iGEM 2017 — Team NCTU_Formosa

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# Team:NCTU Formosa/Notebook

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* Notebook
  + [Protocol](https://2017.igem.org/Team%3ANCTU_Formosa/Protocol)
  + [Lab Notes](https://2017.igem.org/Team%3ANCTU_Formosa/Notebook)
* Team
  + [Team Introduction](https://2017.igem.org/Team%3ANCTU_Formosa/Team)
  + [Attribution](https://2017.igem.org/Team%3ANCTU_Formosa/Attributions)
* Achievement
  + [Medal Criteria](https://2017.igem.org/Team%3ANCTU_Formosa/Medal_Criteria)
* Human Practice
  + [Collaboration](https://2017.igem.org/Team%3ANCTU_Formosa/Collaborations)
  + [HP Silver](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Silver)
  + [HP Gold Integrated](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Gold_Integrated)
  + [Education and Public Engagement](https://2017.igem.org/Team%3ANCTU_Formosa/Engagement)
* Parts
  + [Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Parts)
  + [Basic Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Basic_Part)
  + [Composite Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Composite_Part)
* Wet Lab
  + [Experiment Design](https://2017.igem.org/Team%3ANCTU_Formosa/Experiments)
  + [Fungal Experiment](https://2017.igem.org/Team%3ANCTU_Formosa/Fungal_Experiment)
  + [Fungal Result](https://2017.igem.org/Team%3ANCTU_Formosa/Fungal_Result)
  + [Protein Expression](https://2017.igem.org/Team%3ANCTU_Formosa/Protein_Expression)
  + [Safety](https://2017.igem.org/Team%3ANCTU_Formosa/Safety)
* Modeling
  + [Peptide Prediction Model](https://2017.igem.org/Team%3ANCTU_Formosa/Model)
  + [Disease Occurrence Model](https://2017.igem.org/Team%3ANCTU_Formosa/Disease_Occurrence_Model)
* Project
  + [Description](https://2017.igem.org/Team%3ANCTU_Formosa/Description)
  + [Design](https://2017.igem.org/Team%3ANCTU_Formosa/Applied_Design)
  + [Peptide Prediction](https://2017.igem.org/Team%3ANCTU_Formosa/Peptide_Prediction)
  + [Disease Occurrence Prediction](https://2017.igem.org/Team%3ANCTU_Formosa/Disease_Occurrence_Prediction)
  + [Demonstration](https://2017.igem.org/Team%3ANCTU_Formosa/Demonstrate)
  + [Contribution](https://2017.igem.org/Team%3ANCTU_Formosa/Contribution)
  + [Improvement](https://2017.igem.org/Team%3ANCTU_Formosa/Improve)
* [Home](https://2017.igem.org/Team%3ANCTU_Formosa)

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MENU

[HOME](https://2017.igem.org/Team%3ANCTU_Formosa)

Project

[Description](https://2017.igem.org/Team%3ANCTU_Formosa/Description)
[Design](https://2017.igem.org/Team%3ANCTU_Formosa/Applied_Design)
[Peptide Prediction](https://2017.igem.org/Team%3ANCTU_Formosa/Peptide_Prediction)
[Disease Occurrence Prediction](https://2017.igem.org/Team%3ANCTU_Formosa/Disease_Occurrence_Prediction)
[Demonstration](https://2017.igem.org/Team%3ANCTU_Formosa/Demonstrate)
[Contribution](https://2017.igem.org/Team%3ANCTU_Formosa/Contribution)
[Improvement](https://2017.igem.org/Team%3ANCTU_Formosa/Improve)

Modeling

[Peptide Prediction Model](https://2017.igem.org/Team%3ANCTU_Formosa/Model)
[Disease Occurrence Model](https://2017.igem.org/Team%3ANCTU_Formosa/Disease_Occurrence_Model)

Wet Lab

[Experiment Design](https://2017.igem.org/Team%3ANCTU_Formosa/Experiments)
[Fungal Experiment](https://2017.igem.org/Team%3ANCTU_Formosa/Fungal_Experiment)
[Fungal Result](https://2017.igem.org/Team%3ANCTU_Formosa/Fungal_Result)
[Protein Expression](https://2017.igem.org/Team%3ANCTU_Formosa/Protein_Expression)
[Safety](https://2017.igem.org/Team%3ANCTU_Formosa/Safety)

Parts

[Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Parts)
[Basic Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Basic_Part)
[Composite Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Composite_Part)

Human Practice

[Collaboration](https://2017.igem.org/Team%3ANCTU_Formosa/Collaborations)
[HP Silver](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Silver)
[HP Gold Integrated](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Gold_Integrated)
[Education and Public Engagement](https://2017.igem.org/Team%3ANCTU_Formosa/Engagement)

Achievement

[Medal Criteria](https://2017.igem.org/Team%3ANCTU_Formosa/Medal_Criteria)

Team

[Team Introduction](https://2017.igem.org/Team%3ANCTU_Formosa/Team)
[Attribution](https://2017.igem.org/Team%3ANCTU_Formosa/Attributions)

Notebook

[Protocol](https://2017.igem.org/Team%3ANCTU_Formosa/Protocol)
[Lab Notes](https://2017.igem.org/Team%3ANCTU_Formosa/Notebook)

[![](http://placehold.it/350x150)](https://2017.igem.org/Team%3ANCTU_Formosa)

MENU

[HOME](https://2017.igem.org/Team%3ANCTU_Formosa)

TEAM

[Team](https://2017.igem.org/Team%3ANCTU_Formosa/Team)
[Collaborations](https://2017.igem.org/Team%3ANCTU_Formosa/Collaborations)

