anabolic proBA and ...
... Bacillus subtilis possesses interlinked routes for the synthesis of proline. The ProJ–ProA–ProH route is responsible for the production of proline as an osmoprotectant, and the ProB–ProA–ProI route provides proline for protein synthesis. We show here that the transcription of the anabolic proBA and ...
PAX6 mRNA Transcript Analysis in Various Ocular/Non
... commonly considered to have a housekeeping function (e.g., β-actin and GAPDH) exhibit considerably variable expression levels from one tissue type to another. However, expression profiles for the maintenance/housekeeping genes exhibit similar patterns for each specific tissue type (Figure 1A). As a ...
... commonly considered to have a housekeeping function (e.g., β-actin and GAPDH) exhibit considerably variable expression levels from one tissue type to another. However, expression profiles for the maintenance/housekeeping genes exhibit similar patterns for each specific tissue type (Figure 1A). As a ...
Complete genome sequence of the thermophilic Thermus sp
... studies because protein complexes from extremophiles are easier to crystallize than their mesophilic counterparts [7]. Some of the breakthrough examples of large complexes from thermophiles that have been crystallized are structures of the 70S ribosome [8], the bacterial RNA polymerase [9, 10] and t ...
... studies because protein complexes from extremophiles are easier to crystallize than their mesophilic counterparts [7]. Some of the breakthrough examples of large complexes from thermophiles that have been crystallized are structures of the 70S ribosome [8], the bacterial RNA polymerase [9, 10] and t ...
The Johns Hopkins University - American University of Beirut
... • You need to understand the data they have, and how it is organized • There are often many ways to get to an answer. • Route to get there is not always obvious, but you need to think of alternatives and traps. • Use some query language – each system has its own. • Retrieve data in a specified forma ...
... • You need to understand the data they have, and how it is organized • There are often many ways to get to an answer. • Route to get there is not always obvious, but you need to think of alternatives and traps. • Use some query language – each system has its own. • Retrieve data in a specified forma ...
Genome-wide analysis of the distribution of AP2/ERF transcription
... has made it possible to identify all of the AP2/ERF family members in cabbage for the first time. To identify the four family genes, we conducted extensive BLASTN searches based on B. rapa and A. thaliana nomenclature suggestions [23,7]. Our extensive search for AP2-domain containing proteins identi ...
... has made it possible to identify all of the AP2/ERF family members in cabbage for the first time. To identify the four family genes, we conducted extensive BLASTN searches based on B. rapa and A. thaliana nomenclature suggestions [23,7]. Our extensive search for AP2-domain containing proteins identi ...
Evolutionary aspects of recombination in RNA viruses
... different genomes. Indeed, suggestions have been made that reassortment in segmented RNA viruses and recombination in monopartite RNA viruses represent alternative evolutionary strategies for genetic exchange in this group (Chao et al., 1992). While this idea is fascinating, it is interesting to not ...
... different genomes. Indeed, suggestions have been made that reassortment in segmented RNA viruses and recombination in monopartite RNA viruses represent alternative evolutionary strategies for genetic exchange in this group (Chao et al., 1992). While this idea is fascinating, it is interesting to not ...
The enhancement of ribosomal transcription by the recycling of RNA
... then no longer depend solely on random collisions between the promoter or the spacer enhancer elements and the polymerase. Thus, yet a further mechanism to enhance the rate of ribosomal transcription may occur. Recycling of transcription factors could function either through release of the polymeras ...
... then no longer depend solely on random collisions between the promoter or the spacer enhancer elements and the polymerase. Thus, yet a further mechanism to enhance the rate of ribosomal transcription may occur. Recycling of transcription factors could function either through release of the polymeras ...
factor occupancy and gene expression Effects of sequence variation
... strategy, the distribution of aligned reads at heterozygous variants was not significantly different between the sites of differential allelic occupancy and the matched set of equal allelic occupancy (P = 0.15, two-sided Wilcoxon rank-sum test). (B) The ratio of the rate of motif-disrupting to non-m ...
... strategy, the distribution of aligned reads at heterozygous variants was not significantly different between the sites of differential allelic occupancy and the matched set of equal allelic occupancy (P = 0.15, two-sided Wilcoxon rank-sum test). (B) The ratio of the rate of motif-disrupting to non-m ...
factor occupancy and gene expression Effects of sequence variation
... strategy, the distribution of aligned reads at heterozygous variants was not significantly different between the sites of differential allelic occupancy and the matched set of equal allelic occupancy (P = 0.15, two-sided Wilcoxon rank-sum test). (B) The ratio of the rate of motif-disrupting to non-m ...
