BIOMGC: Systems Biology
What are the limitations and advantages to 2D gel electrophoresis?
- Can only detect medium to high abundance proteins - pH gradients are sometimes inefficient - Labour intensive and somewhat time consuming - Can seperate up to 10,000 proteins compared to 100 or so on 1-D gels
What are some HUPO recommendations?
- Focus on proteomic characterisation of disease - Use of complementary techniques - should involve labs in many countries - use of model organisms - open source - integration of data
What are the three aspects that the HPP are focusing on?
- Identification and characterisation of at least one representative protein from each human gene, including determination of the protein's: abundance and major modifications - determination of the protein profiles of at least one representative protein from every human gene in all major tissues and organs including: immunohistochemical characterisation and sub-cellular localisation - characterisation of both the transient and stable protein-protein interactions and protein complex formation important in: essential biological functions, molecular basis of disease and drug testing, expansion to nucleic acids, lipids and other ligands
What are the other goals of the human genome project?
- To identify all the genes in human DNA, including disease-susceptible genes and map sequence variation - Determine the sequence of the 2.9 billion chemical base pairs that make up human DNA - To sequence and annotate the genomes of key model organisms, namely E.coli, yeast, fly and the laboratory mouse - Store the information in a data base and develop tools for data analysis - transfer related technologies to the private sector - Address the ethical, legal and social issues that may arise from the human genome project
How many new genes have been born?
1,183 due to gene duplication and divergence
How much percent of our genome codes for proteins?
1.5%
How many long non-coding genes does the human genome have?
13,870
How many pseudogenes does the human genome have?
14,181
How big is the human genome?
2.9 Gbp in size (2.9 billion base pairs)
How many genes do humans have?
20,300 genes
How many coding genes does the human genome have?
20,805
How many telephone books (which all had 1000 pages) would you need to hold the sequence of the human genome?
200
How many base pairs does the human genome have?
3,384,269,757
How many single nucleotide polymorphisms are there in the human genome?
3.7 million
How many genes have recently died?
37 which required a mutation that rendered the gene non-functional
How many short non-coding genes does the human genome have?
9,096
How long would it take to read the sequence of the human genome?
9.5 years
How much of our genome is sequenced?
99% of the gene-rich euchromatin region of the genome has been sequenced and annotated with 99.000% accuracy
What is a single nucleotide polymorphism?
A SNP is a 'polymorphism' (difference in A,T, G or C) observed at a position in the genome
Define c-value enigma:
A comparison of genomes from closely related species shows that genome size can vary by a factor of ten or more
What is the ladder of life?
A hierarchy where animals were ultimately classified according to function and complexity, with 'complex' organisms occupying positions further upon the ladder and humanity at the apex
What is a gene?
A segment of DNA sequence corresponding to a single protein or set of alternative proteins variants.
What are transposons?
A transposon (or transposable element) is a small piece of DNA that inserts itself into another place in the genome
What is systems biology?
An approach that determines and integrates the composition and interactions of the key molecules that govern life, thus providing the necessary knowledge to describe and predict the function of biological systems
What are pseudogenes?
Are genomic DNA sequences similar to normal genes but are non-functional; they are regarded as defunct relatives of functional genes
Who proposed the ladder of life?
Aristotle in 384 to 322 BC
Why are they known as selfish DNA?
Because their only function seems to be to make more copies of themselves
Why are they known as junk DNA?
Because there is no obvious benefit to their host
What did the c-value paradox change to enigma?
Because we now know that most of the genomic DNA is non-coding
What can the human genome help with?
Biochemistry, cell biology and physiology
How do you work out the c-value?
By getting the relative molecular weight which is then converted to an absolute value by multiplying it by the atomic mass unit (1 u), which equals one-twelfth of a mass of 12C
How is metagenomics done?
By taking a sample of a particular environment e.g. soil, ocean, thermal vents, gastrointestinal tract etc. Then all DNA is extracted and "shotgun" sequenced and analysed
What can comparative genomics do?
