work of WLB, store them at -20oC Task

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

N

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