Dewey - Blumberg Lab
... Geisinger Health Systems (GHS) • Cohort in this study came from consenting GHS patients who gave blood and DNA samples as well as clinical phenotypes and records • 50, 726 participants • 87 clinical examinations, 658 lab tests, and 7 procedures per participant ...
... Geisinger Health Systems (GHS) • Cohort in this study came from consenting GHS patients who gave blood and DNA samples as well as clinical phenotypes and records • 50, 726 participants • 87 clinical examinations, 658 lab tests, and 7 procedures per participant ...
molecular scissors to study gene function Marta Oliveira
... The Cas9 (CRISPR associated) enzyme is the DNA cutting enzyme – the scissors- of one particular bacteria species (Streptococcus pyogenes) which recognizes the DNA target with the help of a CRISPR RNA. This RNA is generated from the CRISPR loci matching to the target viral DNA and binds to it by base ...
... The Cas9 (CRISPR associated) enzyme is the DNA cutting enzyme – the scissors- of one particular bacteria species (Streptococcus pyogenes) which recognizes the DNA target with the help of a CRISPR RNA. This RNA is generated from the CRISPR loci matching to the target viral DNA and binds to it by base ...
Chapter 19 – Molecular Genetic Analysis and Biotechnology
... • Used not just for copies of gene, but to make gene product – Gene expression ...
... • Used not just for copies of gene, but to make gene product – Gene expression ...
Analysis of Crop Plant Genomes
... Markers have a location and an orientation. When markers in two species are related by descent from a common ancestor, they are called homologues. Comparative mapping data are combinatorial. Species 1 ...
... Markers have a location and an orientation. When markers in two species are related by descent from a common ancestor, they are called homologues. Comparative mapping data are combinatorial. Species 1 ...
How can PCR be used to mutagenize DNA or to introduce novel
... traces of the shyest, rarest animal-urine, feces, scent marks, infinitesimal bits of hair or skin rubbed onto a tree as the elusive creature passes by. ...
... traces of the shyest, rarest animal-urine, feces, scent marks, infinitesimal bits of hair or skin rubbed onto a tree as the elusive creature passes by. ...
Finding disease genes
... • Sequence of protein-coding exons-one ‘exome’ contains coding regions of all ~30,000 genes • Exome contains 30 megabases DNA (whole genome has 3200 megabases) • Detect all SNP variation in a person. Align ‘short reads’ (millions of sequences of ~100 bases against the reference genome) • Requires 40 ...
... • Sequence of protein-coding exons-one ‘exome’ contains coding regions of all ~30,000 genes • Exome contains 30 megabases DNA (whole genome has 3200 megabases) • Detect all SNP variation in a person. Align ‘short reads’ (millions of sequences of ~100 bases against the reference genome) • Requires 40 ...
Rodriguez, Brianna M.
... In class we discussed DNA replication and how our genes sometimes mutate. However, we really didn’t discuss much on how microbes themselves can mutate. While microbial mutations are rare, they do occur, about every one to ten million DNA bases. However, we must take into consideration the fact that ...
... In class we discussed DNA replication and how our genes sometimes mutate. However, we really didn’t discuss much on how microbes themselves can mutate. While microbial mutations are rare, they do occur, about every one to ten million DNA bases. However, we must take into consideration the fact that ...
S2 Text.
... thus explaining the presence of antibacterial activity directed toward Gram-positive bacteria in eggs of immune challenge females. To test for this hypothesis, we searched for the presence of microbial DNA in ovaries and eggs of immune challenged and control females using a PCR assay. Ovaries of few ...
... thus explaining the presence of antibacterial activity directed toward Gram-positive bacteria in eggs of immune challenge females. To test for this hypothesis, we searched for the presence of microbial DNA in ovaries and eggs of immune challenged and control females using a PCR assay. Ovaries of few ...
