From Academia to Industry: There and Back Again

Dr. Zachery Belak, Ph.D.

INTRODUCTION

• Education • Teaching Experiences • Ph.D. and postdoctoral work in Department of

Anatomy and Cell Biology • Industry Experience with Shutout Solutions

Inc. • Postdoctoral Work in Food and Bioproduct

Sciences

INTRODUCTION

• Major Themes: – Comparison of different streams for doing science:

• Academia – Teaching • Academia – Research • Industrial Research • Where do I (or You) fit?

– Passion for science – ‘cause it’s cool ya know? – Benefits of being a generalist – There are many paths a successful scientific career can

take – Taking risks and a willingness to enter new fields and

make them your own.

WHY SCIENCE?

• Collecting Insects, Rocks, Pressing Leaves • Chemistry Set • Microscopy • Astronomy • Projects for every high school science fair from

grade seven to twelve • So... Biology? Chemistry? Astronomy?

UNDERGRAD

• Department of Anatomy and Cell Biology – Human Anatomy – Neuroanatomy – Cell Biology – Embryology

• Summer project with Dr. Troy Harkness working with Saccaromyces cerevisiae

• Honours project with Dr. Nick Ovsenek working with Xenopus laevis

TEACHING

• Biotechnology for the Non-scientist • Introductory Human Anatomy • Teaching Assistant – Medical Human Anatomy

Cadaver Lab • Human Anatomy, Physiology, and Pathology –

McKay Career Training Inc. • Human Anatomy and Physiology – College of

Nursing, University of Regina

GRAD SCHOOL

• Xenopus laevis – The African Clawed Frog • Major model system for vertebrate

development • Originally used in biological assays as a

pregnancy test • The oocyte – pressing the reset switch to turn

a maternal cell into the first pluripotent cell of a new individual.

Messenger Ribonucleoproteins

• Abundant material required for later development accumulates in the cytoplasm

• mRNAs transcribed during oogenesis and stored and stabilized by interaction with proteins = mRNPs

• mRNAs selectively mobilized and translated following fertilization

• Very little known about the structure or function of mRNPs

Yin-Yang 1

• “The protein that does everything”: – Transcription factor that can activate or repress

transcription – Component of mRNPs in Xenopus oocytes

• The questions are: – How does it associate with mRNPs?

• Protein-protein binding • RNA binding activity

– Which RNAs does it bind to?

Fluoride – Friend or Foe?

• Fluoride is widely used in toothpaste and added to water to strengthen tooth enamel

• In high concentrations it causes bone deformities termed skeletal fluorosis

• Problem in areas of the developing world where ground water naturally contains sufficiently high levels of fluoride to cause toxicity

Fluoride – Friend or Foe?

• No molecular studies of whole organsisms • Xenopus tadpoles were the perfect model:

– Live in water so fluoride exposure can be performed by adding it directly to the tank water

– At late stage of development the skeleton is being ossified – converted from cartilage to bone – and so any effects would be most pronounced

– Individuals are sufficiently small they can be processed whole for RNA/Protein extraction

– Individuals sufficiently numerous that large, statistically significant sample sized are easily obtained

• RANKL = Receptor activator of nuclear factor kappa-B ligand – stimulates osteoclast differentiation

• OPG = Osteoprotegerin – Cell surface receptor which inhbits ostoclast differentiation

• BGLAP = Osteocalcin – marker for osteoblast numbers

• So.... No effect on bone formation but inhibition of bone resorbtion = too much bone = osteopetrosis and deformity

Industry – How Did I Get There?

• Shutout Solutions Inc – Begun as a fourth year project in commerce – Initially an idea to remove odours by silver

nanoparticles – Approached by former students – Initially used products produced in South Korea – In 2012 company decided to start an internal

research and development program

Shutout Solutions Inc.

• Took on the role of Head of Research and Development in 2012

• This included: – Start-up of the R&D lab from scratch – Initial purchase of equipment and supplies – Hiring of two research technicians and one

research scientist – Supervision and direction of research program

• A big job to take on

Silver Nanoparticles

• Silver Nanoparticles (AgNPs) – Small particles on the order of 2 – 100 nm

composed of metallic silver – Form a stable colloid in solution – Unique properties including strong plasmon

absorbance • Potentially useful for optic sensors etc. • Some evidence of antimicrobial activity

Silver Nanoparticles

• The company wished to develop nanoparticles in the following areas: – Cleaning products which would deposit AgNPs on

environmental surfaces to make these surfaces self-disinfecting

– Products which would prevent growth of odour-causing bacteria when applied to articles such as shoes and sports equipment

– Development of anti-fouling agents for process water

Silver Nanoparticles

• Major research questions were: – How useful are the antimicrobial properties of

AgNPs? – What is the best size and shape of nanoparticle for

antimicrobial activity? – How to stabilize nanoparticles and successfully

incorporate them in consumer products? – How to selectively deposit nanoparticles on

environmental surfaces?

