Analyzing the Changes in DNA Flexibility Due to Base Modifications
... 66 blocks of data. Each block represents one parameter that is measured from our input pdb file, and contains as many lines as frames in our original dcd file. The first column denotes which frame is being measured, and the nth column contains the measurements for the nth base pair or nth step. Even ...
... 66 blocks of data. Each block represents one parameter that is measured from our input pdb file, and contains as many lines as frames in our original dcd file. The first column denotes which frame is being measured, and the nth column contains the measurements for the nth base pair or nth step. Even ...
Genomic Sequence Data - G3: Genes | Genomes | Genetics
... the sequencing of novel viral genomes from metagenomic datasets and the targeted assembly of genes-of-interest from whole-genome datasets. The motivation for PRICE was to facilitate the assembly of individual genomes of interest using complex, shotgun, metagenomic datasets, derived from virtually a ...
... the sequencing of novel viral genomes from metagenomic datasets and the targeted assembly of genes-of-interest from whole-genome datasets. The motivation for PRICE was to facilitate the assembly of individual genomes of interest using complex, shotgun, metagenomic datasets, derived from virtually a ...
Functional and ecological impacts of horizontal gene transfer in
... still not closely related to homologues in other eukaryotes [42]. A similar situation is found in a putative ferrichrome-binding protein in diatoms, which is highly similar to a bacterial iron-import protein and appears to mediate the uptake of siderophore-bound iron, and further supports an impor ...
... still not closely related to homologues in other eukaryotes [42]. A similar situation is found in a putative ferrichrome-binding protein in diatoms, which is highly similar to a bacterial iron-import protein and appears to mediate the uptake of siderophore-bound iron, and further supports an impor ...
SNP Analysis (GAW15 data)
... the MHC region makes the largest single contribution (relative recurrence risk ~1.8 ) to disease susceptibility7 A set of alleles at the DRB1 locus, many of which share a common polymorphic sequence, the “shared epitope”, explain a large portion, but not all, of the genetic risk within the MHC. ...
... the MHC region makes the largest single contribution (relative recurrence risk ~1.8 ) to disease susceptibility7 A set of alleles at the DRB1 locus, many of which share a common polymorphic sequence, the “shared epitope”, explain a large portion, but not all, of the genetic risk within the MHC. ...
PPTX - Bioinformatics.ca
... How does Segway work? • Goal is to segment the genome into sub-classes. In each case, the tools identify certain data properties that subsets of the genome. Based on the groupings, the presence of known features (e.g. transcription start regions) is scored to suggest the functional meaning of the c ...
... How does Segway work? • Goal is to segment the genome into sub-classes. In each case, the tools identify certain data properties that subsets of the genome. Based on the groupings, the presence of known features (e.g. transcription start regions) is scored to suggest the functional meaning of the c ...
Alu
... A family of SINEs, short interspersed nuclear elements Replicating via LINE-mediated reverse transcription of an RNA polymerase Ⅲ transcript Roughly 280 bp The history of substitution patterns in the human genome Markers to determine genetic distances between human subpopulations – polymorphic Alu i ...
... A family of SINEs, short interspersed nuclear elements Replicating via LINE-mediated reverse transcription of an RNA polymerase Ⅲ transcript Roughly 280 bp The history of substitution patterns in the human genome Markers to determine genetic distances between human subpopulations – polymorphic Alu i ...
Coexpression of Linked Genes in Mammalian
... probe sets in which all perfect match probes perfectly matched to the same Ensembl gene were considered to be valid. The expression level detected by each probe set was obtained as the signal intensity (S) computed from MAS 5.0 algorithm (MAS5) (Hubbell et al. 2002). The S values were averaged among ...
... probe sets in which all perfect match probes perfectly matched to the same Ensembl gene were considered to be valid. The expression level detected by each probe set was obtained as the signal intensity (S) computed from MAS 5.0 algorithm (MAS5) (Hubbell et al. 2002). The S values were averaged among ...
Contrasting Effects of ENU Induced Embryonic Lethal Mutations of
... embryonic death to viable dysmyelination. A previous study identified a candidate gene, QKI, that contains an RNA-binding domain and encodes at least three protein isoforms (QKI-5, -6 and -7). We have determined the genomic structure of QKI, identifying an additional alternative end in cDNAs. Furthe ...
... embryonic death to viable dysmyelination. A previous study identified a candidate gene, QKI, that contains an RNA-binding domain and encodes at least three protein isoforms (QKI-5, -6 and -7). We have determined the genomic structure of QKI, identifying an additional alternative end in cDNAs. Furthe ...
Divergent Evolutionary and Expression Patterns between Lineage
... Identification of A. thaliana Lineage Specific New Genes that Originated through Gene Duplication To identify A. thaliana specific new genes, we selected new genes based on two criteria: first, the gene was not located in any of the syntenic regions between A. thaliana and the rest of three species ...
... Identification of A. thaliana Lineage Specific New Genes that Originated through Gene Duplication To identify A. thaliana specific new genes, we selected new genes based on two criteria: first, the gene was not located in any of the syntenic regions between A. thaliana and the rest of three species ...
