Walk-thru of CAGE exercise
... Going from tags to wigs Showing all tags as blocks in the browser is possible, but dumb – because there are potentially thousands in the window of interest, and we go blind Easy way to summarize is to make nucleotide histograms – whiteboard demo ...
... Going from tags to wigs Showing all tags as blocks in the browser is possible, but dumb – because there are potentially thousands in the window of interest, and we go blind Easy way to summarize is to make nucleotide histograms – whiteboard demo ...
DHPS-WDR83 overlapping SNPs detection in QTL region for meat pH
... checking their suitability to be used on the GoldenGate system with a score >0.6 (designability rank = 1). The position of the selected SNPs was precisely defined on porcine genome (version 10.2) allowing to align the location of the studied QTLR, based on the linkage map, to the physical map (Table ...
... checking their suitability to be used on the GoldenGate system with a score >0.6 (designability rank = 1). The position of the selected SNPs was precisely defined on porcine genome (version 10.2) allowing to align the location of the studied QTLR, based on the linkage map, to the physical map (Table ...
Inheritance of Organelle DNA Sequences in a Citrus–Poncirus
... The apparent segregation of the intergeneric F1 progeny with respect to the P. trifoliata mtDNA configurations suggested that these configurations resulted from influence of the nuclear genome. Nuclear alleles might alter mtDNA organization in the progeny, producing P. trifoliata configurations. Alt ...
... The apparent segregation of the intergeneric F1 progeny with respect to the P. trifoliata mtDNA configurations suggested that these configurations resulted from influence of the nuclear genome. Nuclear alleles might alter mtDNA organization in the progeny, producing P. trifoliata configurations. Alt ...
S. latifolia sex-linked genes, p. 1 Evolutionary strata on
... The ISVS method: A size comparison of homologous introns in previously described X-Y gene pairs in S. latifolia revealed that length variants are common (Figure 1). Among homologous introns in the SlX1/SlY1, SlssX/SlssY and DD44X/DD44Y gene pairs (ATANASSOV et al. 2001; FILATOV 2005c; MOORE et al. 2 ...
... The ISVS method: A size comparison of homologous introns in previously described X-Y gene pairs in S. latifolia revealed that length variants are common (Figure 1). Among homologous introns in the SlX1/SlY1, SlssX/SlssY and DD44X/DD44Y gene pairs (ATANASSOV et al. 2001; FILATOV 2005c; MOORE et al. 2 ...
based methods in the environment and hospital patients
... • mecA PCR products were obtained for all 7 environmental & 27 clinical isolates and corroborated the antibiotic susceptibility testing. • BLASTN analysis of the mecA sequences from clinical and environmental isolates had 98-100% identity to mecA genes from S. aureus spp. • Only two clinical isolate ...
... • mecA PCR products were obtained for all 7 environmental & 27 clinical isolates and corroborated the antibiotic susceptibility testing. • BLASTN analysis of the mecA sequences from clinical and environmental isolates had 98-100% identity to mecA genes from S. aureus spp. • Only two clinical isolate ...
Barley Cbf3 Gene Identification, Expression Pattern, and Map Location
... DREB1 cDNA sequences in public databases and recently reinforced by further cDNA characterization in several plant species by Jaglo et al. (2001). Here, we describe the methods that we employed to obtain barley genes encoding proteins that are highly similar to the Arabidopsis CBF/DREB1 family, and ...
... DREB1 cDNA sequences in public databases and recently reinforced by further cDNA characterization in several plant species by Jaglo et al. (2001). Here, we describe the methods that we employed to obtain barley genes encoding proteins that are highly similar to the Arabidopsis CBF/DREB1 family, and ...
The Microbial World:
... cellulose, lignin, and chitin (the most abundant organic matter on Earth). If it were not for microbial activities involved in natural decay, excessive amounts of organic matter would accumulate in forests and aquatic sediments. In addition, microorganisms are responsible for degradation of toxic c ...
... cellulose, lignin, and chitin (the most abundant organic matter on Earth). If it were not for microbial activities involved in natural decay, excessive amounts of organic matter would accumulate in forests and aquatic sediments. In addition, microorganisms are responsible for degradation of toxic c ...
DNA extraction from frozen fieldcollected and dehydrated herbarium
... specimens, Bruns et al. (1990) successfully extracted and PCRamplified DNA from 31 distinct species. Nevertheless, all taxa used in their work were from the order Agaricales, embrassing species with fleshy and short-lived basidiomata, which are in sharp contrast with the long-lived, coriaceous and w ...