Can identify regions of similarity and difference
What are Class II (DNA transposons) transposons?
Cut and paste without an RNA intermediate
What is sequence- based metagenomics?
Determining what the genes are by identifying the genes and metabolic pathways, comparing it to other communities etc.
What is function- based metagenomics?
Determining what the genes do by screening to identify functions of interest, such as vitamins or antibiotic production, finding the genes that code for functions of interest etc.
Why is proteomics more complex?
Due to: - dynamics - composition and structure - PTMs - Network of interactions - No PCR-equivalent amplification technologies currently available
What is the genetic load?
Every human babies have 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load
Do human males or females have a higher c-value?
Females have a slightly higher c-value due to the two X sex chromosomes
What are Class I (retrotransposons) transposons?
First they are transcribed from DNA to RNA, and the RNA produced is then reverse transcribed to DNA. This copied DNA is then inserted at a new position into the genome
What did we initially think the human genome consisted of?
Greater than 100,000 genes
How much percent of our genome has repetitive sequences?
Greater than 50%
How did Aristotle create the ladder of life?
He distinguished about 500 species of birds, mammals and fishes. He attempted to classify organisms according to form and funcion
What does 2D gel electrophoresis usually use?
Immobilised pH gradients and many types of commercially available IPG strips
When was the project completed?
In 2003
What does genomics mean?
Is an area within genetics that concerns the sequencing and analysis of an organism's genome
What is the suffix -omics used for?
Is used frequently to describe something big, and refers to a field of study in life sciences that focuses on large-scale data/information to understand life summed up in 'omes'
How does the 2D gel electrophoresis work?
It separates on the basis of isoelectric point (pI)
What is comparative genomics?
Its a field of biology research in which the genome sequences of different species - human, mouse and wide variety of other organisms from yeast to chimpanzees - are compared
What is another name for transposons?
Junk DNA or Selfish DNA
What are two types of Long terminal repeats (LTRs)?
Long interspersed Nuclear elements (LINES) and Short interspersed Nuclear elements (SINES)
What is the Whole genome shotgun sequencing strategy?
Many copies of the genome are fragmented. The fragmented genome is then cloned and sequenced. They then realign and reconstruct the sequences.
What has made genomics possible?
New technologies have increased the output
Does genome size correlate with complexity?
No
Was every single base pair in all 24 chromosomes sequenced?
No, only the euchromatic (gene-rich) region has been sequenced of each chromosome. The heterochromatic region is difficult to sequence due to its repetitive nature
Are most of the genome conserved?
No, the sequences diverge at a rate consistent with fixation of neutral alleles by random genetic drift. This strongly suggests that it does not have a function although one can't rule out some unknown function that doesn't depend on sequence.
When was the human proteome project established?
October 7th, 2001
What was the estimated life-span for the project?
Perpetual
What interactions control most cellular functions?
Protein-protein e.g. signal transduction
Which is more complex, genomics or proteomics?
Proteomics
What else can the human genome lead to?
Rapid identification of disease-associated genes and identifying drug targets for new pharmaceuticals
What is the c-value for a male human diploid cell?
Respectively, 6.294 x 10^9bp
What is the c-value for a female human diploid cell?
Respectively, 6.406 x 10^9bp
Who is the president of the Australasian Proteomics Society and a member of HUPO executive committee?
Richard Simpson
What are the two parts to metagenomics?
Sequence- based metagenomics and Function- based metagenomics
What is metagenomics?
Sequencing environmental DNA
Is a small or large fraction of the human genome coding?
Small fraction of the human genome is coding
Why would we want to see similarities and differences?
So we can gain a better understanding of the structure and function of human genes and thereby develop new strategies to combat human diseases
What were gasps in the sequence due to?
Technical limitations
What is C-value?
The amount, in picograms, of DNA contained within a haploid nucleus (e.g. a gamete) or one half the amount in a diploid somatic cell of a eukaryotic organism
What is the c-value paradox called now?
