LAST REVIEW

Question 1

What should be sequenced (5)

Answer 1

– Medical applications
– Evolutionary significance
– Environmental impact
– Food production
– Cost

Question 2

DeNovo

Answer 2

De novo sequencing using genome
fragmentation and automated
technologies (shotgun sequencing)

Question 3

Pimples

Answer 3

– Some of the unknowns showed unexpected codon bias
patterns suggesting acquired genes through horizontal transfer
– Many provide metabolic capacity: Digestive enzymes that
allows P. acnes to live in your pores and to adhere to your cells.
– Many are immune-related allowing P. acnes to sense an attack
(antibiotic) and change to survive.

Question 4

Gut Bacteria

Answer 4

– Sugar uptake. Many secreted proteinsextracellular
monosaccharides we also use selection.
– Environmental sensing. Sensors that interact with transcription
factors allowing to change gene expression depending on
environmental changes.
– Mobile elements (transposons). They spread antibiotic
resistance.

Question 5

RSCU

Answer 5

random synonomous cpdpm usage

Question 6

Euk Vs. Pro

Answer 6

.

Question 7

Massive Parallel (5)

Answer 7

–1) Libraries are made by fragmentation of DNA and ligation to sequence adapters (No E. coli cell system!).
–2) Amplification is done using beads or glass platforms (emPCR)
–3) All sequencing reactions are run at the same time and with simultaneous detection (Massively parallel sequencing)
–4) Shorter read length than with automated Sanger sequencing
–5) Pair-end reads help in aligning to a reference genome

Question 8

SOLID

Answer 8

ligation of flourescently labled oligonucleotides, dinucleotides are read.
–Employs sequencing by ligation.
–The sequence of the DNA is determined by ligation of fluorescently labeled DNA probes using the DNA on the beads as a template.
–The preferential ligation by DNA ligase for matching sequences results in a signal informative of dinucleotide at that position.

Question 9

Transgenic plants

Answer 9

–Rice that produces vitamin A.
–Genetically engineered corn, cotton and other crop plants express such insecticidal proteins.
–Soybeans producing more monosaturated fatty acids.
–Soybeans producing compounds useful as lubricants, paint, and plasticizers.
– Transgenic plants producing vaccine products. Easily to grow and to administer.

Question 10

Why is rice transgenics cool?

Answer 10

its not a gene but a pathway

Question 11

Knockouts

Answer 11

• mutation introduced by recombination
  1) Modify form of gene linked to genes for neomycin resistance and sensitivity to glanciclovir. 2) Deliver modified gene into embryonic stem (ES) cells. 3)Recombinant ES cells are recovered that contain a disrupted or knockout version of the gene of interest

Question 12

CRISPER cRNA

Answer 12

-genome spcific cRNA sequence binding to DNA leads to cas9 cleaves genome dna
-tiggers repair (homo=nuc specific editing) (nonhomo=generatie deletions…knockouts)
CAS has a sequence motif=PAM

Question 13

Retrovirus: Viral Vector

Answer 13

Attacks proliferating cells (many disorders attack cells that rarely divide)
Can integrate into patient genome (insertional mutagenesis)

Question 14

Adenovirus: Viral Vector

Answer 14

Attacks non dividing cells

Does not integrate into patient genome (repeated treatments)

Question 15

Viral vectors in somatic human gene therapy

Retrovirus: Problems

Answer 15

1. immune responce to virus
2. viral insertion
   viral can integrate into the patient genome and distrust vital genes

Question 16

Four factors made ADA-SCID a good candidate for gene therapy

Answer 16

–Gene was cloned and well characterized
–Blood cells can be easily obtained from patients and reintroduced after adding functional copies of the ADA gene.
–Even small amounts of functional ADA will restore partial immune function
–Overproduction of ADA has no toxic effects

Question 17

To proceed with a gene therapy

Answer 17

• The gene must be cloned and well characterized.
• An effective method should be available for delivering the gene into the desired tissue.
• The risks of gene therapy to the patient should be minimal.
• The disease must not be treatable by other strategies.
• Preliminary experiments with animal models or human cell systems should show the effectiveness of the proposed gene therapy trial.