PROJECT

[Description](https://2017.igem.org/Team%3ANCTU_Formosa/Description)
[Design](https://2017.igem.org/Team%3ANCTU_Formosa/Design)
[Experiments](https://2017.igem.org/Team%3ANCTU_Formosa/Experiments)
[Notebook](https://2017.igem.org/Team%3ANCTU_Formosa/Notebook)
[InterLab](https://2017.igem.org/Team%3ANCTU_Formosa/InterLab)
[Contribution](https://2017.igem.org/Team%3ANCTU_Formosa/Contribution)
[Model](https://2017.igem.org/Team%3ANCTU_Formosa/Model)
[Results](https://2017.igem.org/Team%3ANCTU_Formosa/Results)
[Demonstrate](https://2017.igem.org/Team%3ANCTU_Formosa/Demonstrate)
[Improve](https://2017.igem.org/Team%3ANCTU_Formosa/Improve)
[Attributions](https://2017.igem.org/Team%3ANCTU_Formosa/Attributions)

PARTS

[Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Parts)
[Basic Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Basic_Part)
[Composite Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Composite_Part)
[Part Collection](https://2017.igem.org/Team%3ANCTU_Formosa/Part_Collection)

[SAFETY](https://2017.igem.org/Team%3ANCTU_Formosa/Safety)

HUMAN PRACTICES

[Silver HP](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Silver)
[Integrated and Gold](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Gold_Integrated)
[Public Engagement](https://2017.igem.org/Team%3ANCTU_Formosa/Engagement)

AWARDS

[Applied Design](https://2017.igem.org/Team%3ANCTU_Formosa/Applied_Design)
[Entrepreneurship](https://2017.igem.org/Team%3ANCTU_Formosa/Entrepreneurship)
[Hardware](https://2017.igem.org/Team%3ANCTU_Formosa/Hardware)
[Measurement](https://2017.igem.org/Team%3ANCTU_Formosa/Measurement)
[Model](https://2017.igem.org/Team%3ANCTU_Formosa/Model)
[Plant](https://2017.igem.org/Team%3ANCTU_Formosa/Plant)
[Software](https://2017.igem.org/Team%3ANCTU_Formosa/Software)

[JUDGING FORM](https://igem.org/2017_Judging_Form?team=NCTU_Formosa)

NCTU\_Formosa: Lab Note

![](https://static.igem.org/mediawiki/2017/d/d5/Labnote_head.png)

###### Dry Lab

![](https://static.igem.org/mediawiki/2017/4/4f/Ptp_hide.png)

# Week 3.13~3.19

Searching for more information about antifungal diseases

Searching for useful databases: CAMP, PhyAMP

# Week 3.20~3.26

Started building relationship between host, pathogen, disease and peptides

# Week 3.27~4.2

View more bioformatic tools: BLAST, COBLAT, CD search

# Week 4.3~4.9

Searching for more information or paper about fungal diseases

Web crawler of Phi-base, Phytopath,PhytAMP,CAMP

# Week 4.10~4.16

Started building our own database, the building method was established

# Week 4.17~4.23

With the idea of BLAST, COBALT, CDsearch, began to group up different kinds of peptides

# Week 5.1~5.6

Finished grouping up of peptides in new database

Started on studying the Scoring Card Methods (SCM)

# Week 5.15~5.21

Had a meeting with Prof. HO, HSING-YING to learn more about

SCM and confirm previous concept.

Debug of program and database

# Week 5.22~5.28

Web crawler of Uniport

Successfully established our primary SCM

# Week 6.25~7.1

Ask government agencies for disease information

Disease information searching on the Internet

# Week 7.2~7.8

Web crawler of weather information of Central Weather Bureau

# Week 7.9~7.15

Arrange the information of weather

Arrange the information of diseases

Started organizing the website of Parabase

# Week 7.16~7.22

Combining and analyzing data of diseases and weather condition

# Week 7.23~7.29

Combining and analyzing data of diseases and weather condition

# Week 7.30~8.5

Paused for the 5th iGEM Asia-Pacific Conference

Start to discuss the whole concept and the key vision of project and wiki pages

# Week 8.6~8.12

Started to build the model of IoT forecast system

# Week 8.13~8.19

Building the model of IoT forecast system with CNN

# Week 8.20~8.26

IoT forecast system model adjust

Database data updated and utilized

# Week 8.27~9.2

Tried to use other method to build and utilize the model (composite combination model)

Primary test for Parabase on server

# Week 9.3~9.9

Tried to use other methods to build and utilize the model (composite combination model)

# Week 9.10~9.16

Started to link to IoTtalk, testing sensors

# Week 9.17~9.23

Ran the whole process and debug of IoT forecast system

# Week 9.24~9.30

Started beautifying the website of Parabase

# Week 10.01~10.07

Parabase online

Working more and harder on wiki pages

Still debug and utilize the whole system, including SCM model, Parabase and Iot forecast system

# Wiki Freeze

![](https://static.igem.org/mediawiki/2017/c/cb/Ptp_show.png)

###### Wet Lab

![](https://static.igem.org/mediawiki/2017/4/4f/Ptp_hide.png)

# Week 6.18~6.24

Received and resuspended gBlock Sa-AFP1 basic part

Received and resuspended gBlock Sa-AFP2 basic part

Received and resuspended gBlock Rs-AFP2 basic part

Received and resuspended gBlock MiAMP1 basic part

Received and resuspended gBlock LaLTP basic part

gBlock amplification of Sa-AFP1 basic part (Pfu PCR)

gBlock amplification of Sa-AFP2 basic part (Pfu PCR)

gBlock amplification of Rs-AFP2 basic part (Pfu PCR)

gBlock amplification of MiAMP1 basic part (Pfu PCR)

gBlock amplification of LaLTP basic part (Pfu PCR)

