work packages (WP):
WP number:
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1
Start month:
September
Duration: (month)
1
Person months:
1
Title
Sampling, extracting and fixing nematodes
Objective: To collect nematodes from botanical garden and fix them for long time study
Task(s): detailed description of the activities
Task 1.1
Collect the soil and root samples around plant rhizospheres in botanical garden randomly
Task 1.2
Extract the nematodes: using modified Baermann tray method or extract directly from the root under dissecting microscope.
Task 1.3
Pick up the interested groups of nematodes and fix them with TAF for morphological work or fix with DESS for molecular work
Deliverables and timing:
D1: Sampling (September)
D2: Extracting (September)
D3: Fixing (September)
WP number:
2
Start month:
September
Duration: (month)
3
Person months:
2
Title
Preparation and running PCR
Objective: To prepare the DNA templates and amplify them by PCR with different primers
Task(s): detailed description of the activities
Task 2.1
Take the pictures of the nematodes with temporary slides
Task 2.2
For each sample, we cut single nematodes into 2à3 pieces and put them in 20µl of WLB, store them at -20oC
Task 2.2
Extract DNA from nematodes by adding 1µl of protein K for each sample and run the protocol to extract DNA with WLB
Task 2.3
Run PCR with different primers (D2-D3, ITS, COI…) and visualize by gel electrophoresis, send to Macrogen to get sequences
Deliverables and timing:
D1: Preparing DNA templates (September, October)
D2: Running PCR and gel electrophoresis (October to December)
WP number:
3
Start month:
February
Duration: (month)
2
Person months:
1,5
Title
Working with light microscope
Objective: To obtain morphological and morphometric data such as LM pictures, drawings, measurements
Task(s): detailed description of the activities
Task 3.1
Transfer nematodes from fixative solution to glycerin and make permanent slides
Task 3.2
Take LM pictures, draw and measure nematode indices
Task 3.3
Redraw nematodes by illustrator software
Deliverables and timing:
D1: Making permanent slides, taking pictures, measuring (February)
D2: Redrawing by illustrator (March)
WP number:
4
Start month:
April
Duration: (month)
1
Person months:
1
Title
Working with scanning electron microscope
Objective: To obtain SEM pictures
Task(s): detailed description of the activities
Task 4.1
Prepare samples for taking SEM pictures
Task 4.2
Take pictures by scanning electron microscope
Deliverables and timing:
D1: Preparing samples and taking pictures (April)
WP number:
5
Start month:
Mayr
Duration: (month)
1
Person months:
1
Title
Analyzing and combining data
Objective: To compile data and write the thesis
Task(s): detailed description of the activities
Task 5.1
Analyze morphological and molecular data
Task 5.2
Arrange the data and write the thesis
Deliverables and timing:
D1: compiling data and writing the thesis (May)
Summary
S
O
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D
J
F
M
A
M
WP1
x
Task 1.1 Sampling
x
Task 1.2 Extraction
x
Task 1.3 Fixation
x
WP2
x
x
x
x
Task 2.1 Backup pictures from temporary slides
x
x
Task 2.2 Preparation for DNA extraction
x
x
Task 2.3 DNA Extraction
x
x
x
Task 2.4 Running PCR and visualize
x
x
x
WP3
x
x
Task 3.1 Dehydration and making permanent slides
x
Task 3.2 Take LM pictures, draw and measure
x
Task 3.3 Redraw
x
WP4
x
Task 4.1 Prepare samples for taking SEM pictures
x
Task 4.2 Take pictures by scanning electron microscope
x
WP5
x
Task 5.1 Analyze morphological and molecular data
x
Task 5.2 Arrange the data and write the thesis
x
