a toms-turkiye He Heli licobacter cobacter pyl ylori ori %50 - - PowerPoint PPT Presentation

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a toms-turkiye He Heli licobacter cobacter pyl ylori ori %50 - - PowerPoint PPT Presentation

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a toms-turkiye He Heli licobacter cobacter pyl ylori ori %50 %50 He Heli licobacter cobacter pyl ylori ori Peptic ptic Ul Ulcer ers St Stomac mach Cancer ncer PEPTIC ULCERS 300,000 deaths STOMACH CANCER 3rd leading cause

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SLIDE 2

a toms-turkiye

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SLIDE 3
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%50 %50

He Heli licobacter cobacter pyl ylori

  • ri
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He Heli licobacter cobacter pyl ylori

  • ri

Peptic ptic Ul Ulcer ers St Stomac mach Cancer ncer

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PEPTIC ULCERS

300,000 deaths

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SLIDE 7

STOMACH CANCER

3rd leading

cause

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SLIDE 8
  • H. pylori
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SLIDE 9

Penetr netrates tes under er muc ucous

  • us la

layer er Hard d to to cur ure due ue to to ant ntibio ibiotic tic resista sistanc nce.

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CURE CURE

CA CANCER NCER

AIM AIM

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SLIDE 11

2.

  • 2. ACI

CID D REP EPEL ELLENC ENCY

  • 3. INCRE

REAS ASED MOTILI LITY TY 4.

  • 4. SE

SENSI SING 5.

  • 5. KI

KILLING LING

H.

  • H. pylori

lori ER ERADIC ADICATIO TION N . .

1.

  • 1. ACI

CID RES ESIST STANC ANCE

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SLIDE 12

1.

  • 1. ACI

CID RES ESIST STANC ANCE

H.

  • H. pylori

lori ER ERADIC ADICATIO TION N . .

BBa_K1639002

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SLIDE 13

Na Natur turally ally ac acid id res esista istant nt till ill pH pH 5

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SLIDE 14
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OBSERVED EXPECTED

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Bacterial density in OD600nm.

200 400 600 800 1000 1200

Pet45-b gadE Pet45-b gadE Pet45-b gadE Pet45-b gadE Pet45-b gadE pH 7.2 pH 5.0 pH 3.5 pH 2.5 pH 2.0

Cell Viability

Beginning 3 min

  • 1. hour
  • 2. hour

5.hour 9.hour 13.hour

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SLIDE 17

500 1000 1500

Pet45-b gadE

pH 7.2

Beginning 3 min
  • 1. hour
  • 2. hour
5.hour 9.hour 13.hour

500 1000

Pet45-b gadE

pH 5.0

Beginning 3 min
  • 1. hour
  • 2. hour
5.hour 9.hour 13.hour

(-) Control (-) Control

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SLIDE 18

100 200 300 400

Pet45-b gadE

pH 3.5

Beginning 3 min
  • 1. hour
  • 2. hour
5.hour 9.hour 13.hour

100 200 300 400

Pet45-b gadE

pH 2.5

Beginning 3 min
  • 1. hour
  • 2. hour
5.hour 9.hour 13.hour

(-) Control (-) Control

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SLIDE 19

50 100 150 200 250 300

Pet45-b gadE

pH 2.0

Beginning 3 min
  • 1. hour
  • 2. hour
5.hour 9.hour 13.hour

(-) Control

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SLIDE 20
  • 3. INCRE

REAS ASED MOTILI LITY TY 4.

  • 4. SE

SENSI SING 5.

  • 5. KI

KILLING LING 1.

  • 1. ACI

CID RES ESIST STANC ANCE 2.

  • 2. ACI

CID D REP EPEL ELLE LENCY NCY

H.

  • H. pylori

lori ER ERADIC ADICATIO TION N . .

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SLIDE 21

2.

  • 2. ACI

CID D REP EPEL ELLE LENCY NCY

H.

  • H. pylori

lori ER ERADIC ADICATIO TION N . .

BBa_K1639003

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SLIDE 22
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SLIDE 23

OBSERVED EXPECTED

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SLIDE 24
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  • 3. INCRE

REAS ASED MOTILI LITY TY 4.

  • 4. SE

SENSI SING 5.

  • 5. KI

KILLING LING 1.

  • 1. ACI

CID RES ESIST STANC ANCE 2.

  • 2. ACI

CID D REP EPEL ELLE LENCY NCY

H.

  • H. pylori

lori ER ERADIC ADICATIO TION N . .

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  • 3. INCRE

REAS ASED MOTILI LITY TY

H.

  • H. pylori

lori ER ERADIC ADICATIO TION N . .

