An overview of biological technologies

1. Biological Technologies
Carlos Manuel Estévez -Bretón
LISI - Universidad Nacional de Colombia
Laboratorio de investigación
en sistemas inteligentes

2. •Origin
•Biology’s Informa1on
Technology Toolbox
•Omics
•Gene1c engineering
•Synthe1c Biology
•Biopunk & Hacking Culture
•Biotechnology Market
2

3. The Columbia Electronic Encyclopedia™ Copyright © 2013, Columbia University Press.
Licensed from Columbia University Press. All rights reserved. www.cc.columbia.edu/cu/
cup/
“the use of biological processes, as through the exploitation and
manipulation of living organisms or biological systems, in the
development or manufacture of a product or in the
technological solution to a problem. As such, biotechnology is
a general category that has applications in pharmacology,
medicine, agriculture, and many other fields”

4. CME-B
Are the methods that allows to edit biological information
(Nucleic Acids) to obtain desirable characteristics or conditions.
(Aka; Read, Write, Delete)

5. Origin

6. Epipaleolithic

7. Epipaleolithic

8. Epipaleolithic
At about 60,000 years ago technology shifts in Africa. Lithics get smaller in the Late Stone Age, and
appear to have been used in composite tools.
After the end of the last Ice Age, about 18,000 years ago, things got warmer in Eurasia, and
people changed from Ice Age big game hunters to more sedentary foragers in many areas, also
changing to bladlets and microliths. Southern Eurasia and Africa became very rich. In some places a
new type of activity started to take place, horticulture. Horticulture is plant management and
cultivation that is often supplemented with hunting and gathering.
In southwest Eurasia, horticulture starts to take shape between 18,000 and 12,000 years ago. The
ancestors of domestic crops and animals are mixed with wild plants and animals in small villages.
The timing is similar in eastern Eurasia.
In the Americas, Epipaleolithic-like conditions start to appear around 10,000 years ago.

12. Biology’s Information
Technology Toolbox

13. •DNA structure / sequencing
•Restriction enzymes
•PCR
•Genome Editing

15. DNA structure / sequencing

16. Molecular Biology

17. Pairs of Bases
Erwin Chargaff 11 August 1905 – 20
June 2002
Chargaff Rules
In DNA the number of guanine units equals the number of
cytosine units, and the number of adenine units equals the
number of thymine units.
The relative amounts of guanine, cytosine, adenine and
thymine bases varies from one species to another.
1974
NMoS
1949

18. 1953
Francis Crick
April 6, 1928
8 June 1916 – 28 July
2004
Rosalind Elsie Franklin
25 July 1920 – 16
April 1958
1962
Crick, Watson, &
Wilkins
James D. Watson
DNA Structure

19. DNA Replication
TheMeselson–Stahl experiment
1958
«the most beautiful experiment in biology»
Franklin William Stahl
October 8, 1929
«The Replication of DNA in Escherichia coli»
May 24, 1930
Matthew Stanley Meselson

20. Central Dogma of Molecular Biology
1970
DNA —-> DNA
DNA —-> RNA
RNA —-> Protein
Francis Crick

21. The Genetic Code George Gamow
March 4, 1904 – August 19, 1968
Georgiy Antonovich Gamov
"Gamow's diamonds"
http://www.chemistry-blog.com/2012/08/16/the-most-beautiful-wrong-ideas-in-science/
«Possible Relation between
Deoxyribonucleic Acid and
Protein Structures»
IN a communication in Nature of May 30, p. 964, J. D. Watson
and F. H. C. Crick showed that the molecule of
deoxyribonucleic acid, which can be considered as a
chromosome fibre, consists of two parallel chains formed by
only four different kinds of nucleotides. These are either (1)
adenine, or (2) thymine, or (3) guanine, or (4) cytosine with
sugar and phosphate molecules attached to them. Thus the
hereditary properties of any given organism could be
characterized by a long number written in a four-digital
system. On the other hand, the enzymes (proteins), the
composition of which must be completely determined by the
deoxyribonucleic acid molecule, are long peptide chains
formed by about twenty different kinds of amino-acids, and
can be considered as long ‘words’ based on a 20-letter
alphabet. Thus the question arises about the way in which
four-digital numbers can be translated into such ‘words’.
1954