Electrophoresis of PCR product

Digestion of PCR product

Ligation of digestion product

Transformation of Sa-AFP1 basic part ligation product

Transformation of Sa-AFP2 basic part ligation product

Transformation of Rs-AFP2 basic part ligation product

Transformation of MiAMP1 basic part ligation product

Transformation of LaLTP basic part ligation product

# Week 6.25~7.1

Sequencing of MiAMP1- psB1A3 plasmid

Sequencing of Sa-AFP1- psB1A3 plasmid

Sequencing of Sa-AFP2- psB1A3 plasmid

Sequencing of Rs-AFP2- psB1A3 plasmid

Electrophoresis (check the biobrick from IGEM kit)

* K1763424
* K808003
* K1763440
* K1763438

Successful transformation of iGEM kit K1763424 to *E. coil* DH5 α

Successful transformation of iGEM kit K808003 to *E. coil* DH5 α

Successful transformation of iGEM kit K1763440 to *E. coil* DH5 α

Successful transformation of iGEM kit K1763438 to *E. coil* DH5 α

# Week 7.2~7.8

Cultivation of transformed *E. coil*

Cultivation of *E. coil* Rosetta gami

# Week 7.9~7.15

Sequencing of LaLTP - psB1A3 plasmid

Miniprep of pSB1A3 plasmid

Digestion of pSB1A3 plasmid

Electrophoresis for digestion

Cultivation of *E. coil* with pSB1A3 plasmid

Received and resuspended gBlock of predicted peptides

# Week 7.16~7.22

Digestion of K808003 Cr plasmid

Digestion of K848008 Cr plasmid

Digestion of J23101+B0034 Kr plasmid

Ligation of K808003 Cr plasmid

Ligation of K848008 Cr plasmid

Ligation of J23101+B0034 Kr plasmid

Ligation of pSB1A3 plasmid

Start cloning of predicted peptides

gBlock amplification of predicted peptides

* Brevinin-1E (B-1E)
* Pelophylaxin-4 (Pe-4)
* 1095.6 Da venom vasodilator peptide (1095.6)
* Temporin-SN2 (T-SN2)

PfuPCR of predicted peptides sequences

* Brevinin-1E (B-1E)
* Pelophylaxin-4 (Pe-4)
* 1095.6 Da venom vasodilator peptide (1095.6)
* Temporin-SN2 (T-SN2)

Digestion of B-1E plasmid

Digestion of Pe-4 plasmid

Digestion of 1095.6 plasmid

Digestion of T-SN2 plasmid

Ligation of digestion product of B-1E

Ligation of digestion product of Pe-4

Ligation of digestion product of 1095.6

Ligation of digestion product of T-SN2

Ligation of digestion product of pSB1A3

# Week 7.23~7.29

Transformation of B-1E ligation product

Transformation of Pe-4 ligation product

Transformation of 1095.6 ligation product

Transformation of T-SN2 ligation product

# Week 7.30~8.5

Experiment paused for the 5th iGEM Asia-Pacific Conference

# Week 8.6~8.12

Taq-PCR of *E.coil* with transformed gene B-1E

Taq-PCR of *E.coil* with transformed gene Pe-4

Cultivation of transformed *E.coil* with transformed gene B-1E

Cultivation of transformed *E.coil* with transformed gene Pe-4

Sonication *E.coil* Rosetta gami with pSB1A3

Transformation for both DH5 α & Rosatta-gami (RG)

* MiAMP1-psB1A3
* Sa-AFP1- psB1A3
* Sa-AFP2- psB1A3
* Rs-AFP2- psB1A3
* LaLTP-psB1A3

Start cloning of predicted peptides

* M-C
* C-1.4

PfuPCR of predicted peptides sequences

* M-C
* C-1.4

Digestion of PCR product of M-C

Digestion of PCR product of C-1.4

Ligation of digestion product of M-C

Ligation of digestion product of C-1.4

Transformation of M-C ligation product

Transformation of C-1.4 ligation product

# Week 8.13~8.19

Cultivation for more *E.coil* Rosatta-gami (RG)

Peptide tests for best efficiency produced by Rosatta-gami in different time

* MiAMP1-psB1A3
* Sa-AFP1- psB1A3
* Sa-AFP2- psB1A3
* Rs-AFP2- psB1A3
* LaLTP-psB1A3

Miniprep of MiAMP1-psB1A3 plasmid

Miniprep of Sa-AFP1- psB1A3 plasmid

Miniprep of Sa-AFP2- psB1A3 plasmid

Miniprep of Rs-AFP2- psB1A3 plasmid

Miniprep of LaLTP-psB1A3 plasmid

Cultivation for testing logarithmic phase

* MiAMP1 psB1A3
* Sa-AFP1 psB1A3
* Sa-AFP2 psB1A3
* Rs-AFP2 psB1A3
* LaLTP psB1A3
* Rosatta-gami with Cr Kr

SDS-PAGE of produced protein check

* MiAMP1 psB1A3 16HR
* Sa-AFP1 psB1A3 16HR
* Sa-AFP2 psB1A3 16HR
* Rs-AFP2 psB1A3 16HR
* LaLTP psB1A3 16HR
* Rosatta-gami with CrKr 16HR

Optical Density test for testing logarithmic phase

* MiAMP1 psB1A3 16HR 18HR 20HR 22HR
* Sa-AFP1 psB1A3 16HR 18HR 20HR 22HR
* Sa-AFP2 psB1A3 16HR 18HR 20HR 22HR
* Rs-AFP2 psB1A3 16HR 18HR 20HR 22HR
* LaLTP psB1A3 16HR 18HR 20HR 22HR