Phylogenetic Motif Detection by Expectation
... motif discovery as well. At present, few motif discovery methods simultaneously take advantage of both the statistical enrichment of motifs and the preferential conservation of the sequences that match them. One recent study [7] enumerated spaced hexamers that were both preferentially conserved (in ...
... motif discovery as well. At present, few motif discovery methods simultaneously take advantage of both the statistical enrichment of motifs and the preferential conservation of the sequences that match them. One recent study [7] enumerated spaced hexamers that were both preferentially conserved (in ...
Molecular evolution of swine vesicular disease virus
... coxsackie B viruses that contained representatives of the major serotypes of this group and 45 isolates of swine vesicular disease virus (SVDV) from Asia and Europe. Separate analyses of sequence data from two regions of the viral genomes encoding the VP1 and 3BC genes both revealed that the SVDV be ...
... coxsackie B viruses that contained representatives of the major serotypes of this group and 45 isolates of swine vesicular disease virus (SVDV) from Asia and Europe. Separate analyses of sequence data from two regions of the viral genomes encoding the VP1 and 3BC genes both revealed that the SVDV be ...
Recent highlights of the China Rice Functional Genomics Program
... and its promoter, to produce stable transgenic lines with a range of reduced amylose contents. This trait has been incorporated into elite fertility restorer lines as well as cultivars commonly grown in China [23]. In addition, reliable transformation procedures have been developed for most recalcit ...
... and its promoter, to produce stable transgenic lines with a range of reduced amylose contents. This trait has been incorporated into elite fertility restorer lines as well as cultivars commonly grown in China [23]. In addition, reliable transformation procedures have been developed for most recalcit ...
Genetic Markers for Sex Identification in Forensic DNA Analysis
... Nakahori et al. found distinct sequences for AMELX and AMELY with 89% homology between the two [4]. Salido et al. identified 7 exons for AMELX and AMELY (Figure 2) and found that human amelogenin is expressed from both X and Y chromosomes, although the level of expression of AMELY is roughly 10% of ...
... Nakahori et al. found distinct sequences for AMELX and AMELY with 89% homology between the two [4]. Salido et al. identified 7 exons for AMELX and AMELY (Figure 2) and found that human amelogenin is expressed from both X and Y chromosomes, although the level of expression of AMELY is roughly 10% of ...
Low chromosome number angiosperms
... callus and suspension cultures evidencing polyploidization. Karm et al. (1991) analysed plantlet populations generated in vitro from callus from immature flower heads and karyotype analysis was performed too. Later Ogura et al. (1999) compared the difference of changeability of two pair of homologou ...
... callus and suspension cultures evidencing polyploidization. Karm et al. (1991) analysed plantlet populations generated in vitro from callus from immature flower heads and karyotype analysis was performed too. Later Ogura et al. (1999) compared the difference of changeability of two pair of homologou ...
LAB 1: Scientific Method/Tools of Scientific Inquiry
... to load, being sure the tip is in the liquid submerging the gel but NOT deep into the well (you don’t want to poke a hole in the gel!) 5. use a finger from your off hand to steady the micropipettor as shown in the picture and slowly depress the plunger to the first stop to expel the liquid into the ...
... to load, being sure the tip is in the liquid submerging the gel but NOT deep into the well (you don’t want to poke a hole in the gel!) 5. use a finger from your off hand to steady the micropipettor as shown in the picture and slowly depress the plunger to the first stop to expel the liquid into the ...
lac
... labeled galactoside in the presence of inducer. He concluded that lacY must encode an enzyme responsible for transporting the galactoside into cells: called it galactoside permease. ...
... labeled galactoside in the presence of inducer. He concluded that lacY must encode an enzyme responsible for transporting the galactoside into cells: called it galactoside permease. ...
20. Transposable Genetic Elements
... indication of when in the seed's development the breakage occurred. A small white area suggests that the break came late in development, because it gave rise to only a small number of affected cells. A large patch suggests an early break, because many descendant cells are affected. The bottom seed i ...
... indication of when in the seed's development the breakage occurred. A small white area suggests that the break came late in development, because it gave rise to only a small number of affected cells. A large patch suggests an early break, because many descendant cells are affected. The bottom seed i ...
Chromosomes
... • Human chromosomes have repeats of TTAGGG • Telomeres shorten during each cell division in most cells ...
... • Human chromosomes have repeats of TTAGGG • Telomeres shorten during each cell division in most cells ...
RNA transcription and mRNA processing
... cytoplasm; and (4) initially transcription results in a pre-messenger RNA (pre-mRNA) molecule that must be processed before it emerges as a mature mRNA ready for translation. Additionally, mRNAs are much longer-lived in eukaryotes. The first step in transcription is for RNA polymerase to find a gene ...
... cytoplasm; and (4) initially transcription results in a pre-messenger RNA (pre-mRNA) molecule that must be processed before it emerges as a mature mRNA ready for translation. Additionally, mRNAs are much longer-lived in eukaryotes. The first step in transcription is for RNA polymerase to find a gene ...