Grimmer presentation
... Supported by the Intelligence Advanced Research Projects Activity (IARPA) via Department of Interior Interior Business Center (DoI/ICB) contract number D15PC0002. The U.S. Government is authorized to reproduce and distribute reprints for Governmental purposes notwithstanding any copyright annotation ...
... Supported by the Intelligence Advanced Research Projects Activity (IARPA) via Department of Interior Interior Business Center (DoI/ICB) contract number D15PC0002. The U.S. Government is authorized to reproduce and distribute reprints for Governmental purposes notwithstanding any copyright annotation ...
Washington University in St. Louis plays key role in sequencing
... "Once we have the genome of the moss, we will be able to compare the genome of a simple plant to those of complex plants," said Quatrano, an internationally renowned plant scientist. "Knowledge of this plant's genome will allow comparisons between genes to be made that will give us insights as to ge ...
... "Once we have the genome of the moss, we will be able to compare the genome of a simple plant to those of complex plants," said Quatrano, an internationally renowned plant scientist. "Knowledge of this plant's genome will allow comparisons between genes to be made that will give us insights as to ge ...
A Genomic Timeline
... Kary Mullis conceives of the polymerase chain reaction, a chemical DNA replication process that greatly quicken the pace of genetic science and technology development. ...
... Kary Mullis conceives of the polymerase chain reaction, a chemical DNA replication process that greatly quicken the pace of genetic science and technology development. ...
a version - SEA
... After the isolation and sequencing of Mycobacterium phage LittleLaf, various bioinformatic tools were utilized in the annotation of its genome; these tools included the annotation software DNA Master, the gene prediction software GeneMark, the Starterator and Phamerator reports, Shine-Dalgarno value ...
... After the isolation and sequencing of Mycobacterium phage LittleLaf, various bioinformatic tools were utilized in the annotation of its genome; these tools included the annotation software DNA Master, the gene prediction software GeneMark, the Starterator and Phamerator reports, Shine-Dalgarno value ...
Molecular and Genomics-Based Diagnostics for Medical Microbiology
... Increase in speed, decreasing costs and discriminatory power of NGS make it an ideal tool for routine use in diagnostic microbiology laboratories Replace several existing tests performed on the same isolate, notably identification of antibiotic-resistance mechanisms, virulence determinants and genot ...
... Increase in speed, decreasing costs and discriminatory power of NGS make it an ideal tool for routine use in diagnostic microbiology laboratories Replace several existing tests performed on the same isolate, notably identification of antibiotic-resistance mechanisms, virulence determinants and genot ...
news and views feature
... eukaryotes — several of which are completed, with many others being explored — range from less than 3 million bp for an intracellular microsporidian to the 4 billion found in the human genome, and more. The genomes of eukaryotes are, however, often greatly inflated by the presence of considerable am ...
... eukaryotes — several of which are completed, with many others being explored — range from less than 3 million bp for an intracellular microsporidian to the 4 billion found in the human genome, and more. The genomes of eukaryotes are, however, often greatly inflated by the presence of considerable am ...
slides
... Classification • Gene expression data is commonly used in the classification of a biological sample. - Tumor subtypes - Response to certain types of treatment (e.g. chemotherapy). • Most approaches focus on classification of two, or at most three classes, and have high rates of error when run on se ...
... Classification • Gene expression data is commonly used in the classification of a biological sample. - Tumor subtypes - Response to certain types of treatment (e.g. chemotherapy). • Most approaches focus on classification of two, or at most three classes, and have high rates of error when run on se ...
Table S1.
... When single nucleotide variations occur in at least 1% of the population, they are considered polymorphisms or SNPs (Single Nucleotide Polymorphism). ...
... When single nucleotide variations occur in at least 1% of the population, they are considered polymorphisms or SNPs (Single Nucleotide Polymorphism). ...
13-2 Manipulating DNA
... Knowing the sequence of an organism’s DNA allows researchers to study specific genes, to compare them with the genes of other organisms, and to try to discover the functions of different genes and gene combinations. ...