Cultivation for more plasmid of M-C

Cultivation for more plasmid of C-1.4

Miniprep of M-C plasmid

Miniprep of C-1.4 plasmid

# Week 8.20~8.26

TaqPCR of M-C plasmid

TaqPCR of C-1.4 plasmid

Digestion of PCR product of M-C

Digestion of PCR product of C-1.4

Sequencing of Pe-4- pSB1A3 plasmid

Sequencing of B-1E- pSB1A3 plasmid

Cultivation for testing OD value

* MiAMP1 psB1A3
* Sa-AFP1 psB1A3
* Sa-AFP2 psB1A3
* Rs-AFP2 psB1A3
* LaLTP psB1A3
* Rosatta-gami with CrKr

Ligation of digestion product of M-C

Ligation of digestion product of C-1.4

Transformation of M-C ligation product

Transformation of C-1.4 ligation product

# Week 8.27~9.2

SDS-PAGE of produced protein check

* MiAMP1 psB1A3 16HR
* Sa-AFP1 psB1A3 16HR
* Sa-AFP2 psB1A3 16HR
* Rs-AFP2 psB1A3 16HR
* LaLTP psB1A3 16HR
* Rosatta-gami with CrKr

Cultivation for peptides

* MiAMP1 psB1A3
* Sa-AFP1 psB1A3
* Sa-AFP2 psB1A3
* Rs-AFP2 psB1A3
* LaLTP psB1A3
* Rosatta-gami with CrKr

SDS-PAGE with urea added to make peptides refolded

* MiAMP1 psB1A3
* Sa-AFP1 psB1A3
* Sa-AFP2 psB1A3
* Rs-AFP2 psB1A3
* LaLTP psB1A3
* psB1A3
* Rosatta-gami (normal)

# Week 9.3~9.9

Cultivation for testing logarithmic phase (Rosatta-gami)

* MiAMP1 psB1A3
* Sa-AFP1 psB1A3
* LaLTP psB1A3
* Pe-4 psB1A3
* B-1E psB1A3

Cultivation for plasmid

* M-C
* C-1.4

Miniprep for sequencing plasmid

* M-C
* C-1.4

# Week 9.10~9.16

Sequencing of M-C plasmid sample

Repeat DNA experiments for validated peptides, MiAMP1, Sa-AFP1, Sa- AFP2, Rs-AFP2, LaLTP

Pfu-PCR for MiAMP1, Sa-AFP1, Sa-AFP2, Rs-AFP2, LaLTP Digestion for PCR product

Ligation for MiAMP1, Sa-AFP1, Sa-AFP2, Rs-AFP2, LaLTP plasmids

Transformation for ligation product

Sonication for peptide

* MiAMP1
* LaLTP
* Sa-AFP1
* Sa-AFP2
* Rs-AFP2
* Pe-4
* B-1E

# Week 9.17~9.23

SDS-PAGE with urea added to make peptides refolded

* MiAMP1
* LaLTP
* Sa-AFP1
* Sa-AFP2
* Rs-AFP2
* Pe-4
* B-1E

# Week 9.24~9.30

Miniprep of Rs-AFP2, LaLTP plasmid for sequencing

Transformation for more E.coil to produce more plasmid

# Wiki Freeze

![](https://static.igem.org/mediawiki/2017/c/cb/Ptp_show.png)

###### Fungal Experiment

![](https://static.igem.org/mediawiki/2017/4/4f/Ptp_hide.png)

# Week 4.24~4.30

First visit to Dr. Tsai at Taiwan Agricultural Research Institute, Taichung

First visit to Professor Lee, Department of Plant Pathology of National Chung Hsing University

Got some experimental fungi from Taiwan Agricultural Research Institute

# Week 5.1~5.7

Second visit to Dr. Tsai.

# Week 5.8~5.14

Started wet lab fungal experiments design

Started fungi culture (plates from Dr. Tsai)

# Week 7.16~7.22

Started wet lab fungal experiment training for more team members

Started training experiments

# Week 8.13~8.19

Visit Professor Chia-Lin Chung, Department of Plant Pathology and Microbiology, National Taiwan University

# Week 8.27~9.2

Experiments failed, debug and adjusted experiment methods and protocols

# Week 9.3~9.9

Visited Dr. Tsai again

# Week 9.10~9.16

Adjusted and tested new method

# Week 9.17~9.23

Inhibition zone test using NaN3 against *Botrytis cinerea* (training)

Spore germination test using NaN3 against *Botrytis cinerea* (training)

Plant infection test of Botrytis cinerea

# Week 9.24~9.30

Spore germination test using sonication product of Sa-AFP1 transformed *E. coli* liquid against *Botrytis cinerea*

Spore germination test using sonication product of Sa-AFP2 transformed *E. coli* liquid against *Botrytis cinerea*

Spore germination test using sonication product of Rs-AFP2 transformed *E. coli* liquid against *Botrytis cinerea*

Plant infection test of *Botrytis cinerea*

# Week 10.01~10.07

Spore germination test using sonication product of Sa-AFP1 transformed *E. coli* liquid against *Botrytis cinerea*

Spore germination test using sonication product of Sa-AFP1 transformed *E. coli* liquid against *Botrytis cinerea*

Spore germination test using sonication product of Sa-AFP2 transformed *E. coli* liquid against *Botrytis cinerea*

Spore germination test using sonication product of Rs-AFP2 transformed *E. coli* liquid against *Botrytis cinerea*