... strategy, the distribution of aligned reads at heterozygous variants was not significantly different between the sites of differential allelic occupancy and the matched set of equal allelic occupancy (P = 0.15, two-sided Wilcoxon rank-sum test). (B) The ratio of the rate of motif-disrupting to non-m ...
factor occupancy and gene expression Effects of
... strategy, the distribution of aligned reads at heterozygous variants was not significantly different between the sites of differential allelic occupancy and the matched set of equal allelic occupancy (P = 0.15, two-sided Wilcoxon rank-sum test). (B) The ratio of the rate of motif-disrupting to non-m ...
... strategy, the distribution of aligned reads at heterozygous variants was not significantly different between the sites of differential allelic occupancy and the matched set of equal allelic occupancy (P = 0.15, two-sided Wilcoxon rank-sum test). (B) The ratio of the rate of motif-disrupting to non-m ...
Replication timing and transcriptional control: beyond
... There are only two mammalian loci for which both replication-timing switches and origin localization have been studied. At the mouse immunoglobulin IgH locus, new origins are activated in pre-B cells when the promoter region of this locus becomes transcriptionally active and switches from late to ea ...
... There are only two mammalian loci for which both replication-timing switches and origin localization have been studied. At the mouse immunoglobulin IgH locus, new origins are activated in pre-B cells when the promoter region of this locus becomes transcriptionally active and switches from late to ea ...
An Introduction to Streptomyces
... In the early steps of microbiology, many organisms now belonging to the class of Actinobacteria, such as Mycobacterium leprae were considered as species somewhere between fungi and bacteria (Hopwood, 1999). In the light of new discoveries such as the: composition of the Actinobacteria cell wall (lik ...
... In the early steps of microbiology, many organisms now belonging to the class of Actinobacteria, such as Mycobacterium leprae were considered as species somewhere between fungi and bacteria (Hopwood, 1999). In the light of new discoveries such as the: composition of the Actinobacteria cell wall (lik ...
Mechanisms of translational regulation in bacteria
... render the ribosome binding site of a gene inaccessible and hence an evolutionary pressure to suppress structure formation around the translation start site is expected. Here, we investigated the impact of this selective force on the codon usage at the beginning of genes in E. coli and around 400 ot ...
... render the ribosome binding site of a gene inaccessible and hence an evolutionary pressure to suppress structure formation around the translation start site is expected. Here, we investigated the impact of this selective force on the codon usage at the beginning of genes in E. coli and around 400 ot ...
Staphylococcus aureus CC395 harbours a novel
... differed slightly from dru types dt11a (5a-2d-4a-0-2d-5b-3a-2 g3b-4e-3e) found in S. aureus strain WIS, dt11ax (5a-2d-4a-0-2d6f-3a-2 g-3b-4e-3e) found in S. schleiferi strain TSCC54, and dt11c (5a-2d-4a-0-2d-5b-3a-2 g-4b-4e-3e) found in S. capitis strain CR01 and S. aureus strain 08BA02176 (repeat s ...
... differed slightly from dru types dt11a (5a-2d-4a-0-2d-5b-3a-2 g3b-4e-3e) found in S. aureus strain WIS, dt11ax (5a-2d-4a-0-2d6f-3a-2 g-3b-4e-3e) found in S. schleiferi strain TSCC54, and dt11c (5a-2d-4a-0-2d-5b-3a-2 g-4b-4e-3e) found in S. capitis strain CR01 and S. aureus strain 08BA02176 (repeat s ...
Alternative Splicing in Higher Plants
... with the annotation of the genome and the relatively low gene number • The complexity of human development is difficult to explain using only 30,000 genes • Humans have had a recent expansion of the transposable element Alu in the genome - 4% of human protein coding genes contain at least one Alu - ...
... with the annotation of the genome and the relatively low gene number • The complexity of human development is difficult to explain using only 30,000 genes • Humans have had a recent expansion of the transposable element Alu in the genome - 4% of human protein coding genes contain at least one Alu - ...
A rule-based kinetic model of RNA polymerase II C
... RNAPII enzyme. The model represents the kinases and phosphatases that act on these repeats during initiation, elongation, 30 end maturation and RNAPII recycling. We demonstrate that this model can help explain both genome-wide patterns of RNAPII phosphorylation on yeast genes, and changes in phospho ...
... RNAPII enzyme. The model represents the kinases and phosphatases that act on these repeats during initiation, elongation, 30 end maturation and RNAPII recycling. We demonstrate that this model can help explain both genome-wide patterns of RNAPII phosphorylation on yeast genes, and changes in phospho ...