... Knowing the sequence of an organism’s DNA allows researchers to study specific genes, to compare them with the genes of other organisms, and to try to discover the functions of different genes and gene combinations. ...
A Lite Introduction toComparative Genomics
... Application: Phenotyping Using SNPs • SNP: Single Nucleotide Polymorphism - change in one base between two instances of the same gene • Used as genetic flags to identify traits, esp. for genetic diseases • CG goal: Identify as many SNPs as possible • Challenges – Data: need sequenced genomes from m ...
... Application: Phenotyping Using SNPs • SNP: Single Nucleotide Polymorphism - change in one base between two instances of the same gene • Used as genetic flags to identify traits, esp. for genetic diseases • CG goal: Identify as many SNPs as possible • Challenges – Data: need sequenced genomes from m ...
glossary of technical terms
... The field of science and engineering relating to the adaptation of living organisms or biological processes to industrial and commercial applications. ...
... The field of science and engineering relating to the adaptation of living organisms or biological processes to industrial and commercial applications. ...
Inhibitors of a microbial metabolic pathway as potential antibiotics
... threat for public health. Antibiotics and antifungal agents usually target either cell wall formation, general protein synthesis or DNA replication. Innovative molecules against new targets are urgently needed. We propose to find inhibitors of a microbial metabolic pathway that has not been explored ...
... threat for public health. Antibiotics and antifungal agents usually target either cell wall formation, general protein synthesis or DNA replication. Innovative molecules against new targets are urgently needed. We propose to find inhibitors of a microbial metabolic pathway that has not been explored ...
Genomewide Motif Recognition with a Dictionary Model
... words from an observed sequence. Moving from the same premises, we consider words that can be spelled in a variety of forms (hence accounting for varying degrees of conservation of the same motif across genome locations). The overall frequency of occurrence of each word in the sequence and the param ...
... words from an observed sequence. Moving from the same premises, we consider words that can be spelled in a variety of forms (hence accounting for varying degrees of conservation of the same motif across genome locations). The overall frequency of occurrence of each word in the sequence and the param ...
Biogeography of the Carpathians
... remains poorly understood when compared with the arctic-alpine plant species which have been extensively studied in the last decade. Erythronium dens-canis L. is disjunctly distributed from the Iberian Peninsula to the Ukraine without extending above the Alps. It is a typical deciduous forest geophy ...
... remains poorly understood when compared with the arctic-alpine plant species which have been extensively studied in the last decade. Erythronium dens-canis L. is disjunctly distributed from the Iberian Peninsula to the Ukraine without extending above the Alps. It is a typical deciduous forest geophy ...
Bioinformatics and Supercomputing
... • Phylogenetic Trees and Clustering are effective methods to support biology data analysis. • Using these tools, scientists can have a comprehensive understanding and comparison of results from different solutions • Should be used in conjunction with other scientific research and methods • Can fill ...
... • Phylogenetic Trees and Clustering are effective methods to support biology data analysis. • Using these tools, scientists can have a comprehensive understanding and comparison of results from different solutions • Should be used in conjunction with other scientific research and methods • Can fill ...
Identifying Mutations Responsible for Rare Disorders Using New
... Schematic of the FLVCR2 mutations found in two patients (F1 and F3). A. The four mutations in FLVCR2 identified in F1 and F3 using whole exome sequencing as visualized using the Integrative Genomics Viewer from the Broad Institute (http://www.broadinstitute.org/igv). B Mutations in FLVCR2 are shown ...
... Schematic of the FLVCR2 mutations found in two patients (F1 and F3). A. The four mutations in FLVCR2 identified in F1 and F3 using whole exome sequencing as visualized using the Integrative Genomics Viewer from the Broad Institute (http://www.broadinstitute.org/igv). B Mutations in FLVCR2 are shown ...
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.