Plant infection test of *Botrytis cinerea*

# Week 10.08~10.14

Inhibition zone test using Pe-4 pure peptide against *Botrytis
cinerea*

Inhibition zone test using M-C pure peptide against *Botrytis
cinerea*

Inhibition zone test using 1095.6 pure peptide against *Botrytis
cinerea*

Inhibition zone test using T-SN2 pure peptide against *Botrytis
cinerea*

Inhibition zone test using B-1E pure peptide against *Botrytis
cinerea*

Inhibition zone test using C-1,4 pure peptide against *Botrytis
cinerea*

Spore germination test using Pe-4 pure peptide against *Botrytis
cinerea*

Spore germination test using M-C pure peptide against *Botrytis
cinerea*

Spore germination test using 1095.6 pure peptide against *Botrytis
cinerea*

Spore germination test using T-SN2 pure peptide against *Botrytis
cinerea*

Spore germination test using B-1E pure peptide against *Botrytis
cinerea*

Spore germination test using C-1,4 pure peptide against *Botrytis
cinerea*

Plant infection test using Pe-4 pure peptide against *Botrytis
cinerea*

Plant infection test using M-C pure peptide against *Botrytis
cinerea*

Plant infection test using 1095.6 pure peptide against *Botrytis
cinerea*

Plant infection test using T-SN2 pure peptide against *Botrytis
cinerea*

Plant infection test using B-1E pure peptide against *Botrytis
cinerea*

Plant infection test using C-1,4 pure peptide against *Botrytis
cinerea*

Plant infection test using Pe-4 pure peptide against *Botrytis
cinerea*

Plant infection test using M-C pure peptide against *Botrytis
cinerea*

Plant infection test using 1095.6 pure peptide against *Botrytis
cinerea*

Plant infection test using T-SN2 pure peptide against *Botrytis
cinerea*

Plant infection test using B-1E pure peptide against *Botrytis
cinerea*

Plant infection test using C-1,4 pure peptide against *Botrytis
cinerea*

# Week 10.15~10.21

Result double confirm of Inhibition zone test

* Pe-4
* M-C
* 1095.6
* T-SN2
* B-1E
* C-1,4

Result double confirm of Spore germination test

* Pe-4
* M-C
* 1095.6
* T-SN2
* B-1E
* C-1,4

Result double confirm of Plant infection test

* Pe-4
* M-C
* 1095.6
* T-SN2
* B-1E
* C-1,4

# Week 10.21~10.28

Result triple confirm of Inhibition zone test

* Pe-4
* M-C
* 1095.6
* T-SN2
* B-1E
* C-1,4

Result triple confirm of Spore germination test

* Pe-4
* M-C
* 1095.6
* T-SN2
* B-1E
* C-1,4

Result triple confirm of Plant infection test

* Pe-4
* M-C
* 1095.6
* T-SN2
* B-1E
* C-1,4

# Week 10.29~11.04

Spore germination test of validated peptides

Inhibition zone test of validated peptides

Result confirmed and checked

# Wiki Freeze

![](https://static.igem.org/mediawiki/2017/c/cb/Ptp_show.png)

Untitled Document

* + [**Home**](https://2017.igem.org/Team%3ANCTU_Formosa)
* + **Project**
  + [Description](https://2017.igem.org/Team%3ANCTU_Formosa/Description)
  + [Design](https://2017.igem.org/Team%3ANCTU_Formosa/Applied_Design)
  + [Peptide Prediction](https://2017.igem.org/Team%3ANCTU_Formosa/Peptide_Prediction)
  + [Disease Occurrence Prediction](https://2017.igem.org/Team%3ANCTU_Formosa/Disease_Occurrence_Prediction)
  + [Demonstration](https://2017.igem.org/Team%3ANCTU_Formosa/Demonstrate)
  + [Contribution](https://2017.igem.org/Team%3ANCTU_Formosa/Contribution)
  + [Improvement](https://2017.igem.org/Team%3ANCTU_Formosa/Improve)
* + **Modeling**
  + [Peptide Prediction Model](https://2017.igem.org/Team%3ANCTU_Formosa/Model)
  + [Disease Occurrence Model](https://2017.igem.org/Team%3ANCTU_Formosa/Disease_Occurrence_Model)
* + **Wet Lab**
  + [Experiment Design](https://2017.igem.org/Team%3ANCTU_Formosa/Experiments)
  + [Fungal Experiment](https://2017.igem.org/Team%3ANCTU_Formosa/Fungal_Experiment)
  + [Fungal Result](https://2017.igem.org/Team%3ANCTU_Formosa/Fungal_Result)
  + [Protein Expression](https://2017.igem.org/Team%3ANCTU_Formosa/Protein_Expression)
  + [Safety](https://2017.igem.org/Team%3ANCTU_Formosa/Safety)
* + **Parts**
  + [Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Parts)
  + [Basic Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Basic_Part)
  + [Composite Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Composite_Part)
* + **Human Practice**
  + [Collaboration](https://2017.igem.org/Team%3ANCTU_Formosa/Collaborations)
  + [HP Silver](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Silver)
  + [HP Gold Integrated](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Gold_Integrated)
  + [Education and Public Engagement](https://2017.igem.org/Team%3ANCTU_Formosa/Engagement)
* + **Achievement**
  + [Medal Criteria](https://2017.igem.org/Team%3ANCTU_Formosa/Medal_Criteria)
* + **Team**
  + [Team Introduction](https://2017.igem.org/Team%3ANCTU_Formosa/Team)
  + [Attribution](https://2017.igem.org/Team%3ANCTU_Formosa/Attributions)
* + **Notebook**
  + [Protocol](https://2017.igem.org/Team%3ANCTU_Formosa/Protocol)
  + [Lab Notes](https://2017.igem.org/Team%3ANCTU_Formosa/Notebook)

[![](https://static.igem.org/mediawiki/2017/b/bf/HQ_menu_logo.jpg)](https://2017.igem.org)


[![](https://static.igem.org/mediawiki/2017/8/8b/HQ_page_logo.jpg)](https://2017.igem.org)

