1 Putranto Webinar Biotech Fun UEU 2020

Biotech is fun!
Ilmu Kekinian dan Masa Depan
www.thespruceeats.com Riza Arief Putranto
Presented in Webinar Series Bioteknologi Universitas Esa Unggul

From Office via Zoom – July 15th 2020
Biology to Biotechnology
“Our world is built on biology and once we begin to

understand it, it then becomes a technology, a
biotechnology”
― Ryan Bethencourt
Biotechnology
Bios (Biology), Teuchos (Tools), Logos (Knowledge)
"A set of techniques that utilize living organisms or parts of

living organisms, to produce or modify products, improve
the ability of plants and animals, develop microorganisms
for special uses that are useful for human life".
Do you know this fruit? Do you like it?
www.exoticfruitbox.com
Copyright @rizaputranto 2020

Do you know this fruit? Do you like it?
• Papaya is native to Mexico. However, it

grows naturally in the Caribbean and
Florida too.
• According to the Food and Agriculture
Organization of the United Nations
(FAO), India produces the most
papayas – over 5 million tons in 2013.
• It can be added to salads, smoothies,
and other dishes.
• Papayas have A, B vitamins, alpha and
beta-carotene, lutein and zeaxanthin,
vitamin E, calcium, potassium, vitamin
K, and lycopene (antioxidant)

Something inside the papaya regulates its maturity
Papaya is a climacteric fruit, a

stage of fruit ripening
associated with increased
ethylene production and a rise
in cellular respiration.
Papaya fruit expansion and

ripening stages for candidate
gene expression analysis. (A)
Color development in fruit flesh
of SunUp (top row) and Kapoho
(bottom row). (B) Expansion size
(ES) of developing papaya fruit
compared with mature fruit. (C)
Fruit ripening stages based on
change in fruit skin color.
Blas et al. 2010. Plant Physiology, 152(4), 2013.

This speed of maturity is encoded by macromolecule
• Let us extract something from inside the papaya’s

cells using salts and normal liquid soap.
• You will need also a filter, a becker glass, an
enlenmeyer, and an ethanol
In the end, you will obtain a white-ish jelly as an