... specimens, Bruns et al. (1990) successfully extracted and PCRamplified DNA from 31 distinct species. Nevertheless, all taxa used in their work were from the order Agaricales, embrassing species with fleshy and short-lived basidiomata, which are in sharp contrast with the long-lived, coriaceous and w ...
A nomenclature for restriction enzymes, DNA methyltransferases
... preferred. However, they will be divided into subtypes as indicated below. One new type of REase will be added. This is Type IV, which will include those systems that cleave only methylated DNA as their substrate and show only weak speci®city, such as the McrA, McrBC and Mrr systems of Escherichia c ...
... preferred. However, they will be divided into subtypes as indicated below. One new type of REase will be added. This is Type IV, which will include those systems that cleave only methylated DNA as their substrate and show only weak speci®city, such as the McrA, McrBC and Mrr systems of Escherichia c ...
Computational Biology
... Observation: 3-6 % of all cytosines are methylated in human DNA. This methylation occurs (almost) exclusively when cytosine is followed by a guanine base -> CpG dinucleotide. 5-methyl-cytosine SAM: S-adenosyl-methionine SAH: S-adenosyl-homocysteine ...
... Observation: 3-6 % of all cytosines are methylated in human DNA. This methylation occurs (almost) exclusively when cytosine is followed by a guanine base -> CpG dinucleotide. 5-methyl-cytosine SAM: S-adenosyl-methionine SAH: S-adenosyl-homocysteine ...
AP Biology Study Guide
... 2. Describe the diverse roles and abundance of prokaryotic life. 3. Compare the characteristics of the three domains of life. Explain why biologists consider Archaea to be more closely related to Eukarya than to Bacteria. 4. Compare the different shapes of prokaryotes. 5. Describe the structures and ...
... 2. Describe the diverse roles and abundance of prokaryotic life. 3. Compare the characteristics of the three domains of life. Explain why biologists consider Archaea to be more closely related to Eukarya than to Bacteria. 4. Compare the different shapes of prokaryotes. 5. Describe the structures and ...
03_SAC_pseudogenes_final_pap
... scores. Using data from functional or comparative genomic studies over the last five years, previously non-annotated genes have been discovered in yeast (Velvelescu et al. 1997; Cliften, 2001). However as new sequencing techniques develop and more efficient computational tools are available, new ins ...
... scores. Using data from functional or comparative genomic studies over the last five years, previously non-annotated genes have been discovered in yeast (Velvelescu et al. 1997; Cliften, 2001). However as new sequencing techniques develop and more efficient computational tools are available, new ins ...
Figure 1 - York College of Pennsylvania
... Figure 4: Comparison of zebrafish and human PPT1. Human and zebrafish PPT1 amino acid sequences were aligned using CLUSTALW. Dashes in sequences allow optimal alignment for amino acid insertions/deletions. Identical amino acids are highlighted by asterisks and conserved are highlighted by dots. ...
... Figure 4: Comparison of zebrafish and human PPT1. Human and zebrafish PPT1 amino acid sequences were aligned using CLUSTALW. Dashes in sequences allow optimal alignment for amino acid insertions/deletions. Identical amino acids are highlighted by asterisks and conserved are highlighted by dots. ...
Array Differences in Genomic Coverage and Data Quality Impact
... In addition to loss of coverage, discordant calls have the potential to negatively impact GWAS results in other ways. While achieving the highest possible call rate is desirable, including questionable calls at the expense of accuracy can quickly compromise the integrity of the results. The evidence ...
... In addition to loss of coverage, discordant calls have the potential to negatively impact GWAS results in other ways. While achieving the highest possible call rate is desirable, including questionable calls at the expense of accuracy can quickly compromise the integrity of the results. The evidence ...
The distribution of substitutions reflects features of homologous
... sequence similarity [2, 3]. This point is the subject to discussion [4], but to a moment is used commonly [5–7]. Numerous approaches for homologous recombination events detection are available [8–10]. However, alternative methods also can provide insights into features of recombination process. In [ ...
... sequence similarity [2, 3]. This point is the subject to discussion [4], but to a moment is used commonly [5–7]. Numerous approaches for homologous recombination events detection are available [8–10]. However, alternative methods also can provide insights into features of recombination process. In [ ...
Microarray Data Analysis Statistical 吳漢銘 助理教授 陽明大學 臨床醫學研究所
... The Scaling Factor- In general, the scaling factor should be around three, but as long as it is not greater than five, the chip should be okay. The scaling factor (SF) should remain consistent across the experiment. ...
... The Scaling Factor- In general, the scaling factor should be around three, but as long as it is not greater than five, the chip should be okay. The scaling factor (SF) should remain consistent across the experiment. ...
