Bhupi dicty
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Transcript of Bhupi dicty
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Summer Training PresentationsDepartment of Molecular and Human Genetics
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Understanding of the life cycle of Dictyostelium
discoideum and cloning of putative gene
Mentor:
Dr. Shweta Saran
Developmental Biology Lab
SLS JNU, New Delhi.
Presented By:
Bhupender Verma
M.Sc. (F) MHG BHU
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Introduction Dictyostelium discoideum are single
cellular organisms
Live on decaying logs and feed on
bacteria
Dictyostelium discoideum follow asexual
cycle-
• when there is plenty of food available
• Live solitary
• Are haploid
• Reproduce by binary fission
Also called as “Social amoebae”
During starvation organisms aggregate
and migrating slug is formed that
culminates in a fruiting body to release
spores
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Figure: Scott F. Gilbert-Developmental Biology 8th edition
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Domain – Eukarya
Kingdom- Amoebozoa
Superphylum- Conosa
Phylum- Mycetozoa
Class- Dictyostelia
Order- dictyosteliida
Family- Dictyosteliidae
Genus- Dictyostelium
Species- D. discoideum
Classification:
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Life cycle
In lab Dicty are grown in HL5 liquid media at 22ºC.
In nutrient rich conditions Dicty divide by binary fission
and remain solitary.
For studying their development a concentrated solution
is transferred to the NNA plates.
In the absence of nutrients, these myxomoebae join
together to form moving streams of cells converging at a
central point.
Different developmental stages that can be observed:
• Tight aggregate
• Migrating slug (pseudoplasmodium or grex) – slimy
sheath encased
• Fruiting body
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Vegetative loose aggregate mound migratory slug
Early culminant fruiting body
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Cloning of the putative gene:
Strategy:
• Design the primers
• Gradient PCR for optimizing annealing conditions
• Standard PCR for obtaining amplified insert
• Digestion of vector and insert with HindIII and PstI
• Liagtion of insert to the vector
•Transform bacteria with recombinant vector
• Isolate cloned plasmid and digest for checking if insert is
desirable
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Gradient PCR for optimizing annealing conditions:
5 kb
1.5 kb
500 bp
5 kb
1.5 kb
500 bp
Design the primers
• Gradient PCR
• Standard PCR
• Digestion with HindIII
and PstI
• Liagtion
• Bacterial
transformaton
• Isolate cloned plasmid
and digest for checking
if insert is desirable
1 2 3 4 5 6 7 8 9 10 M 11 12 13 14 15 16 17 18 19 20
21 22 23 24 25 26 27 28 29 30 M 31 32 33 34 35 36
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Standard PCR for obtaining amplified insert:
5 kb
1.5 kb
500 bp
Design the primers
• Gradient PCR
• Standard PCR
• Digestion with HindIII
and PstI
• Liagtion
• Bacterial
transformaton
• Isolate cloned plasmid
and digest for checking
if insert is desirable
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pDrive cloning vector-
Design the primers
• Gradient PCR
• Standard PCR
• Digestion with HindIII
and PstI
• Liagtion
• Bacterial
transformaton
• Isolate cloned plasmid
and digest for checking
if insert is desirable
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Digestion of vector and insert with HindIII and PstI
5 kb
1.5 kb
500 bp
Design the primers
• Gradient PCR
• Standard PCR
• Digestion with HindIII
and PstI
• Liagtion
• Bacterial
transformaton
• Isolate cloned plasmid
and digest for checking
if insert is desirable
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Checking insert from fallout size:
5 kb
1.5 kb
500 bp
5 kb
1.5 kb
500 bp
Design the primers
• Gradient PCR
• Standard PCR
• Digestion with HindIII
and PstI
• Liagtion
• Bacterial
transformaton
• Isolate cloned plasmid
and digest for checking
if insert is desirable
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Cloning two segments of a putative gene
in pDrive vector for making Knockout-
1. Insert 1 – obtained from digestion (HindIII & NotI) of cloning
vector as pop out
2. pDrive vector – already had other insert so digest with (HindIII &
NotI) & obtain vector-BSR
3. Ligate insert to vector
4. Transform bacteria
5. Grow bacteria and isolate plasmid
6. Digest plasmid for checking proper ligation
7. Proceed with the colony that had proper insert
8. PCR of insert 2
9. Digest insert 2
10.Ligation
11.Transformation
12.Isolate plasmid and check
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1. Insert 1-as pop out
2. pDrive -had other
insert
3. Ligation of insert 1
4. Transform E.coli
5. Grow E.coli &
isolate plasmid
6. Digest plasmid for
check
7. Proceed with sample
having proper insert
8. PCR of insert 2
9. Digest insert 2
10.Ligation
11.Transformation
12.Isolate plasmid and
check
Digestion with HindIII & NotI
+BSR
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5 kb
1.5 kb
500 bp
Check after elution from
agarose gel:
1. Insert 1-as pop out
2. pDrive -had other
insert
3. Ligation of insert 1
4. Transform E.coli
5. Grow E.coli &
isolate plasmid
6. Digest plasmid for
check
7. Proceed with sample
having proper insert
8. PCR of insert 2
9. Digest insert 2
10.Ligation
11.Transformation
12.Isolate plasmid and
check
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1. Insert 1-as pop out
2. pDrive -had other
insert
3. Ligation of insert 1
4. Transform E.coli
5. Grow E.coli &
isolate plasmid
6. Digest plasmid for
check
7. Proceed with sample
having proper insert
8. PCR of insert 2
9. Digest insert 2
10.Ligation
11.Transformation
12.Isolate plasmid and
check
For checking again digest
with HindII & NotI
5 kb
1.5 kb
500 bp
5 kb
1.5 kb
500 bp
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1. Insert 1-as pop out
2. pDrive -had other
insert
3. Ligation of insert 1
4. Transform E.coli
5. Grow E.coli &
isolate plasmid
6. Digest plasmid for
check
7. Proceed with sample
having proper insert
8. PCR of insert 2
9. Digest insert 2
10.Ligation
11.Transformation
12.Isolate plasmid and
check
For checking again digest
with HindII & NotI
5 kb
1.5 kb
500 bp
5 kb
1.5 kb
500 bp
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After insert1 what do we have?
pDrive-Insert1-BSR
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1. Insert 1-as pop out
2. pDrive -had other
insert
3. Ligation of insert 1
4. Transform E.coli
5. Grow E.coli &
isolate plasmid
6. Digest plasmid for
check
7. Proceed with sample
having proper insert
8. PCR of insert 2
9. Digestion of insert 2
10.Ligation
11.Transformation
12.Isolate plasmid and
check
5 kb
1.5 kb
500 bp
Digestion with HindIII &
BamhI:
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1. Insert 1-as pop out
2. pDrive -had other
insert
3. Ligation of insert 1
4. Transform E.coli
5. Grow E.coli &
isolate plasmid
6. Digest plasmid for
check
7. Proceed with sample
having proper insert
8. PCR of insert 2
9. Digestion of insert 2
10.Ligation
11.Transformation
12.Isolate plasmid and
check
Now we are ready with a DNA segment that is “insert1-BSR-insert2”This insert can be used for knocking out this putative genesAnd my insert is still under study
Result:
pDrive Insert1-BSR-Insert2
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RICARDO ESCALANTE and JUAN J. VICENTE- Dictyostelium
discoideum: a model system for differentiation and patterning(2000)
L. Eichinger, J. A. Pachebat, G. Glockner- The genome of the social
amoeba Dictyostelium discoideum (2005)
Developmental biology- Scott F. Gilbert- 8th edition.
References:
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Thank you!