extracted product from papaya’s cells

This is how papaya’s genome (its DNA) looks like
GGGACAGGGGGAGCCCTATAATTGGACAAGTCTGGGATCCTTGAGTCCTACTCAGCCCCAGCGGAGGTGAAGGACGTCCTTCCCCAGGAGCCGGTGAGAAGCGCAGTCGGGGGCACGGGGATGAGCTCAGGGG
CCTCTAGAAAGAGCTGGGACCCTGGGAACCCCTGGCCTCCAGGTAGTCTCAGGAGAGCTACTCGGGGTCGGGCTTGGGGAGAGGAGGAGCGGGGGTGAGGCAAGCAGCAGGGGACTGGACCTGGGAAGGGC
TGGGCAGCAGAGACGACCCGACCCGCTAGAAGGTGGGGTGGGGAGAGCAGCTGGACTGGGATGTAAGCCATAGCAGGACTCCACGAGTTGTCACTATCATTTATCGAGCACCTACTGGGTGTCCCCAGTGTCCTC
Francis Crick
AGATCTCCATAACTGGGGAGCCAGGGGCAGCGACACGGTAGCTAGCCGTCGATTGGAGAACTTTAAAATGAGGACTGAATTAGCTCATAAATGGAACACGGCGCTTAACTGTGAGGTTGGAGCTTAGAATGTGAA
GGGAGAATGAGGAATGCGAGACTGGGACTGAGATGGAACCGGCGGTGGGGAGGGGGTGGGGGGATGGAATTTGAACCCCGGGAGAGGAAGATGGAATTTTCTATGGAGGCCGACCTGGGGATGGGGAGATA
AGAGAAGACCAGGAGGGAGTTAAATAGGGAATGGGTTGGGGGCGGCTTGGTAAATGTGCTGGGATTAGGCTGTTGCAGATAATGCAACAAGGCTTGGAAGGCTAACCTGGGGTGAGGCCGGGTTGGGGCCGG
GCTGGGGGTGGGAGGAGTCCTCACTGGCGGTTGATTGACAGTTTCTCCTTCCCCAGACTGGCCAATCACAGGCAGGAAGATGAAGGTTCTGTGGGCTGCGTTGCTGGTCACATTCCTGGCAGGTATGGGGGCGG
GGCTTGCTCGGTTCCCCCCGCTCCTCCCCCTCTCATCCTCACCTCAACCTCCTGGCCCCATTCAGGCAGACCCTGGGCCCCCTCTTCTGAGGCTTCTGTGCTGCTTCCTGGCTCTGAACAGCGATTTGACGCTCTCTGG
GCCTCGGTTTCCCCCATCCTTGAGATAGGAGTTAGAAGTTGTTTTGTTGTTGTTGTTTGTTGTTGTTGTTTTGTTTTTTTGAGATGAAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCTCGGCTCACT
GCAAGCTCCGCCTCCCAGGTCCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCACATGCCACCACACCCGACTAACTTTTTTGTATTTTCAGTAGAGACGGGGTTTCACCATGTTGGCCAGGC
TGGTCTGGAACTCCTGACCTCAGGTGATCTGCCCGTTTCGATCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCTGGCTGGGAGTTAGAGGTTTCTAATGCATTGCAGGCAGATAGTGAATACCAGACA
CGGGGCAGCTGTGATCTTTATTCTCCATCACCCCCACACAGCCCTGCCTGGGGCACACAAGGACACTCAATACATGCTTTTCCGCTGGGCGCGGTGGCTCACCCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGG
GAGGATCACTTGAGCCCAGGAGTTCAACACCAGCCTGGGCAACATAGTGAGACCCTGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGCCACACACCTGTGCTCTCAGCTACTCAGGAGGCTGAGGCAGG
AGGATCGCTTGAGCCCAGAAGGTCAAGGTTGCAGTGAACCATGTTCAGGCCGCTGCACTCCAGCCTGGGTGACAGAGCAAGACCCTGTTTATAAATACATAATGCTTTCCAAGTGATTAAACCGACTCCCCCCTCAC
James Watson
CCTGCCCACCATGGCTCCAAAGAAGCATTTGTGGAGCACCTTCTGTGTGCCCCTAGGTACTAGATGCCTGGACGGGGTCAGAAGGTCGCTTTTGGGATTACCTGCTCTCAGCTTTGTCTCTCTCTCTTCCCTTCTGACT
CAGTCTCTCACACTCGTCCTGGCTCTGTCTCTGTCCTTCCCTAGCTCTTTTATATAGAGACAGAGAGATGGGGTCTCACTGTGTTGCCCAGGCTGGTCTTGAACTTCTGGGCTCAAGCGATCCTCCCGCCTCGGCCTCCC
AAAGTGCTGGGATTAGAGGCATGAGCCACCTTGCCCGGCCTCCTAGCTCCTTCTTCGTCTCTGCCTCTGCCCTCTGCATCTGCTCTCTGCATCTGTCTCTGTCTCCTTCTCTCGGCCTCTGCCCCGTTCCTTCTCTCCCTCT
TGGGTCTCTCTGGCTCATCCCCATCTCGCCCGCCCCATCCCAGCCCTTCTCCCCGCCTCCCACTGTGCGACACCCTCCCGCCCTCTCGGCCGCAGGGCGCTGATGGACGAGACCATGAAGGAGTTGAAGGCCTACAAA
TCGGAACTGGAGGAACAACTGACCCCGGTGGCGGAGGAGACGCGGGCACGGCTGTCCAAGGAGCTGCAGGCGGCGCAGGCCCGGCTGGGCGCGGACATGGAGGACGTGTGCGGCCGCCTGGTGCAGTACCG
CGGCGAGGTGCAGGCCATGCTCGGCCAGAGCACCGAGGAGCTGCGGGTGCGCCTCGCCTCCCACCTGCGCAAGCTGCGTAAGCGGCTCCTCCGCGATGCCGATGACCTGCAGAAGCGCCTGGCAGTGTACCAGG
• Deoxyribonucleic acid (DNA) is a molecule composed of two
CCGGGGCCCGCGAGGGCGCCGAGCGCGGCCTCAGCGCCATCCGCGAGCGCCTGGGGCCCCTGGTGGAACAGGGCCGCGTGCGGGCCGCCACTGTGGGCTCCCTGGCCGGCCAGCCGCTACAGGAGCGGGCCC
polynucleotide chains that coil around each other to form a