# Team:NCTU Formosa/Experiments

navigation

[![](https://static.igem.org/mediawiki/2017/e/e9/Nav_pic.jpeg)](https://2017.igem.org/Team%3ANCTU_Formosa)

* Notebook
  + [Protocol](https://2017.igem.org/Team%3ANCTU_Formosa/Protocol)
  + [Lab Notes](https://2017.igem.org/Team%3ANCTU_Formosa/Notebook)
* Team
  + [Team Introduction](https://2017.igem.org/Team%3ANCTU_Formosa/Team)
  + [Attribution](https://2017.igem.org/Team%3ANCTU_Formosa/Attributions)
* Achievement
  + [Medal Criteria](https://2017.igem.org/Team%3ANCTU_Formosa/Medal_Criteria)
* Human Practice
  + [Collaboration](https://2017.igem.org/Team%3ANCTU_Formosa/Collaborations)
  + [HP Silver](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Silver)
  + [HP Gold Integrated](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Gold_Integrated)
  + [Education and Public Engagement](https://2017.igem.org/Team%3ANCTU_Formosa/Engagement)
* Parts
  + [Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Parts)
  + [Basic Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Basic_Part)
  + [Composite Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Composite_Part)
* Wet Lab
  + [Experiment Design](https://2017.igem.org/Team%3ANCTU_Formosa/Experiments)
  + [Fungal Experiment](https://2017.igem.org/Team%3ANCTU_Formosa/Fungal_Experiment)
  + [Fungal Result](https://2017.igem.org/Team%3ANCTU_Formosa/Fungal_Result)
  + [Protein Expression](https://2017.igem.org/Team%3ANCTU_Formosa/Protein_Expression)
  + [Safety](https://2017.igem.org/Team%3ANCTU_Formosa/Safety)
* Modeling
  + [Peptide Prediction Model](https://2017.igem.org/Team%3ANCTU_Formosa/Model)
  + [Disease Occurrence Model](https://2017.igem.org/Team%3ANCTU_Formosa/Disease_Occurrence_Model)
* Project
  + [Description](https://2017.igem.org/Team%3ANCTU_Formosa/Description)
  + [Design](https://2017.igem.org/Team%3ANCTU_Formosa/Applied_Design)
  + [Peptide Prediction](https://2017.igem.org/Team%3ANCTU_Formosa/Peptide_Prediction)
  + [Disease Occurrence Prediction](https://2017.igem.org/Team%3ANCTU_Formosa/Disease_Occurrence_Prediction)
  + [Demonstration](https://2017.igem.org/Team%3ANCTU_Formosa/Demonstrate)
  + [Contribution](https://2017.igem.org/Team%3ANCTU_Formosa/Contribution)
  + [Improvement](https://2017.igem.org/Team%3ANCTU_Formosa/Improve)
* [Home](https://2017.igem.org/Team%3ANCTU_Formosa)

☰

MENU

[HOME](https://2017.igem.org/Team%3ANCTU_Formosa)

Project

[Description](https://2017.igem.org/Team%3ANCTU_Formosa/Description)
[Design](https://2017.igem.org/Team%3ANCTU_Formosa/Applied_Design)
[Peptide Prediction](https://2017.igem.org/Team%3ANCTU_Formosa/Peptide_Prediction)
[Disease Occurrence Prediction](https://2017.igem.org/Team%3ANCTU_Formosa/Disease_Occurrence_Prediction)
[Demonstration](https://2017.igem.org/Team%3ANCTU_Formosa/Demonstrate)
[Contribution](https://2017.igem.org/Team%3ANCTU_Formosa/Contribution)
[Improvement](https://2017.igem.org/Team%3ANCTU_Formosa/Improve)

Modeling

[Peptide Prediction Model](https://2017.igem.org/Team%3ANCTU_Formosa/Model)
[Disease Occurrence Model](https://2017.igem.org/Team%3ANCTU_Formosa/Disease_Occurrence_Model)

Wet Lab

[Experiment Design](https://2017.igem.org/Team%3ANCTU_Formosa/Experiments)
[Fungal Experiment](https://2017.igem.org/Team%3ANCTU_Formosa/Fungal_Experiment)
[Fungal Result](https://2017.igem.org/Team%3ANCTU_Formosa/Fungal_Result)
[Protein Expression](https://2017.igem.org/Team%3ANCTU_Formosa/Protein_Expression)
[Safety](https://2017.igem.org/Team%3ANCTU_Formosa/Safety)

Parts

[Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Parts)
[Basic Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Basic_Part)
[Composite Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Composite_Part)

Human Practice

[Collaboration](https://2017.igem.org/Team%3ANCTU_Formosa/Collaborations)
[HP Silver](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Silver)
[HP Gold Integrated](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Gold_Integrated)
[Education and Public Engagement](https://2017.igem.org/Team%3ANCTU_Formosa/Engagement)

Achievement

[Medal Criteria](https://2017.igem.org/Team%3ANCTU_Formosa/Medal_Criteria)

Team

[Team Introduction](https://2017.igem.org/Team%3ANCTU_Formosa/Team)
[Attribution](https://2017.igem.org/Team%3ANCTU_Formosa/Attributions)

Notebook

[Protocol](https://2017.igem.org/Team%3ANCTU_Formosa/Protocol)
[Lab Notes](https://2017.igem.org/Team%3ANCTU_Formosa/Notebook)

[![](http://placehold.it/350x150)](https://2017.igem.org/Team%3ANCTU_Formosa)

MENU

[HOME](https://2017.igem.org/Team%3ANCTU_Formosa)

TEAM

[Team](https://2017.igem.org/Team%3ANCTU_Formosa/Team)
[Collaborations](https://2017.igem.org/Team%3ANCTU_Formosa/Collaborations)