BBa_K1639004 BBa_K1639005 BBa_K1639006

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a) A MUTANT FORM OF HNS

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OBSERVED EXPECTED

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b) Changing

MotA& MotB to

PomA&PotB

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MotB (E. coli)

PomB

(V. cholerae)

PotB (chimeric)

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HNS PotB59 / PomA 0.25 0.40

24h 24h 24h 24h

HNS-T108I (-) Control

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SLIDE 35 motility 1 2 3 4 5 6 7 8 9 10

HNS-T108I PotB59/PomA Wild type HNS (-) control

10 9 8 3

Motility by fold

Compar ared ed moti tili lities ties: : HNS-T108I > PotB59/PomA > > Wild type HNS > (-) control

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SLIDE 36
  • 3. INCRE

REAS ASED MOTILI LITY TY 4.

  • 4. SE

SENSI SING 5.

  • 5. KI

KILLING LING 1.

  • 1. ACI

CID RES ESIST STANC ANCE 2.

  • 2. ACI

CID D REP EPEL ELLE LENCY NCY

H.

  • H. pylori

lori ER ERADIC ADICATIO TION N . .

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SLIDE 37

4.

  • 4. SE

SENSI SING

H.

  • H. pylori

lori ER ERADIC ADICATIO TION N . .

BBa_K1639014 BBa_K1639000 BBa_K1639001

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SLIDE 38

4.

  • 4. SE

SENSI SING

H.

  • H. pylori

lori ER ERADIC ADICATIO TION N . .

BBa_K1639014 BBa_K1639000 BBa_K1639001

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And Logic Gates

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Toehold-RNA Switches

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The presence of Trigger RNA in the cell unwinds the hairpine structure. Then RBS sets free and causes the production of TEV Protease

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SLIDE 43

We used GFP instead of TEV protease

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IPTG (-) IPTG (+) pColA ToeHold GFP + Trigger RNA pColA ToeHold GFP

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pColA-ToeHold GFP pColA-ToeHold GFP + Trigger RNA

IPTG

+ +

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SLIDE 46

50 100 150 200 250 300

− + − + Toehold Toehold+Trigger

Cell Lysate Fold Change

Avg
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SLIDE 47
  • 3. INCRE

REAS ASED MOTILI LITY TY 4.

  • 4. SE

SENSI SING 1.

  • 1. ACI

CID RES ESIST STANC ANCE 2.

  • 2. ACI

CID D REP EPEL ELLE LENCY NCY 5.

  • 5. KI

KILLING LING

H.

  • H. pylori

lori ER ERADIC ADICATIO TION N . .

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SLIDE 48

5.

  • 5. KI

KILLING LING

H.

  • H. pylori

lori ER ERADIC ADICATIO TION N . .

BBa_K1639007 BBa_K1639008

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SLIDE 49

Ant

nti i

Micr

icrobial

  • bial

Pept

ptide ide

Pexig xiganan anan

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OBSERVED EXPECTED

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OBSERVED EXPECTED

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Barry ry J. Ma . Marsh shall all

2005 Nobel Prize laureate in Physiology or Medicine

‘If you achieved just

  • ne of your goals that

would be exciting enough.’

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6.

  • 6. CA

CANCE CER SWITCH

STOMA OMACH CH CA CANCER NCER TR TREA EATMENT TMENT

BBa_K1639015 BBa_K1639016 BBa_K1639010 BBa_K1639011 BBa_K1639009

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SLIDE 56

miRNA switch working mechanism

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SLIDE 57
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SLIDE 58

Human

Practices

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Going public:

iGEM for little kids

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Outreach:

Street Interview

Interviewed with;

1)Patients 2)Doctors 3)People

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iGEM Meetup: Synbio Day

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A very new approach to medicine;

VIRTUAL HOSPITAL

where synthetic biology meets medicine in future

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SLIDE 63
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Collaborations

Mentored AUC Turkey iGEM team Held a meetup with 3 other regional teams Connected our team to the iGEM Rhizi (created by Paris Bettencourt iGEM) Prepared a VH video of UCL iGEM Team’s project ‘Mind the Gut’ Joined to the iGEM Academy YouTube channel (Created by Tinity iGEM)

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Safety: Suicide Switch

BBa_K1639022

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ACHIEVEM HIEVEMENTS ENTS

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pColA lA (ATOMS OMS) pSB SB1C3 1C3-T7 T7 (ATOMS OMS)