AGGCCTGGGGCGAGCGGCTGCGCGCGCGGATGGAGGAGATGGGCAGCCGGACCCGCGACCGCCTGGACGAGGTGAAGGAGCAGGTGGCGGAGGTGCGCGCCAAGCTGGAGGAGCAGGCCCAGCAGATACG
CCTGCAGGCCGAGGCCTTCCAGGCCCGCCTCAAGAGCTGGTTCGAGCCCCTGGTGGAAGACATGCAGCGCCAGTGGGCCGGGCTGGTGGAGAAGGTGCAGGCTGCCGTGGGCACCAGCGCCGCCCCTGTGCCC
double helix carrying genetic instructions
AGCGACAATCACTGAACGCCGAAGCCTGCAGCCATGCGACCCCACGCCACCCCGTGCCTCCTGCCTCCGCGCAGCCTGCAGCGGGAGACCCTGTCCCCGCCCCAGCCGTCCTCCTGGGGTGGACCCTAGTTTAATA
• Nucleotides bonded together with covalent bonds
AAGATTCACCAAGTTTCACGCATCTCGCTTTTGGGATTACCTGCTCTCAGCTTTGTCTCTCTCTCTTCCCTTCTGACTCAGTCTCTCACACTCGTCCTGGCTCTGTCTCTGTCCTTCCCTAGCTCTTTTATATAGAGACAGA
GAGATGGGGTCTCACTGTGTTGCCCAGGCTGGTCTTGAACTTCTGGGCTCAAGCGATCCTCCCGCCTCGGCCTCCCAAAGTGCTGGGATTAGAGGCATGAGCCACCTTGCCCGGCCTCCTAGCTCCTTCTTCGTCTCT
o Adenine (A) hydrogen bonds with Thymine (T)
GCCTCTGCCCTCTGCATCTGCTCTCTGCATCTGTCTCTGTCTCCTTCTCTCGGCCTCTGCCCCGTTCCTTCTCTCCCTCTTGGGTCTCTCTGGCTCATCCCCATCTCGCCCGCCCCATCCCAGCCCTTCTCCCCGCCTCCCAC
o Cytosine (C) hydrogen bonds with Guanine (G)
TGTGCGACACCCTCCCGCCCTCTCGGCCGCAGGGCGCTGATGGACGAGACCATGAAGGAGTTGAAGGCCTACAAATCGGAACTGGAGGAACAACTGACCCCGGTGGCGGAGGAGACGCGGGCACGGCTGTCCA
AGGAGCTGCAGGCGGCGCAGGCCCGGCTGGGCGCGGACATGGAGGACGTGTGCGGCCGCCTGGTGCAGTACCGCGGCGAGGTGCAGGCCATGCTCGGCCAGAGCACCGAGGAGCTGCGGGTGCGCCTCGCCT
CCCACCTGCGCAAGCTGCGTAAGCGGCTCCTCCGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCG
ATGCGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGA
www.podcastscience.fm
This is how papaya’s genome (its DNA) looks like
GGGACAGGGGGAGCCCTATAATTGGACAAGTCTGGGATCCTTGAGTCCTACTCAGCCCCAGCGGAGGTGAAGGACGTCCTTCCCCAGGAGCCGGTGAGAAGCGCAGTCGGGGGCACGGGGATGAGCTCAGGGG
CCTCTAGAAAGAGCTGGGACCCTGGGAACCCCTGGCCTCCAGGTAGTCTCAGGAGAGCTACTCGGGGTCGGGCTTGGGGAGAGGAGGAGCGGGGGTGAGGCAAGCAGCAGGGGACTGGACCTGGGAAGGGC
TGGGCAGCAGAGACGACCCGACCCGCTAGAAGGTGGGGTGGGGAGAGCAGCTGGACTGGGATGTAAGCCATAGCAGGACTCCACGAGTTGTCACTATCATTTATCGAGCACCTACTGGGTGTCCCCAGTGTCCTC
AGATCTCCATAACTGGGGAGCCAGGGGCAGCGACACGGTAGCTAGCCGTCGATTGGAGAACTTTAAAATGAGGACTGAATTAGCTCATAAATGGAACACGGCGCTTAACTGTGAGGTTGGAGCTTAGAATGTGAA
GGGAGAATGAGGAATGCGAGACTGGGACTGAGATGGAACCGGCGGTGGGGAGGGGGTGGGGGGATGGAATTTGAACCCCGGGAGAGGAAGATGGAATTTTCTATGGAGGCCGACCTGGGGATGGGGAGATA
AGAGAAGACCAGGAGGGAGTTAAATAGGGAATGGGTTGGGGGCGGCTTGGTAAATGTGCTGGGATTAGGCTGTTGCAGATAATGCAACAAGGCTTGGAAGGCTAACCTGGGGTGAGGCCGGGTTGGGGCCGG
GCTGGGGGTGGGAGGAGTCCTCACTGGCGGTTGATTGACAGTTTCTCCTTCCCCAGACTGGCCAATCACAGGCAGGAAGATGAAGGTTCTGTGGGCTGCGTTGCTGGTCACATTCCTGGCAGGTATGGGGGCGG
GGCTTGCTCGGTTCCCCCCGCTCCTCCCCCTCTCATCCTCACCTCAACCTCCTGGCCCCATTCAGGCAGACCCTGGGCCCCCTCTTCTGAGGCTTCTGTGCTGCTTCCTGGCTCTGAACAGCGATTTGACGCTCTCTGG
GCCTCGGTTTCCCCCATCCTTGAGATAGGAGTTAGAAGTTGTTTTGTTGTTGTTGTTTGTTGTTGTTGTTTTGTTTTTTTGAGATGAAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGGGATCTCGGCTCACT
GCAAGCTCCGCCTCCCAGGTCCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCACATGCCACCACACCCGACTAACTTTTTTGTATTTTCAGTAGAGACGGGGTTTCACCATGTTGGCCAGGC
TGGTCTGGAACTCCTGACCTCAGGTGATCTGCCCGTTTCGATCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCTGGCTGGGAGTTAGAGGTTTCTAATGCATTGCAGGCAGATAGTGAATACCAGACA
CGGGGCAGCTGTGATCTTTATTCTCCATCACCCCCACACAGCCCTGCCTGGGGCACACAAGGACACTCAATACATGCTTTTCCGCTGGGCGCGGTGGCTCACCCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTGG
GAGGATCACTTGAGCCCAGGAGTTCAACACCAGCCTGGGCAACATAGTGAGACCCTGTCTCTACTAAAAATACAAAAATTAGCCAGGCATGGTGCCACACACCTGTGCTCTCAGCTACTCAGGAGGCTGAGGCAGG
AGGATCGCTTGAGCCCAGAAGGTCAAGGTTGCAGTGAACCATGTTCAGGCCGCTGCACTCCAGCCTGGGTGACAGAGCAAGACCCTGTTTATAAATACATAATGCTTTCCAAGTGATTAAACCGACTCCCCCCTCAC
CCTGCCCACCATGGCTCCAAAGAAGCATTTGTGGAGCACCTTCTGTGTGCCCCTAGGTACTAGATGCCTGGACGGGGTCAGAAGGTCGCTTTTGGGATTACCTGCTCTCAGCTTTGTCTCTCTCTCTTCCCTTCTGACT
CAGTCTCTCACACTCGTCCTGGCTCTGTCTCTGTCCTTCCCTAGCTCTTTTATATAGAGACAGAGAGATGGGGTCTCACTGTGTTGCCCAGGCTGGTCTTGAACTTCTGGGCTCAAGCGATCCTCCCGCCTCGGCCTCCC
AAAGTGCTGGGATTAGAGGCATGAGCCACCTTGCCCGGCCTCCTAGCTCCTTCTTCGTCTCTGCCTCTGCCCTCTGCATCTGCTCTCTGCATCTGTCTCTGTCTCCTTCTCTCGGCCTCTGCCCCGTTCCTTCTCTCCCTCT
TGGGTCTCTCTGGCTCATCCCCATCTCGCCCGCCCCATCCCAGCCCTTCTCCCCGCCTCCCACTGTGCGACACCCTCCCGCCCTCTCGGCCGCAGGGCGCTGATGGACGAGACCATGAAGGAGTTGAAGGCCTACAAA
TCGGAACTGGAGGAACAACTGACCCCGGTGGCGGAGGAGACGCGGGCACGGCTGTCCAAGGAGCTGCAGGCGGCGCAGGCCCGGCTGGGCGCGGACATGGAGGACGTGTGCGGCCGCCTGGTGCAGTACCG
CGGCGAGGTGCAGGCCATGCTCGGCCAGAGCACCGAGGAGCTGCGGGTGCGCCTCGCCTCCCACCTGCGCAAGCTGCGTAAGCGGCTCCTCCGCGATGCCGATGACCTGCAGAAGCGCCTGGCAGTGTACCAGG
A chromatogram
CCGGGGCCCGCGAGGGCGCCGAGCGCGGCCTCAGCGCCATCCGCGAGCGCCTGGGGCCCCTGGTGGAACAGGGCCGCGTGCGGGCCGCCACTGTGGGCTCCCTGGCCGGCCAGCCGCTACAGGAGCGGGCCC
AGGCCTGGGGCGAGCGGCTGCGCGCGCGGATGGAGGAGATGGGCAGCCGGACCCGCGACCGCCTGGACGAGGTGAAGGAGCAGGTGGCGGAGGTGCGCGCCAAGCTGGAGGAGCAGGCCCAGCAGATACG
CCTGCAGGCCGAGGCCTTCCAGGCCCGCCTCAAGAGCTGGTTCGAGCCCCTGGTGGAAGACATGCAGCGCCAGTGGGCCGGGCTGGTGGAGAAGGTGCAGGCTGCCGTGGGCACCAGCGCCGCCCCTGTGCCC
An Illumina Next-Seq 550,
AGCGACAATCACTGAACGCCGAAGCCTGCAGCCATGCGACCCCACGCCACCCCGTGCCTCCTGCCTCCGCGCAGCCTGCAGCGGGAGACCCTGTCCCCGCCCCAGCCGTCCTCCTGGGGTGGACCCTAGTTTAATA
Next Generation Sequencer
AAGATTCACCAAGTTTCACGCATCTCGCTTTTGGGATTACCTGCTCTCAGCTTTGTCTCTCTCTCTTCCCTTCTGACTCAGTCTCTCACACTCGTCCTGGCTCTGTCTCTGTCCTTCCCTAGCTCTTTTATATAGAGACAGA
GAGATGGGGTCTCACTGTGTTGCCCAGGCTGGTCTTGAACTTCTGGGCTCAAGCGATCCTCCCGCCTCGGCCTCCCAAAGTGCTGGGATTAGAGGCATGAGCCACCTTGCCCGGCCTCCTAGCTCCTTCTTCGTCTCT
GCCTCTGCCCTCTGCATCTGCTCTCTGCATCTGTCTCTGTCTCCTTCTCTCGGCCTCTGCCCCGTTCCTTCTCTCCCTCTTGGGTCTCTCTGGCTCATCCCCATCTCGCCCGCCCCATCCCAGCCCTTCTCCCCGCCTCCCAC
TGTGCGACACCCTCCCGCCCTCTCGGCCGCAGGGCGCTGATGGACGAGACCATGAAGGAGTTGAAGGCCTACAAATCGGAACTGGAGGAACAACTGACCCCGGTGGCGGAGGAGACGCGGGCACGGCTGTCCA
AGGAGCTGCAGGCGGCGCAGGCCCGGCTGGGCGCGGACATGGAGGACGTGTGCGGCCGCCTGGTGCAGTACCGCGGCGAGGTGCAGGCCATGCTCGGCCAGAGCACCGAGGAGCTGCGGGTGCGCCTCGCCT
CCCACCTGCGCAAGCTGCGTAAGCGGCTCCTCCGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCG
ATGCGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGACCTGCACGCGATGCCGATGA
Papaya genome decoded: the scientists were happy J
http://archives.starbulletin.com/2008/04/24/news/story09.html Ming R et al. 2008 Nature, 452(7190), 991-996.
• A UH-led international team of 85 scientists has deciphered the genetic code of a disease-resistant papaya.
• Scientists pose with some of the papayas used in research at Snyder Hall on the University of Hawaii-Manoa campus
(scientists Maqs Alam, Qingyi Yu and Shaobin Hou; papaya farmer Ken Kamiya; scientist Dennis Gonsalves; business
development manager Tak Sugimura; and Stephanie Whalen of the Hawaii Agriculture Research Center).