Rapid Detection of Human Enteric Pathogens (Viruses and Bacteria) in... Resources from Jordan Using Polymerase Chain Reaction (PCR)
... Dept. of Biological Sciences. Yarmouk University, Irbid- Jordan. Abstract: The monitoring programs in Jordan that are implemented on water quality with regard to detection of microbial contamination from water resources, rely mainly on time consuming conventional culture methods. Therefore to ensure ...
... Dept. of Biological Sciences. Yarmouk University, Irbid- Jordan. Abstract: The monitoring programs in Jordan that are implemented on water quality with regard to detection of microbial contamination from water resources, rely mainly on time consuming conventional culture methods. Therefore to ensure ...
Praktikum der Microarray-Datenanalyse
... • H0comp : The genes in G are at most as often differentially expressed as the genes in G c . • H0self : No genes in G are differentially expressed. • The presented 2 × 2 table methods test H0comp . ...
... • H0comp : The genes in G are at most as often differentially expressed as the genes in G c . • H0self : No genes in G are differentially expressed. • The presented 2 × 2 table methods test H0comp . ...
Characterization of transcription factor binding sites by
... Competitive bandshifts (EMSA) → rel. binding constants of oligonucletides Alignment of in vivo sites → base frequency matrix (from 10-100 sequences) in vitro selection (SELEX) → base frequency matrix (up to 200 sequences) SAGE/SELEX → base frequency matrix (up to 10’000 binding sequences) Exhaustive ...
... Competitive bandshifts (EMSA) → rel. binding constants of oligonucletides Alignment of in vivo sites → base frequency matrix (from 10-100 sequences) in vitro selection (SELEX) → base frequency matrix (up to 200 sequences) SAGE/SELEX → base frequency matrix (up to 10’000 binding sequences) Exhaustive ...
Diversity of Lactase Persistence Alleles in Ethiopia
... inserted into the pGL3hLPH1085 promoter construct with luciferase as a reporter, as previously described.8,11 Transfections were conducted with Caco-2 cells and the results are shown in Figure 1. A significant increase in luciferase activity was observed for the 14009*G construct in comparison with ...
... inserted into the pGL3hLPH1085 promoter construct with luciferase as a reporter, as previously described.8,11 Transfections were conducted with Caco-2 cells and the results are shown in Figure 1. A significant increase in luciferase activity was observed for the 14009*G construct in comparison with ...
Microbial Gene Transfer: An Ecological
... ambient microbial flora. However, both approaches usually require some cultivation of the recipient, which may result in a dramatic underestimation of the ambient transfer frequency. Novel methods are just evolving to study in situ gene transfer processes, including the use of green fluorescent prot ...
... ambient microbial flora. However, both approaches usually require some cultivation of the recipient, which may result in a dramatic underestimation of the ambient transfer frequency. Novel methods are just evolving to study in situ gene transfer processes, including the use of green fluorescent prot ...
Author`s personal copy
... terrestrial ecosystems. These effects, in turn, exert selective pressures on all components of the biosphere. Direct selection on organisms occurs through harvesting, artificial selection and attempts to control parasites, pests and pathogens. One of the most dramatic pieces of evidence for the infl ...
... terrestrial ecosystems. These effects, in turn, exert selective pressures on all components of the biosphere. Direct selection on organisms occurs through harvesting, artificial selection and attempts to control parasites, pests and pathogens. One of the most dramatic pieces of evidence for the infl ...
The Concept of Microbial Species
... has a straightforward answer that can satisfy all biologists. The traditional answer focused on the extremely small size of organisms under investigation; however, this leaves little room for distinction on the basis of taxonomy because practically all organisms have a microscopic stage during their ...
... has a straightforward answer that can satisfy all biologists. The traditional answer focused on the extremely small size of organisms under investigation; however, this leaves little room for distinction on the basis of taxonomy because practically all organisms have a microscopic stage during their ...
Population Phenotypes of Neuropsychiatric Copy Number Variants
... – Gene Fusion: Splicing of genes together as a result of intronic deletions – Excision or Duplication of Functional Domains – Disruption of Coding Sequences – Position Effects: Position and coding of a gene has changed – Perturbation of Long-Range Gene Regulation CNVs can alter human physiological f ...
... – Gene Fusion: Splicing of genes together as a result of intronic deletions – Excision or Duplication of Functional Domains – Disruption of Coding Sequences – Position Effects: Position and coding of a gene has changed – Perturbation of Long-Range Gene Regulation CNVs can alter human physiological f ...
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use either ""shotgun"" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before.