The c-value enigma
What is the c-value paradox?
The c-value paradox takes its name from our inability to account for the content of the genome in terms of known function
What is the BAC-by-BAC approach?
The chromosomes are dye-stained, creating bands on them. Each band is a physical location that contains known genetic markers. Then they annotate each chromosomes and its genes with known linked genetic landmarks, such as single nucleotide polymorphisms, short tandem repeats, and other variations in the genetic sequence. Then they fragmented the genome into large segments, cloning them into bacterial artificial chromosomes, and ordering them using linked genetic markers. Overlapping sequences at the end of each fragment are used to assemble a contiguous map of each chromosome. Then they fragmented each large fragment into smaller fragments, and determining the sequence of each of these fragments by automated Sanger sequencing. The complete sequence is assembled by comparing each individual sequence and aligning them to see where the sequences overlap. Used a dideoxy sequencing chromatogram or electropherogram
What does genome mean?
The genome is the entire DNA content that is present within one cell of an organism
What is proteomics?
The global analysis of intra and extra-cellular proteins, providing the identity, structure, function, and post-translation modifications of individual gene products
What is interactome?
The global protein-protein interactions in cells and biological fluids (e.g. plasma)
Whose DNA was sequences?
The international human genome sequencing consortium collected blood samples from anonymous female volunteers and sperm samples from anonymous male volunteers. Large number of samples were collected, and the laboratories used 11 of those sample from 450 collected. Not even the volunteers know if their genome was selected The Celera Genomics used blood and sperm samples donated initially by 21 volunteers of different race, but only used 5 samples (2 males and 3 females). Age, sex and ethnogeographic group were recorded. 130ml of whole blood were collected from both males and females, and 6 semen samples from the males were collected over 6 weeks.
Who were responsible for sequencing our genome?
The international human genome sequencing consortium heads; Francis S. Collins and Art Patrinos and the Celera Genomics head; J. Craig Venter
How was the human genome sequenced?
The international human genome sequencing consortium used the 'BAC-by-BAC approach' and the Celera Genomics used the 'Whole genome shotgun sequencing approach'
What is the modern evolutionary theory?
The modern understanding of evolution is perfectly consistent with the presence or large amounts of junk DNA in a genome
How much did the human genome project cost?
The project cost 2.7 billion dollars
What is proteome?
The protein complement of the genome
What is the ultimate goal of the human genome project?
The ultimate goal of this initiative is to understand the human genome
Who first created the world genomics?
Thomas H. Roderick in 1986
What was the major aim of the human proteome project?
To map the human proteome
How will mapping the proteome be done?
Using gene-centric approach focusing on three aspects
How are diseases usually treated?
Usually treated at the protein level with therapeutic agents (drugs) targeting proteins
How is the human proteome being mapped?
With the use of 2D gel electrophoresis and Tandem mass spectrometry
Do humans have a richer collection of protein domain architectures than other eukaryotes?
Yes
Do proteins carry out nearly all controlled biological functions?
Yes
Can proteins be pharmaceuticals themselves?
Yes e.g. insulin or EPO
Is comparative genomics effective?
Yes, it is a powerful tool for studying evolutionary changes among organisms, helping to identify genes that are conserved among species, as well as genes that give each organism its unique characteristics.
How many times was each base pair sequenced?
on average 10 times each
What are the pros and cons of the BAC-by-BAC approach?
pros: - Very rigorous - High degree of success (less than 1 in 10,000 base error rate) - More thorough than WGSS strategy - Fewer gaps than WGSS strategy cons: - slow - maps suffered from poor continuity
What are the pros and cons for the Whole genome shotgun sequencing strategy?
pros: - fast - also high degree of success (low error rate) cons: - more gaps - not as thorough - relied heavily on chromosomal maps generated by the IHGSC
How many genes does the worm and fly have?
worm: 20,000 ( very similar to humans: 20,300) fly: 13,500 genes