PROJECT

[Description](https://2017.igem.org/Team%3ANCTU_Formosa/Description)
[Design](https://2017.igem.org/Team%3ANCTU_Formosa/Design)
[Experiments](https://2017.igem.org/Team%3ANCTU_Formosa/Experiments)
[Notebook](https://2017.igem.org/Team%3ANCTU_Formosa/Notebook)
[InterLab](https://2017.igem.org/Team%3ANCTU_Formosa/InterLab)
[Contribution](https://2017.igem.org/Team%3ANCTU_Formosa/Contribution)
[Model](https://2017.igem.org/Team%3ANCTU_Formosa/Model)
[Results](https://2017.igem.org/Team%3ANCTU_Formosa/Results)
[Demonstrate](https://2017.igem.org/Team%3ANCTU_Formosa/Demonstrate)
[Improve](https://2017.igem.org/Team%3ANCTU_Formosa/Improve)
[Attributions](https://2017.igem.org/Team%3ANCTU_Formosa/Attributions)

PARTS

[Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Parts)
[Basic Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Basic_Part)
[Composite Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Composite_Part)
[Part Collection](https://2017.igem.org/Team%3ANCTU_Formosa/Part_Collection)

[SAFETY](https://2017.igem.org/Team%3ANCTU_Formosa/Safety)

HUMAN PRACTICES

[Silver HP](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Silver)
[Integrated and Gold](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Gold_Integrated)
[Public Engagement](https://2017.igem.org/Team%3ANCTU_Formosa/Engagement)

AWARDS

[Applied Design](https://2017.igem.org/Team%3ANCTU_Formosa/Applied_Design)
[Entrepreneurship](https://2017.igem.org/Team%3ANCTU_Formosa/Entrepreneurship)
[Hardware](https://2017.igem.org/Team%3ANCTU_Formosa/Hardware)
[Measurement](https://2017.igem.org/Team%3ANCTU_Formosa/Measurement)
[Model](https://2017.igem.org/Team%3ANCTU_Formosa/Model)
[Plant](https://2017.igem.org/Team%3ANCTU_Formosa/Plant)
[Software](https://2017.igem.org/Team%3ANCTU_Formosa/Software)

[JUDGING FORM](https://igem.org/2017_Judging_Form?team=NCTU_Formosa)

NCTU\_Formosa: Experiment Design

![](https://static.igem.org/mediawiki/2017/8/81/Designexp_head.png)

###### The Procedure of Wet Lab Experiments

![](https://static.igem.org/mediawiki/2017/0/05/Peptide-Flow.png)

# Strains

- Fungal experiments: *Botrytis cinerea*

     (Because of their high infectiousness to many kinds of hosts (around 200 types of species) and also the short lifespan)

- DNA cloning: *E. coli* DH5α

- Peptide cloning: *E. coli* BL21 Rosetta-Gami

- Peptide expression: *E. coli* BL21 Rosetta-Gami

# 1.Experimental Validation for Parabase

     We did the experimental validation for our prediction system using the predicted peptides.

- Inhibition Zone: the measurement of inhibiting mycelia

- Spore Germination: the measurement of inhibiting spores

- Botany Experiment: the observation of the disease occurring in reality

# 2.Further Application in Agriculture

     For the ultimate goal of realizing the system in farmlands, we first attempted to cost down by producing peptides from *E. coli* to prepare for the mass production.

     We added several peptides already known to be antifungal to do the following experiments.

(1)Cloning

     After filtering samples that were not suitable to apply to farms, we tried to transform samples into *E. coli*. We have submitted [Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Part) to iGEM.

(2)Protein Expression

     We then tried to express them by SDS-PAGE.

# 3. Future Work

     For the proteins expressed, we will do the three fungal experiments to do double check, then attempt to apply them into farmlands by the use of IoT and the disease occurrence model.

     For the proteins that aren’t suitable to be expressed by SDS-PAGE, we will try other expression methods.

# 4. How to select the predicted antifungal peptides to do the validation?

     We collected unknown peptides from UniProt database and calculated their scores through the scoring card. After calculating the scores, we selected hundreds of peptides which scores were higher than the threshold.

     Then the peptides would pass through some filters, and then chose our final peptides for wet lab experiments:

First , we deleted the peptides which amino acid lengths were longer than one hundred amino acids or lower than ten amino acids because the lengths of most antifungal peptides are between this range. Second, we checked the UniProt to confirm the sequence correctness of peptides and ensure they were not signal peptides or propeptides. Last, searching the original function of the peptide. If the group of peptides had the same original function, we would only choose the one which possessed the highest score. After filtering the peptides, we have chosen six peptides for following wet lab experiments.