Linkage Disequilibrium and Inference of Ancestral
... among populations, with Africa tending to have low LD and with populations that are more derived or isolated having the highest LD (Dunning et al. 2000; Kidd et al. 2000; Reich et al. 2001; Bonnen et al. 2002). A number of population genetic inferences can be drawn from surveys of multilocus-SNP gen ...
... among populations, with Africa tending to have low LD and with populations that are more derived or isolated having the highest LD (Dunning et al. 2000; Kidd et al. 2000; Reich et al. 2001; Bonnen et al. 2002). A number of population genetic inferences can be drawn from surveys of multilocus-SNP gen ...
Rapid divergence and diversification of mammalian duplicate gene
... developed a phylogenetic method that classifies evolutionary processes driving the retention of duplicate genes by quantifying divergence between their spatial gene expression profiles and that of their single-copy orthologous gene in a closely related sister species. Results: Here, we apply our cla ...
... developed a phylogenetic method that classifies evolutionary processes driving the retention of duplicate genes by quantifying divergence between their spatial gene expression profiles and that of their single-copy orthologous gene in a closely related sister species. Results: Here, we apply our cla ...
- eScholarship@UMMS - University of Massachusetts
... and control cells, using ChIP-seq (Supplemental Fig. S1; Johnson et al. 2007; Mardis 2007; Robertson et al. 2007). Three primary fibroblast cell lines were used in this study: an HGPS patient fibroblast (HGPS), a normal cell line from the father of the HGPS patient (Father), and an age-matched norma ...
... and control cells, using ChIP-seq (Supplemental Fig. S1; Johnson et al. 2007; Mardis 2007; Robertson et al. 2007). Three primary fibroblast cell lines were used in this study: an HGPS patient fibroblast (HGPS), a normal cell line from the father of the HGPS patient (Father), and an age-matched norma ...
Alternative Splicing in Higher Plants
... How many isoforms can a locus have? – Wang and Brendel found that alternative splicing at a locus creates a finite number of isoforms • ~60% of the transcribed loci in rice exhibit only a single isoform (no alternative splicing) – Campbell found similar results: • 68.3% of rice loci have only one is ...
... How many isoforms can a locus have? – Wang and Brendel found that alternative splicing at a locus creates a finite number of isoforms • ~60% of the transcribed loci in rice exhibit only a single isoform (no alternative splicing) – Campbell found similar results: • 68.3% of rice loci have only one is ...
Effective transfer of chromosomes carrying leaf rust resistance
... was present in all hybrids examined (Fig. 1c, d). This consideration led us to suppose that triticale cv. Bogo and the F1 to BC2F5 hybrids of (Ae. tauschii × S. cereale) × triticale cv. Bogo could carry the dominant allele of the Ph1 gene. This assumption explained the appearance of 3D chromosomes i ...
... was present in all hybrids examined (Fig. 1c, d). This consideration led us to suppose that triticale cv. Bogo and the F1 to BC2F5 hybrids of (Ae. tauschii × S. cereale) × triticale cv. Bogo could carry the dominant allele of the Ph1 gene. This assumption explained the appearance of 3D chromosomes i ...
Human genome
The human genome is the complete set of nucleic acid sequence for humans (Homo sapiens), encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. Human genomes include both protein-coding DNA genes and noncoding DNA. Haploid human genomes, which are contained in germ cells (the egg and sperm gamete cells created in the meiosis phase of sexual reproduction before fertilization creates a zygote) consist of three billion DNA base pairs, while diploid genomes (found in somatic cells) have twice the DNA content. While there are significant differences among the genomes of human individuals (on the order of 0.1%), these are considerably smaller than the differences between humans and their closest living relatives, the chimpanzees (approximately 4%) and bonobos. Humans share 50% of their DNA with bananas.The Human Genome Project produced the first complete sequences of individual human genomes, with the first draft sequence and initial analysis being published on February 12, 2001. The human genome was the first of all vertebrates to be completely sequenced. As of 2012, thousands of human genomes have been completely sequenced, and many more have been mapped at lower levels of resolution. The resulting data are used worldwide in biomedical science, anthropology, forensics and other branches of science. There is a widely held expectation that genomic studies will lead to advances in the diagnosis and treatment of diseases, and to new insights in many fields of biology, including human evolution.Although the sequence of the human genome has been (almost) completely determined by DNA sequencing, it is not yet fully understood. Most (though probably not all) genes have been identified by a combination of high throughput experimental and bioinformatics approaches, yet much work still needs to be done to further elucidate the biological functions of their protein and RNA products. Recent results suggest that most of the vast quantities of noncoding DNA within the genome have associated biochemical activities, including regulation of gene expression, organization of chromosome architecture, and signals controlling epigenetic inheritance.There are an estimated 20,000-25,000 human protein-coding genes. The estimate of the number of human genes has been repeatedly revised down from initial predictions of 100,000 or more as genome sequence quality and gene finding methods have improved, and could continue to drop further. Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA molecules, regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been elucidated.