Do you know how big is Papaya genome?
ASGPB Hawaii Papaya Genome Project
Ming R et al. 2008 Nature, 452(7190), 991-996.
How big is the Papaya genome?

Papaya genome is only 1/10 of human genome (3.000 Mbp). Human
genome if spread can reach the distance of the Sun to Pluto for 17 times.
So, papaya genome if spread can reach almost twice Sun to Pluto.
Papaya with a physical appearance as a tree only has three times of

genome size against Arabidopsis (a-10 cm herb)
www.wikimedia.org With bigger size of genome, papaya has less number of genes

Problem in papaya production: a viral (uncontrolled) disease
Papaya was introduced to Hawaii in the 1800s, and PRSV belongs to the genus Potyvirus
the production of papaya in Hawaii grew into a Filamentous and flexuous virions
major industry. That industry faced a crisis in 1992, 760-800 x 12 nm (ssRNA virus)
however, when the papaya ringspot virus (PRSV)
was first identified in Puna, the center of Hawaiian
papaya production.
PRSV affects papaya production throughout the

The vector: Aphids
world. The virus interferes with the plant's ability (Myzus persicae)
www.apsnet.org
to photosynthesize. Affected plants are stunted and
often produce deformed and inedible fruit. Papaya
production in Hawaii dropped from 55.8 million
pounds to 35.6 million pounds between 1992 and
1998 as a result of the virus.
The virus, PRSV, is transmitted nonpersistently by

aphid vectors and does not multiply in the vector. Papaya trees die
The disease cycle can start with aphids feeding on because of the virus
infected papaya for as little as 15 seconds and
subsequently feeding on a healthy papaya.
www.agbioforum.org

Transgenic papaya is the answer for the problem of PRSV
Using particle bombardment inserting a viral coat protein gene into a plant to
give the plant immunity to the virus.
In the early 1990s scientists at Cornell and the University of Hawaii (led by
Dennis Gonsalves) developed a transgenic papaya that was resistant to PRSV.
The Cornell researchers tried to clone and fine-tune the Coat Protein genes of
PRSV for more than hundreds trials. At that time they used classic forward
genetics to identify the genes.
The newly disease-resistant papaya,