Untitled Document

* + [**Home**](https://2017.igem.org/Team%3ANCTU_Formosa)
* + **Project**
  + [Description](https://2017.igem.org/Team%3ANCTU_Formosa/Description)
  + [Design](https://2017.igem.org/Team%3ANCTU_Formosa/Applied_Design)
  + [Peptide Prediction](https://2017.igem.org/Team%3ANCTU_Formosa/Peptide_Prediction)
  + [Disease Occurrence Prediction](https://2017.igem.org/Team%3ANCTU_Formosa/Disease_Occurrence_Prediction)
  + [Demonstration](https://2017.igem.org/Team%3ANCTU_Formosa/Demonstrate)
  + [Contribution](https://2017.igem.org/Team%3ANCTU_Formosa/Contribution)
  + [Improvement](https://2017.igem.org/Team%3ANCTU_Formosa/Improve)
* + **Modeling**
  + [Peptide Prediction Model](https://2017.igem.org/Team%3ANCTU_Formosa/Model)
  + [Disease Occurrence Model](https://2017.igem.org/Team%3ANCTU_Formosa/Disease_Occurrence_Model)
* + **Wet Lab**
  + [Experiment Design](https://2017.igem.org/Team%3ANCTU_Formosa/Experiments)
  + [Fungal Experiment](https://2017.igem.org/Team%3ANCTU_Formosa/Fungal_Experiment)
  + [Fungal Result](https://2017.igem.org/Team%3ANCTU_Formosa/Fungal_Result)
  + [Protein Expression](https://2017.igem.org/Team%3ANCTU_Formosa/Protein_Expression)
  + [Safety](https://2017.igem.org/Team%3ANCTU_Formosa/Safety)
* + **Parts**
  + [Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Parts)
  + [Basic Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Basic_Part)
  + [Composite Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Composite_Part)
* + **Human Practice**
  + [Collaboration](https://2017.igem.org/Team%3ANCTU_Formosa/Collaborations)
  + [HP Silver](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Silver)
  + [HP Gold Integrated](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Gold_Integrated)
  + [Education and Public Engagement](https://2017.igem.org/Team%3ANCTU_Formosa/Engagement)
* + **Achievement**
  + [Medal Criteria](https://2017.igem.org/Team%3ANCTU_Formosa/Medal_Criteria)
* + **Team**
  + [Team Introduction](https://2017.igem.org/Team%3ANCTU_Formosa/Team)
  + [Attribution](https://2017.igem.org/Team%3ANCTU_Formosa/Attributions)
* + **Notebook**
  + [Protocol](https://2017.igem.org/Team%3ANCTU_Formosa/Protocol)
  + [Lab Notes](https://2017.igem.org/Team%3ANCTU_Formosa/Notebook)

[![](https://static.igem.org/mediawiki/2017/b/bf/HQ_menu_logo.jpg)](https://2017.igem.org)

[![](https://static.igem.org/mediawiki/2017/8/8b/HQ_page_logo.jpg)](https://2017.igem.org)

# Team:NCTU Formosa/Results

[![](http://placehold.it/350x150)](https://2017.igem.org/Team%3ANCTU_Formosa)

MENU

[HOME](https://2017.igem.org/Team%3ANCTU_Formosa)

TEAM

[Team](https://2017.igem.org/Team%3ANCTU_Formosa/Team)
[Collaborations](https://2017.igem.org/Team%3ANCTU_Formosa/Collaborations)

PROJECT

[Description](https://2017.igem.org/Team%3ANCTU_Formosa/Description)
[Design](https://2017.igem.org/Team%3ANCTU_Formosa/Design)
[Experiments](https://2017.igem.org/Team%3ANCTU_Formosa/Experiments)
[Notebook](https://2017.igem.org/Team%3ANCTU_Formosa/Notebook)
[InterLab](https://2017.igem.org/Team%3ANCTU_Formosa/InterLab)
[Contribution](https://2017.igem.org/Team%3ANCTU_Formosa/Contribution)
[Model](https://2017.igem.org/Team%3ANCTU_Formosa/Model)
[Results](https://2017.igem.org/Team%3ANCTU_Formosa/Results)
[Demonstrate](https://2017.igem.org/Team%3ANCTU_Formosa/Demonstrate)
[Improve](https://2017.igem.org/Team%3ANCTU_Formosa/Improve)
[Attributions](https://2017.igem.org/Team%3ANCTU_Formosa/Attributions)

PARTS

[Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Parts)
[Basic Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Basic_Part)
[Composite Parts](https://2017.igem.org/Team%3ANCTU_Formosa/Composite_Part)
[Part Collection](https://2017.igem.org/Team%3ANCTU_Formosa/Part_Collection)

[SAFETY](https://2017.igem.org/Team%3ANCTU_Formosa/Safety)

HUMAN PRACTICES

[Silver HP](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Silver)
[Integrated and Gold](https://2017.igem.org/Team%3ANCTU_Formosa/HP/Gold_Integrated)
[Public Engagement](https://2017.igem.org/Team%3ANCTU_Formosa/Engagement)

AWARDS

[Applied Design](https://2017.igem.org/Team%3ANCTU_Formosa/Applied_Design)
[Entrepreneurship](https://2017.igem.org/Team%3ANCTU_Formosa/Entrepreneurship)
[Hardware](https://2017.igem.org/Team%3ANCTU_Formosa/Hardware)
[Measurement](https://2017.igem.org/Team%3ANCTU_Formosa/Measurement)
[Model](https://2017.igem.org/Team%3ANCTU_Formosa/Model)
[Plant](https://2017.igem.org/Team%3ANCTU_Formosa/Plant)
[Software](https://2017.igem.org/Team%3ANCTU_Formosa/Software)

[JUDGING FORM](https://igem.org/2017_Judging_Form?team=NCTU_Formosa)

# Results

Here you can describe the results of your project and your future plans.

##### What should this page contain?

* Clearly and objectively describe the results of your work.
* Future plans for the project.
* Considerations for replicating the experiments.

##### You should also describe what your results mean:

* Interpretation of the results obtained during your project. Don't just show a plot/figure/graph/other, tell us what you think the data means. This is an important part of your project that the judges will look for.
* Show data, but remember all measurement and characterization data must be on part pages in the Registry.
* Consider including an analysis summary section to discuss what your results mean. Judges like to read what you think your data means, beyond all the data you have acquired during your project.

##### Project Achievements

You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.

* A list of linked bullet points of the successful results during your project
* A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.

##### Inspiration

See how other teams presented their results.

* [2014 TU Darmstadt](https://2014.igem.org/Team%3ATU_Darmstadt/Results/Pathway)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Results)
* [2014 Paris Bettencourt](https://2014.igem.org/Team%3AParis_Bettencourt/Results)

[![](https://static.igem.org/mediawiki/2017/b/bf/HQ_menu_logo.jpg)](https://2017.igem.org)