Model Organisms and the Human Genome Project Flashcards
Definition
a method of DNA sequencing first commercialized by Applied Biosystems, based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication
Sanger sequencing
Definition
free-living (not parasitic), transparent nematode (roundworm), about 1 mm in length, that lives in temperate soil environments
Caenorhabditis elegans
What are the advantages of zebrafish as a model organism?
Difference between individuals occurs due to what?
SNP and Copy Number Variations
Define
Deuterostome
a subtaxon of the Bilateria branch of the subkingdom Eumetazoa, within Animalia, and are distinguished from protostomes by their deuterostomic embryonic development; in deuterostomes, the first opening (the blastopore) becomes the anus, while in protostomes, it becomes the mouth
What are the advantages of using nematodes as a model organism?
Definition
a class of DNA sequencing methods currently under active development
Third generation sequencing
Definition
Scientific name for the zebrafish
Danio rerio
Definition
a small mammal of the order Rodentia, characteristically having a pointed snout, small rounded ears, and a long naked or almost hairless tail. Scientific name for the mouse
Mus musculus
Define
Phylogenetic tree
a diagram that represents evolutionary relationships among organisms
Why was the Human Genome Project started?
- Make a complete and accurate sequence of the human genome
- Identify all genes
- Understand the tole of genes in cell differentiation, development, ageing, metabolism etc.
- Personalised medicine
- Role in disease
Definition
an approach used to identify genes (or set of genes) responsible for a particular phenotype of an organism
Forward genetics
What are the disadvantages of mice as model organisms?
Define
Euchromatin
chromosome material which does not stain strongly except during cell division. It represents the major genes and is involved in transcription
Definition
the whole set of molecular interactions in a particular cell
Interactome
Definition
a subtaxon of the Bilateria branch of the subkingdom Eumetazoa, within Animalia, and are distinguished from protostomes by their deuterostomic embryonic development; in deuterostomes, the first opening (the blastopore) becomes the anus, while in protostomes, it becomes the mouth
Deuterostome
What are the disadvantages of using yeast as a model organism?
Define
SINEs
Short sequences of non-coding DNA present at high frequencies in various eukaryotic genomes
What collection of sequencing methods does Monash use?
Next generation sequencing
Definition
Short sequences of non-coding DNA present at high frequencies in various eukaryotic genomes
SINEs
Definition
a method of DNA sequencing (determining the order of nucleotides in DNA) based on the “sequencing by synthesis” principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation, rather than chain termination with dideoxynucleotides
Pyrosequencing
Definition
an international research effort to determine the DNA sequence of the entire human genome
Human genome project
Definition
the study of transcriptomes and their functions
Transcriptomics
Definition
a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is known generally as the common fruit fly (though inaccurately) or vinegar fly
Drosophila melanogaster
Define
Mus musculus
a small mammal of the order Rodentia, characteristically having a pointed snout, small rounded ears, and a long naked or almost hairless tail. Scientific name for the mouse
Define
Copy number variation (CNV)
a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals in the human population
Define
Genomics
the branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes
Why are human not feasible to conduct research on?
Low progeny numbers
Can not genetically manipulate
High cost
Not true breeding
Long generation time
ETHICS
Definition
chromosome material which does not stain strongly except during cell division. It represents the major genes and is involved in transcription
Euchromatin
Definition
A cloning method based on the generation of random large fragments of DNA which are inserted (cloned) into vectors to form a genome library—a large number of different recombinant DNA molecules
Shot gun cloning
What was the original method used to sequence the genome?
Sanger sequencing
Define
Saccharomyces cerevisiae
a species of yeast. It has been instrumental to winemaking, baking, and brewing since ancient times
Define
Forward genetics
an approach used to identify genes (or set of genes) responsible for a particular phenotype of an organism
Definition
the branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes
Genomics
Definition
a diagram that represents evolutionary relationships among organisms
Phylogenetic tree
Define
Third generation sequencing
a class of DNA sequencing methods currently under active development
Define
Danio rerio
Scientific name for the zebrafish
Definition
the study of proteomes and their functions
Proteomics
What are the advantages of mice as model organisms?
Roughly what percentage of the human genome encode proteins?
~2%
What are the disadvantages of using nematodes as a model organism?