Rainbow papaya
Photograph: See D Jan/Getty Images/iStockphoto
www.bio-rad.com springernature.com

At that time 1990’s, bioinformatics is not yet there, if so…
Coat protein (CP) protein modelling of PRSV UniProtKB - Q15ED7
Red colors: pocket activity
KQKEKEKDDAIDGNDVSTSTKTGERDRDVNVGTSGTFTVPRIRS
FTDKMILPRVKGKTVLNLNHLLQYNPQQIDISNTRATQSQFEKW
YGGVRNDYGLNDNEMQVMLNGLMVWCIENGTSPDISGVWV
MMDGENQVDYPIKPLIEHASPSFRQIMAHFSNAAEAYIAMRNA
TERYMPRYGLKRNLTDISLARYAFDFYEVNSKTPDRAREAHMQ
MKAAALRNANRRMFGIDGSVSDKEENTERHTVEDVNRD
Bioinformatics helps to shorten

the wet lab activities, making it
more focused.
The new study has found that the

transgenic insertions (CP genes)
occurred in only three places in
the papaya genome, and that no
nuclear genes were disrupted.

Bioinformatics are now the “trending biotechnology”
16000
PDB at a Glance 2018
14000
43,823 Distinct Protein Sequences
12000
38,074 Structures of Human Sequences
9,953 Nucleic Acid Containing Structures
Deposited sequences
10000
8000
Approx. 119 thousands new protein structures 2018-2020
6000
PDB at a Glance 2020 (April)
4000 162,816 Distinct Protein Sequences
47,077 Structures of Human Sequences
2000 11,761 Nucleic Acid Containing Structures
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Bioinformatics related to databasing, BIG DATA analysis and modeling
If you know how to play DOTA 2, then you gotta love bioinformatics!
These are protein models, validated

and close to its natural forms

Debates upon transgenic “Rainbow” papaya occurs
i.pinimg.com
The Papaya GMO plants saved an $11-million industry — despite the ignition of the GMO wars
90% of the Papaya planted in the world today are transgenic

However, some plants showed naturally occurred transgenic
Genetically Modified Organisms (GMOs) are still a subject

of debate because of its unknown effect to human, thus
we know some of unique alimentations were naturally
engineered (by nature): sweet potatoes such as Ubi
Cilembu.
Kyndt T et al. 2015, Proceedings of the National Academy of Sciences, 201419685.
The researchers collected 291 sweet

potato samples from cultivated sources
across the globe along with nine wild
sources and subjected them all to DNA
analysis—they found that all of the
cultivated potatoes carried at least
two stretches of Agrobacterium DNA,
while the wild species carried one.
blog.regopantes.com

Anyone has seen RAMPAGE movie in 2018?
• Primatologist Davis Okoye, a former US Army Special Forces soldier and

member of an anti-poaching unit, works at the San Diego Wildlife
Sanctuary.
• He has befriended a rare albino western lowland gorilla named
George, exposed to the biochemical substances causing George to
grows considerably larger and more aggressive.
• Dr. Kate Caldwell explains that the biochemicals was developed by
Energyne to rewrite genes on a massive scale. She had hoped to
advance CRISPR research as a potential cure for diseases, but
discovered Energyne's plans to use it as a biological weapon.
The movie introduced the word

“CRISPR” for the first time. What is that?
moviesanywhere.com
Nowadays, we live in a world of CRISPR
Keywords to CRISPR:
• Genome editing
• Cut and edit
• Non-transgenic
CRISPR technology is a simple yet

powerful tool for editing genomes. It
allows researchers to easily alter DNA
sequences and modify gene function.
Its many potential applications include
correcting genetic defects, treating and
preventing the spread of diseases and
improving crops.
https://massivesci.com/videos/david-baltimore-crispr-condensed-matters/

What is CRISPR/Cas? Clustered Regularly Interspaced Short Palindromic Repeats – Caspase (Cas) associated protein
o Mode of Action Option 1. NHEJ generates a “random”

o Original defence system in bacteria Streptococcus and Neisseria against virus
mutation due to an synonymous DNA repair.
o Three components:
ü RNA-guided Cas9 nuclease o Mode of Action Option 2. HDR generates a ”more
ü crRNA (CRISPR RNA) directed” mutation thanks to a template introduced within
ü a partially complementary trans-acting crRNA (tracrRNA) the system. The latest is called “precise genome editing”
DNA-Binding domain Nuclease domain
Plant DNA
MoA Option 1 MoA Option 2
https://fr.wikipedia.org
Delete/Change
Visualized figure from NBT Platform, 2018 Non-Homologous End Joining (NHEJ) Change with template
Homology Directed Repair (HDR)