Synthesis and Characterization of AgNPs

• Synthesis using methods of inorganic chemistry • Characterization using:

– Transmission electron microscopy – Dynamic light scattering – UV-Visual spectroscopy – Scanning electron microscopy to assess surface

deposition

• Little experience in these areas so it was a huge challenge

Assessing Antimicrobial Activity of AgNPs

• Used a number of standard microbiological assays: – Minimum inhibitory concentration assay – Suspension culture antimicrobial assay

• Developed new methods for examining antimicrobial activity on surfaces bearing AgNPs

• Testing on a variety of bacteria and fungi

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Back to Academia – Why?

• Good environment at Shutout and enjoyed the science

• Lack of opportunity for publication • Reduced opportunity for interaction with other

scientists • Research focus strictly controlled by company

management • Many non-scientific administrative duties • This isn’t a bad thing – just not the best fit for me

The Eskiw Lab

• Joined the lab of Dr. Chris Eskiw in April 2016 • Focus of the lab is on the influence of

nutritional state on genome organization

Genome Organization

• Why is it important? • We know of DNA as a set of “instructions” for

cells to operate • But....

– How those instructions are organized is as important as their content

– Think of the library – all the books are useless unless we have a way of organizing them so the required information can be accessed at the required time

Genome Organization

• Human cells contain 23 chromosomes – each chromosome is a single molecule of DNA associated with various proteins

• We usually think of chromosomes looking like this:

Genome Organization

• But chromosomes only appear this way when they are compactly packaged for distribution to daughter cells during cell division

• Normally chromosomes are “unpacked” in the nucleus to allow the DNA to accessed and “read” in the process of transcription

• The following image shows different chromosomes stained in the nucleus of a cell in their “unpacked” state

Genome Organization

• Successful organization of the genome is critical: – Defects in genome organization lead to premature

aging, e.g. Progeria • Caloric restriction retards aging and extends

lifespan • Could there therefore be an effect of caloric

restriction on genome organization that underlies it’s anti-aging effects?

Genome Organization

• An important step in answering this question is: – To what extent to the chromosomes overlap or

intermingle when they are in their “unpacked” or extended condition in the nucleus?

Probing Genome Organization

• 5-ethynyl-2'-deoxyuridine (EdU) is an analog of the nucleotide tymidine

• It is incorporated in DNA during replication • EdU is applied to cells during which time their

DNA incorporates some EdU • The EdU is then removed and the cells are

allowed to undergo several divisons • After this process the cells will contain a mixture

of chromosomes, some labelled with EdU and some not

Probing Genome Organization

• EdU can be detected in the cells by reaction with a fluorescent molecule and imaged by fluoresence microscopy

• This shows some areas of the nucleus are labelled – corresponding the labelled chromosomes, and some are unlabelled

Toward the Future

• How can we tell if the labelled chromosome intermingles or overlaps with the unlabelled ones?

• SILVER NANOPARTICLES!!!! • Cells will be treated with AgNPs modified to react

with the EdU label • Imaging by high-resolution transmission electron

microscopy should determine if labelled and unlabelled chromosomes intermingle in the nucleus

Toward the Future

• Current Research Challenges: – Fluoresence labelling confirms we can selectively label

some chromosomes with EdU while others are unlablled

– Synthesis of sufficiently small (2-5 nm) AgNPs – Modification of AgNPs to react with EdU – Successfully reacting modified AgNPs with sections of

cells prepared for TEM – Design and implementation of appropriate controls to

ensure AgNPs observed by TEM are in fact present on EdU labelled DNA

My Observations

• Important thing is to do what you love – science – and to be able to make a living at it

• There are my career routes available • One should choose based on what is the best fit • Don’t be biased against either academia or

industry • Don’t look at it as advantages or disadvantages of

various career routes but instead as what is the best fit

• The best fit could be a blend of options

My Observations

• Teaching – Steady pay – Great rewards – No grant applications – No bench work – Not much opportunity for discovery – “You don’t really understand something yourself

until you have to teach it to someone else” – Reasonably low stress for the right kind of person

My Observations • Research

– Long hours – Ability to pursue your own interests – Opportunity for pure research – Mobility in terms of changing labs/projects – Bench work – Contact with the scientific community – More opportunity for collaboration – Greater access to facilities and equipment – Funding can be difficult and uncertain – Ultimately at the PI level have to take responsibility for the

research program – Opportunity for publication

My Observations • Industry

– Good hours – Good pay, steady work – No grant applications – Less opportunity for pure research – Research focus determined by the company – Starting/continuing projects determined by management – Good facilities/adequate funding for the work to be done – Less interaction with the scientific community – Less potential for publication – Less mobility for changing projects/labs/research focus – Bench work

CONCLUSION

• Many career paths available in the sciences – there’s no one right answer

• Find the best fit for you • It is a great honour to be able to do what you love

and make a living at it and one should always be thankful for that

• Don’t be afraid of entering a new field and making it your own – science is all about stepping into the unkown

• Have FUN!