Definition
a method that is used to help understand the function of a gene by analyzing the phenotypic effects of specific engineered gene sequences
Reverse genetics
Define
Interactome
the whole set of molecular interactions in a particular cell
Define
Drosophila melanogaster
a species of fly (the taxonomic order Diptera) in the family Drosophilidae. The species is known generally as the common fruit fly (though inaccurately) or vinegar fly
Define
Shot gun cloning
A cloning method based on the generation of random large fragments of DNA which are inserted (cloned) into vectors to form a genome library—a large number of different recombinant DNA molecules
Define
Sanger sequencing
a method of DNA sequencing first commercialized by Applied Biosystems, based on the selective incorporation of chain-terminating dideoxynucleotides by DNA polymerase during in vitro DNA replication
Define
Human genome project
an international research effort to determine the DNA sequence of the entire human genome
How does Sanger Sequencing work?
What are the disadvantages of using Drosophila as a model organism?
What are the advantages of using yeast as a model organism?
What is clone-by-clone sequencing?
In clone-by-clone sequencing, the genome is broken up into large chunks, 150 kilobases long (150,000 base pairs). The location of these chunks on the chromosomes is recorded (mapped) to help with assembling them in order after sequencing. The chunks are then inserted into Bacterial Artificial Chromosomes (BACs) and put inside bacterial cells to grow. The chunks of DNA are copied each time the bacteria divide to produce lots of identical copies. The DNA in the individual bacterial clones is then broken down into even smaller, overlapping fragments. Each fragment is 500 base pairs long so that they are a more manageable size for sequencing. These fragments are put into a vector that has a known DNA sequence. The DNA fragments are then sequenced, starting with the known sequence of the vector and extending out into the unknown sequence of the DNA. Following sequencing, the small fragments of DNA are pieced together by identifying areas of overlap to reform the large chunks that were originally inserted into the BACs. This ‘assembly’ is carried out by computers which spot areas of overlap and piece the DNA sequence together. Then, by following the map constructed at the beginning, the large chunks can be assembled back into the chromosomes as part of the complete genome sequence.
Define
Pyrosequencing
a method of DNA sequencing (determining the order of nucleotides in DNA) based on the “sequencing by synthesis” principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation, rather than chain termination with dideoxynucleotides
Definition
an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait
Genome-wide association study (GWAS)
Definition
chromosome material of different density from normal (usually greater), in which the activity of the genes is modified or suppressed
Heterochromatin
Define
LINES
a group of non-long terminal repeat retrotransposons which are widespread in the genome of many eukaryotes
What are the two types of first generation sequencing methods?
Sanger sequencing
Capillary electrophoresis sequencing
Define
Transcriptomics
the study of transcriptomes and their functions
Definition
a group of non-long terminal repeat retrotransposons which are widespread in the genome of many eukaryotes
LINES
Definition
a field of molecular biology that attempts to make use of the vast wealth of data given by genomic and transcriptomic projects (such as genome sequencing projects and RNA sequencing) to describe gene (and protein) functions and interactions
Functional genomics
Definition
a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals in the human population
Copy number variation (CNV)
Define
Capillary electrophoresis sequencing
a family of electrokinetic separation methods performed in submillimeter diameter capillaries and in micro- and nanofluidic channels
Define
Genome-wide association study (GWAS)
an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait
Define
Proteomics
the study of proteomes and their functions
Definition
a species of yeast. It has been instrumental to winemaking, baking, and brewing since ancient times
Saccharomyces cerevisiae
What things do you need to consider when studying model organisms?
- What question can be asked in the animal?
- Is it feasible?
- Is it ethical?
- What are the genetics, has the genome been sequenced?
- Can it be genetically manipulated?
- What are the drawbacks?
Define
Heterochromatin
chromosome material of different density from normal (usually greater), in which the activity of the genes is modified or suppressed
Definition
a family of electrokinetic separation methods performed in submillimeter diameter capillaries and in micro- and nanofluidic channels
Capillary electrophoresis sequencing
Define
Functional genomics
a field of molecular biology that attempts to make use of the vast wealth of data given by genomic and transcriptomic projects (such as genome sequencing projects and RNA sequencing) to describe gene (and protein) functions and interactions
Definition
the haploid set of chromosomes in a gamete or microorganism, or in each cell of a multicellular organism
Genome
Define
Genome
the haploid set of chromosomes in a gamete or microorganism, or in each cell of a multicellular organism
What are the Next Generation Sequencing methods?
Pyrosequencing
Sequencing by synthesis
Define
Caenorhabditis elegans
free-living (not parasitic), transparent nematode (roundworm), about 1 mm in length, that lives in temperate soil environments
True or False:
Transcriptomics and proteomics are not genome sequencing techniques
True
What are the disadvantages of the zebrafish as a model organism?
Define
Reverse genetics
a method that is used to help understand the function of a gene by analyzing the phenotypic effects of specific engineered gene sequences
What are the advantages of using Drosophila as a model organism?