Nowadays, we can create synthetic plasmids in computer
Insert the sgRNA into the in silico construct
sgRNA S gene
…AUUUAGUGCGUGAUCUCCCUCAGGGUUUUUCGGCUUUAGAACCAUUGGUAG..
•Bacterial Resistance(s) Ampicillin
•Growth Temperature 37°C In parallel, the collateral reporter
•Growth Strain(s) DH5alpha containing parts of the target
sequence (sgRNA) is also built
•Gene/Insert name SARS-CoV-2 S and synthesized
•Species SARS CoV 2
•Insert Size (bp) 3819
•Mutation Codon optimized and C-terminal 19 amino acids deletion
•Entrez Gene S (a.k.a. GU280_gp02, spike glycoprotein)
•Promoter CMV
•Tag / Fusion Protein 3xFlag (C terminal on backbone)
•Cas protein Cas12a
•Cloning method Restriction Enzyme

•5ʹ cloning site HindIII (unknown if destroyed)
•3ʹ cloning site BamHI (unknown if destroyed)
•5ʹ sequencing primer CMV-F

CRISPR-based SHERLOCK for COVID-19 test
(Specific High sensitivity Enzymatic Reporter unLOCKing)
Kellner et al. (2019). SHERLOCK: nucleic acid detection with CRISPR nucleases. Nature Protocols, 14(10).
Joung J, et al. (2020). Point-of-care testing for COVID-19 using SHERLOCK diagnostics. medRxiv, 2020.05.04.20091231.
Specificity
• This specific high-sensitivity
Target genes enzymatic reporter unlocking
ORf1ab and S (SHERLOCK), allows
multiplexed, portable, and
1. RT-RPA ultra-sensitive detection of
Cas13a
RNA or DNA from clinically
relevant samples.
• SHERLOCK assays uses

recombinase-mediated
polymerase pre-amplification
of DNA or RNA and
subsequent Cas13- detection
via fluorescence and
colorimetric readouts that
Sensitivity provide results in <1 h with a
setup time of less than 15
min.

CRISPR controversy, create greatness or Deadpool?
He Jiankui, a Chinese researcher, at the Human Genome
Editing Conference in Hong Kong on Wednesday,
November 28, 2018. He claims to have made the
world’s first gene-edited babies.
www.vox.com
https://mg.co.za
CRISPR is currently being trialled as therapeutics
“I’m hopeful that this is the first in a
wave of new treatment options for
patients with β-thalassemia and
Ex-vivo sickle cell disease,” says Jacob Corn,
a University of California, Berkeley,
researcher who has used CRISPR to
In-vitro fix sickle cell mutations in human
cells in the lab.
Both diseases are ideal for fixing

with gene editing, since their
precise cause is known: mutations
in a gene that makes a subunit of
hemoglobin, the protein that carries
oxygen throughout the blood.
Genomic Resource Centre: Genes and human disease, World Health Organization.
http://www.who.int/genomics/public/geneticdiseases/en/index2.html

CRISPR and other biotech are growing markets
The global CRISPR market is

estimated to expand at a CAGR of
23.95% over the forecasting period
2019-2028. The increasing lifestyle-
Jennifer Doudna
oriented diseases, the rising
prevalence of genetic diseases and
the growing application of drugs are
the primary factors driving the
growth of the CRISPR market.
Emmanuelle Charpentier
Feng Zhang
https://labiotech.eu/features/crispr-cas9-
review-gene-editing-tool/

Being a biotechnologist
during the pandemic era is
a blessing in disguise, and
in the future we need more
biotechnologists.
Private collection, the Indonesian Research Institute for Biotechnology and Bioindustry (2015)

The current gold standard for COVID-19 test is biotech!
RT-qPCR
Requires temperature cycling
Swab sample Requires 2 primers (F and R)

Typically >1.5 hours of PCR running
Typical yield ~ 0.2 mg
Nucleic acid extraction Real-time detection

Sensitive to sample purity
Polymerase chain reaction (PCR)
Accurate to 98%
method, specifically Real-time PCR or
Sensitive and specific Reverse Transcriptase Quantitative PCR
Amplification
Repeatability (RT-qPCR) is the most commonly used
technology for pathogen nucleic acid
detection and has been considered as a
Imporant factors of massive testing: “gold standard” for disease diagnostics
Detection 1. Amount of RT-qPCR machines due to high sensitivity and specificity.
2. Sufficient reagents
3. Number of well-trained personnel