Our ur No Novel el Pl Plas asmids mids

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SLIDE 69

MAIN REFERENCES

[1] Ma, Z., Gong, S., Richard, H., Tucker, D., Conway, T., & Foster, J. (n.d.). GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12. Molecular Microbiology, 1309-1320. [2] Croxen, M., Sisson, G., Melano, R., & Hoffman, P. (2006). The Helicobacter pylori Chemotaxis Receptor TlpB (HP0103) Is Required for pH Taxis and for Colonization of the Gastric Mucosa. Journal of Bacteriology, 2656-2665. [3] Nishino, Y., Onoue, Y., Kojima, S., & Homma, M. (2015). Functional chimeras of flagellar stator proteins between E. coli MotB and Vibrio PomB at the periplasmic region in Vibrio or E. coli. MicrobiologyOpen, 323-331. [4] Donato, G., & Kawula, T. (1998). Enhanced Binding of Altered H-NS Protein to Flagellar Rotor Protein FliG Causes Increased Flagellar Rotational Speed and Hypermotility in Escherichia coli. Journal of Biological Chemistry, 24030-24036. [5] Green, A., Silver, P., Collins, J., & Yin, P. (n.d.). Toehold Switches: De-Novo-Designed Regulators of Gene Expression. Cell, 925-939. [6] Lewis V Wray Jr., Jill M Zalieckas, Susan H Fisher. Bacillus subtilis Glutamine Synthetase Controls Gene Expression through a Protein- Protein Interaction with Transcription Factor TnrA. Cell Volume 107, Issue 4, 16 November 2001, Pages 427–435 [7] Vendeville, A., Winzer, K., Heurlier, K., Tang, C., & Hardie, K. (n.d.). Making 'sense' of metabolism: Autoinducer-2, LUXS and pathogenic
  • bacteria. Nature Reviews Microbiology Nat Rev Micro, 383-396.
[8] Zhang XL, Jiang AM, Ma ZY, Li XB, Xiong YY, Dou JF, Wang JF. The synthetic antimicrobial peptide pexiganan and its nanoparticles (PNPs) exhibit the anti-helicobacter pylori activity in vitro and in vivo. Molecules 2015, 20(3), 3972-3985; doi:10.3390/molecules20033972 [9] Zhao, C., Dwyer, M., Yu, A., Wu, Y., Fang, S., & Middelberg, A. (2015). A simple and low-cost platform technology for producing pexiganan antimicrobial peptide in E. coli. Biotechnol. Bioeng. Biotechnology and Bioengineering, 957-964.
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SLIDE 70
  • Prof. Dr. Esra Gündüz
  • Prof. Dr. Mehmet Gündüz
  • Assist. Prof. Muradiye Acar
  • Assist. Prof. Dr. Sultan Çiftçi Yılmaz
  • Assist. Prof. Dr. Ömer Faruk Hatipoğlu
  • Dr. Sadık Çiğdem

Ayşe Çelik Burak Yılmaz Mustafa Semih Elitok

IN INSTR STRUCT UCTORS ORS & A & ADVISORS VISORS

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SLIDE 71
  • Dr. Akihiko Ishijima

We’d like thank you to Dr.Akihiko for providing us amino acid sequence of PotB59 protein

  • Dr. Andrea Schuller

For their big support and advices about DAMP4 and Pexiganan’s mechanism

  • Dr. Chunxia Zhao

We’d also thank you to Dr.Chunxia for answering our questions about Pexiganan

  • Dr. Bernard Binetruy

Special thanks to Dr.Bernard for providing of CAGop promoter’s sequence

ACK CKNO NOWLEDGEMENTS WLEDGEMENTS

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SP SPONSORS ONSORS

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SLIDE 73

Thanks

for your patience

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SLIDE 74

EXTRA SLIDES

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SLIDE 75
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SLIDE 76
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SLIDE 77
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SLIDE 78
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SLIDE 79
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GadE TlpB

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HNS-T108I Potb59/PomA

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SLIDE 82

pAlst-TnrA pLsr-LsrR

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SLIDE 83

Toehold Switch Trigger RNA

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SLIDE 84

DAMP-Pexiganan TEV Protease

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SLIDE 85

Project Finding Part Designing Experiment Plans Experiments Interlab Study Wiki Diagrams & Drawings Team Video Virtual Hospital Other Human Practices Poster Designing Presentation Preperation

Abdullah Uçar Ahmet Faruk Payamoğlu Alperen Sefa Toker Aslıhan Büşra Öğretici Ayşenur Toygar Bahadır Benli Berke Kahraman Büşra Gülnihal Soylu Fethi Önal Furkan Güneş Furkan Sacit Ceylan Hilal Şahin Kevser Sıddıka Yiğit Kübra Yıldırım Mikail Doğan Muhammed Fatih Aktaş Mustafa Yılmaz Nurgeldi Bazarov Ömer Enes Önür Selcan İçtaş Şahika Betül Yaylı Şeymanur Erol Turan Kaya

                                                                                                                             