About OMICS Group

OMICS Group International is an amalgamation of Open Access publications and worldwide international science conferences and events. Established in the year 2007 with the sole aim of making the information on Sciences and technology ‘Open Access’, OMICS Group publishes 400 online open access scholarly journals in all aspects of Science, Engineering, Management and Technology journals. OMICS Group has been instrumental in taking the knowledge on Science & technology to the doorsteps of ordinary men and women. Research Scholars, Students, Libraries, Educational Institutions, Research centers and the industry are main stakeholders that benefitted greatly from this knowledge dissemination. OMICS Group also organizes 300 International conferences annually across the globe, where knowledge transfer takes place through debates, round table discussions, poster presentations, workshops, symposia and exhibitions.

About OMICS Group Conferences

OMICS Group International is a pioneer and leading science event organizer, which publishes around 400 open access journals and conducts over 300 Medical, Clinical, Engineering, Life Sciences, Pharma scientific conferences all over the globe annually with the support of more than 1000 scientific associations and 30,000 editorial board members and 3.5 million followers to its credit.

OMICS Group has organized 500 conferences, workshops and national symposiums across the major cities including San Francisco, Las Vegas, San Antonio, Omaha, Orlando, Raleigh, Santa Clara, Chicago, Philadelphia, Baltimore, United Kingdom, Valencia, Dubai, Beijing, Hyderabad, Bengaluru and Mumbai.

YEDITEPE UNIVERSITY GENETICS AND BIOENGINEERING DEPT.

Assist. Prof. Dr. Hüseyin Çimen huseyin.cimen@yeditepe.edu.tr

YEDITEPE PROTEOMICS and MASS SPECTROMETRY LABORATORY

ISTANBUL, TURKIYE

OMICS Aug 4th,2014

About me…

Undergraduate (BSc): 2006 Molecular Biology and Genetics Middle East Technical University, TURKEY

Graduate (PhD): 2012 Biochemistry, Microbiology and

Molecular Biology (BMMB) Eberly College of Science,

Pennsylvania State University, PA

Research: 2011 - 2012 Biochemistry John C. Edwards Medicine School Marshall University, WV

Molecular Biology ve Genetics Lab

Microbial Genetics Lab

Mol. Diagnostic Lab Nanobiotechnology Lab

Plant Biotechnology Lab

Imaging Lab

Biomaterials Lab

Bioinformatics Lab Functional Genetics Lab

YEDITEPE UNIVERSITY STEM CELL AND GENE THERAPY EXCELLENCE CENTER

Protemics Lab

YEDITEPE PROTEOMICS and MASS SPECTROMETRY LABORATORY

•Protein ID •Protein structure, function, folding and interaction analysis

•Post-translational modification (PTM; acetylation) analysis of complex biological samples

•Biomarker discovery and characterization Thermo Dionex

UltiMate 3000

nano-HPLC nanoESI-qTOF

Bruker Compact

Allison Doerr, Nature Methods 10 (2013)

Discovery-based Targeted Proteomic Studies: Gel-based and/or off-gel protein sample preparation and purification

Stanley Fields, Science 291 (2001)

Reproducible - Quantitative Highly Sensitive Protein ID and Biomarker Discovery

Katie Vicari,, Nature Methods 10 (2012)

Biochemistry Proteomics Targeted Proteomics

Where is Waldo?

Vancouver Canucks Fan Zone, 2011 http://www.gigapixel.com/image/gigapan-canucks-g7.html

Where is Waldo?

Where is Waldo?

Where is Waldo?

HERE?

Vancouver Canucks Fan Zone, 2011 http://www.gigapixel.com/image/gigapan-canucks-g7.html

Mitochondrial functions and cancer: Elevated glycolytic metabolism and oxygen use in cancer cells

Douglas C. Wallace, Nature Reviews Cancer

Inner

Membrane

Matrix

ND6 ND4L

ND5

ND4 ND3

ND1 ND2

Cyt b COX I

COX II COX III

ATP6

ATP8

Krebs Cycle

e- e-

e- e-

H+H+ H+H+

Cyt C e- e-

H+H+ O2 H+H+ H2O

ADP ATP

Cyt C

e-

O2

Q

H+`H+

NADH

NAD+

H+ H+ H+ H+H+H+

Cyt C

H+`

e-

O2

O2- .

O2- .

e- e-

Peter S. Rabinwitch after Mandavilli et al, Mutation Research 509 (2002) 127–151

Electron Transport Chain

2OH- OH-

COMPLEX I II III IV V nDNA 39 4 10 10 16 mtDNA 7 0 1 3 2

Inner memb.