SARS-CoV-2 Detection vs Mutation is biotech!
Is the virus able to overcome the detection
system due to its mutation?
GISAID Comments on the Discussion of Different Types or Clades of
the hCoV-19 Virus and their Origin
As the outbreak evolves over time and more data becomes available,
several colleagues have analyzed and proposed different "types" of
the virus and their origin. Depending on choice of definitions one can
classify the circulating virus strains into a different number of clades
based on genetic variants. These are part of the natural evolution of
the virus currently not known to be associated with any differences
in virulence.
Changes in prevalence of these variants in the short term are

expected and often driven by chance or so-called founder effects
rather than immediate evolutionary pressure. GISAID's daily
summaries of strains distinguishes clades based on genetic marker
variants but this is subject to change following the viral evolution.
It is important to note that there is currently not enough data from

the early outbreak period to interpret the early history of global
transmissions from few genomes in detail.
https://www.gisaid.org/references/statements-clarifications/different-types-or-
clades-of-the-virus-and-their-origin/#c501

Biotechnology from classic to modern products
www.liputan6.com www.pekanbarunews.com www.inquirer.com www.fool.com
• Tempe fermentation • Nata de Coco • Insuline production • RNA vaccines

• It is made by a natural fermentation • The first example of this • Target: S protein
culturing and controlled • Acetobacter xylinum is the occurred in 1978, Herbert • No infectious virus needs
fermentation process that living organism that carries Boyer, University of to be handled
binds soybeans into a out the fermentation of California, took a version • Vaccines are typically
cake form using a fungus Nata de Coco. of the human insulin gene immunogenic
Rhizopus oligosporus, • Nata de Coco is a bacterial and inserted into the • Rapid production possible
usually marketed under cellulose that forms over bacterium Escherichia coli
the name tempeh starter a sugary medium made by to produce synthetic
A. xylinum. "human" insulin.

The future biotechnology: from Genomics to CRISPR!
Bioinformatics
Comparative genomics
Protein modelling
Synthetic genes
A new phase - genetic engineering

Basic DNA knowledge A detection tool
DNA sequencing A future tool
Genomics (DNA) Cisgenic (CRISPR)

Thank you for your attention
“I think the biggest innovations of the 21st
century will be at the intersection of
biology and technology.” - Steve Jobs
Riza Arief Putranto, DEA, Dr

Head of Research Division
Genomics, Transriptomics & Bioinformatics
PT Riset Perkebunan Nusantara

Jl. Salak No.1A Bogor, Indonesia 16128
Ph. +62 251 8333382
Fax. +62 251 8315985
Email rizaputranto@rpn.co.id
ResearcherID | LinkedIn | ORCID | Scopus ID

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Biotech is fun!

Ilmu Kekinian dan Masa Depan

www.thespruceeats.com Riza Arief Putranto

Presented in Webinar Series Bioteknologi Universitas Esa Unggul

“Our world is built on biology and once we begin to

Bios (Biology), Teuchos (Tools), Logos (Knowledge)

"A set of techniques that utilize living organisms or parts of

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• Papaya is native to Mexico. However, it

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Papaya is a climacteric fruit, a

Papaya fruit expansion and

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• Let us extract something from inside the papaya’s

In the end, you will obtain a white-ish jelly as an

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http://archives.starbulletin.com/2008/04/24/news/story09.html Ming R et al. 2008 Nature, 452(7190), 991-996.

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Ming R et al. 2008 Nature, 452(7190), 991-996.

How big is the Papaya genome?

Papaya with a physical appearance as a tree only has three times of

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PRSV affects papaya production throughout the

The virus, PRSV, is transmitted nonpersistently by

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The newly disease-resistant papaya,

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Bioinformatics helps to shorten

The new study has found that the

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These are protein models, validated

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Genetically Modified Organisms (GMOs) are still a subject

Kyndt T et al. 2015, Proceedings of the National Academy of Sciences, 201419685.

The researchers collected 291 sweet

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• Primatologist Davis Okoye, a former US Army Special Forces soldier and

The movie introduced the word

CRISPR technology is a simple yet

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o Mode of Action Option 1. NHEJ generates a “random”

DNA-Binding domain Nuclease domain

MoA Option 1 MoA Option 2

Homology Directed Repair (HDR)

Insert the sgRNA into the in silico construct

•Cloning method Restriction Enzyme

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• SHERLOCK assays uses

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Both diseases are ideal for fixing

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The global CRISPR market is

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Swab sample Requires 2 primers (F and R)

Nucleic acid extraction Real-time detection

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Changes in prevalence of these variants in the short term are

It is important to note that there is currently not enough data from

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www.liputan6.com www.pekanbarunews.com www.inquirer.com www.fool.com

• Tempe fermentation • Nata de Coco • Insuline production • RNA vaccines

Copyright @rizaputranto 2020