Matrix

ND6 ND4L

ND5

ND4 ND3

ND1 ND2

Cyt b COX I

COX II COX III

ATP6

ATP8

H2O

ADP ATP

Q

Cyt C

NADH +H+

Krebs Cycle

Acetyl-CoA

NAD+

Pi

Regulation of Oxidative Phosphorylation Comlexes

Lysine-NH2

Protein

Acetyl-CoA CoA

NAD+

Protein

Lysine-NH-CO-CH3

Acetylated

Mitochondrial Proteome: >20 % acetylation (Kim SC et.al 2006)

ac-NDUFA9

Cimen H et al. (2010), Ahn BH et al. (2008), Scott I et al. (2012), and Kim SC et al. (2006).

ac-SdhA

2

1

GCN5L1 SIRT3, SIRT4, and SIRT5 2

1

NAM O-acyl-ADP-ribose

REFERENCE CENTRE of BORON STUDIES

• BOREN (National Boron Research Institute, TURKIYE) – Efficiency and spectrum of scientific studies

on boron

• APPLICATION: – Glass, ceramic, flame retardants, cement,

metallurgy, energy, cleaning, bleaching, agriculture, cosmetics, health

– BNCT: boron neutron capture therapy in cancer

• Concentrated Borates – Ulexite – Tincal – Colemanite

• Refined Borates

– Borik Acid – Boraks Pentahidrat – Boraks Dekahidrat – Etibor- 48 – Sodyum Perborat Monohidrat – Sodyum Perborat Tetrahidrat – Borax Anhydroust – Boron Oxide

• Speciality Boron Products – Tarımbor (Agricultural Boron) – Ahsapbor (Wood Boron) – Zinc Borate – Cellulosic Insulation Material – Boron Nitride – Boron-Cement (Boron-Added-Cement) – Elementel Boron – Sodium Borohydride – Trimetyl Borate – Boron Carbide

REFERENCE CENTRE of BORON STUDIES

Interaction between sodium borate and NAD+ may affect Sirtuins, NAD+ dependent deacetylases.

BORON vs NAD+

(Hunt CD, 2012)

72 h incubation with Serum starvation for 24 h

Cell harvest and sample preparation

Cellular, metabolic, and proteomic analyses

Hep3B cells incubated with Sodium Borate supplemented media

BORON vs NAD+

0

200

400

600

800

1000

1 2 3 4

Con NaB

NaB treatment decreased cell proliferation rate

Time (Days)

Cel

l Via

bilit

y (%

)

Percent cell viability measured through metabolic activity of cultured HEP3B cells treated with NaB.

Acetyl-K

GAPDH

NaB treatment (μg /ml) 0 15

A B

IB analysis demonstrated >10% decrease in whole cell acetylome

020406080

100120

NaB treatment decreased overall protein acetylation

0 15 NaB treatment (μg /ml)

Rel

ativ

e Ac

etyl

atio

n (%

)

020406080

100120

Acetyl-K

NaB treatment (μg /ml) 0 15

A B

IB analysis demonstrated >10% decrease in mitochondrial acetylome

NaB treatment decreased overall mitochondrial protein acetylation

0 15 NaB treatment (μg /ml)

Rel

ativ

e Ac

etyl

atio

n (%

)

HSP60

NaB treatment enhanced SIRT3 activity

0

20

40

60

80

100

120

140

0 15 NaB treatment (μg /ml)

Rel

ativ

e SI

RT3

Act

ivity

(%)

CycLex® SIRT3 Deacetylase Fluorometric Assay Kit

NaB – NAD interaction elevated SIRT3 activity.

*

0

50

100

150

200

250

300

NaB treatment affects metabolism

0 15 NaB treatment (μg /ml)

Rel

ativ

e Le

vel (

%)

NaB – NAD interaction elevates NAD+/NADH ratio.

NAD+ / NADH Ratio

NaB treatment (μg /ml) 0 15

C IV

C V

C III

C II

C I

HSP60

A B

OXPHOS Ab cocktail: ATPSA (CV), UQCRC2 (CIII), MTCO1 (CIV), SDHB (CII), NDUFB8 (CI)

* * * *

*

NaB treatment reduced OXPHOS complexes

NaB treatment (μg /ml)

Rel

ativ

e O

XPH

OS

(%)

0 15 0 15 0 15 0 15 0 15

NaB reduced mitochondrial biogenesis.

CV CIII CIV CII CI

*

020406080

100120140

NaB treatment lowered ROS production

0 15 NaB treatment (μg /ml)

Rel

ativ

e R

OS

Leve

l (%

)

Abcam DCFDA Cellular ROS Detection Assay Kit NaB reduced ROS generation (>70%).

WCL

MITO

ACETYLATION

SIRT3 activity

BORON treatment enhances mitophagy in order to increase mitochondrial quality upon deacetylation.

NAD+/NADH 103%

NaB Treatment (15 μg/ml)

Cell Viability

Cancer cell proliferation hampered by BORON

Summary

Future Prospects and Acknowledgement

• Mitochondrial structure analysis with electron microscopy

• Drug supplementation along with boron

• Specific column development for boron-interacting proteins

LAB MEMBERS: Graduate: MSc Berna USTUNER MSc Eray Esendir Firdevs Cansu ATILGAN Bihter YAVUZ Technician: Binnur Herand KIRATLI

Special Thanks:

Yeditepe SAHIN Lab members

FUNDING: Yeditepe UNIVERSITY

THANKS

OMICS Aug 4th,2014

Department web: www.genetik.yeditepe.edu.tr

Yeditepe Biyoteknology Society: yeditepebiotech.com fb.com/pages/Yeditepe-University-Biotechnology-Society

YEDITEPE GENETICS AND BIONEGINEERING PROTEOMICS and MASS SPECTROMETRY LAB.

Let Us Meet Again

We welcome you all to our future conferences of OMICS Group

International

Please Visit: www.omicsgroup.com

www.conferenceseries.com www.proteomicsconference.com