22. Sequencing

23. First Generation Sequencing

24. Sangre dideoxy Seq.
Is a method based on the selective incorporation
of chain-terminating dideoxynucleotides by DNA
polymerase during in vitro DNA replication. The
initial method required that each read start be
cloned for production of single-stranded DNA.
1977
13 August 1918 – 19 November 2013
Frederick Sanger
1958
1980
DNA fragments are labelled with
a radioactive or fluorescent tag
on the primer (1), in the new DNA
strand with a labeled dNTP, or
with a labeled ddNTP.

25. Maxam-Gilbert Seq.
Is a method of DNA sequencing based on the
selective incorporation of chain-terminating
dideoxynucleotides by DNA polymerase during in
vitro DNA replication.
1977
October 28, 1942
Allan Maxam
March 21, 1932
Walter Gilbert
The improvement of Sanfer´s chain-termination method makes that
Maxam–Gilbert sequencing fall out of favour due to its technical
complexity prohibiting its use in standard molecular biology kits,
extensive use of hazardous chemicals, and difficulties with scale-up
1980
Sanger, Berg, & Gilbert

26. Convencional Sequencing
• Can sequence up to 1,000 bp, and per-base 'raw'
accuracies as high as 99.999%. In the context of
high-throughput shotgun genomic sequencing,
Sanger sequencing costs on the order of $0.50 per
kilobase.
24
Jay Shendure & Hanlee Ji, Nature Biotechnology 26, 1135 - 1145 (2008)

27. Next Generation Sequencing

28. PacBio
Single molecule real time sequencing (SMRT) is a parallelized single
molecule DNA sequencing method. Single molecule real time sequencing
utilizes a zero-mode waveguide (ZMW).[1] A single DNA polymerase
enzyme is affixed at the bottom of a ZMW with a single molecule of DNA as
a template.

29. Illumina
1. Prepare genomic DNA
2. ALach DNA to surface
3. Bridge amplificaPon
4. Fragement become
double stranded
5. Denature the double
stranded molecules
6. Complete amplificaPon
7. Determine first base
8. Image first base
9. Determine second base
10. Image second base
11. Sequence reads over
mulPple cycles
12. Align data.
>50 milliion clusters/flow
cell, each 1000 copies of
the same template, 1
billion bases per run, 1% of
the cost of capillary-based
method.
(From: hLp://
www.illumina.com/
downloads/
SS_DNAsequencing.pdf)

30. Method Read length Accuracy (single
read not
consensus)
Reads per run Time per run Cost per 1 million
bases (in US$)
Advantages Disadvantages
Single-molecule
real-time
sequencing (Pacific
Biosciences)
10,000 bp to 15,000
bp avg (14,000 bp
N50); maximum read
length >40,000 base
87% single-read
accuracy
50,000 per SMRT
cell, or 500–1000
megabases
30 minutes to 4 hour $0.13–$0.60
Longest read length.
Fast. Detects 4mC,
5mC, 6mA
Moderate throughput.
Equipment can be very
expensive.
Ion semiconductor
(Ion Torrent)
up to 400 bp 98 % up to 80 million 2 hours $1
Less expensive
equipment. Fast.
Homopolymer errors.
Pyrosequencing
(454)
700 bp 100 % 1 million 24 hours $10 Long read size. Fast.
Runs are expensive.
Homopolymer errors.
Sequencing by
synthesis (Illumina)
50 to 300 bp 99.9% (Phred30)
up to 6 billion (TruSeq
paired-end)
1 to 11 days,
depending upon
sequencer and
specified read length
$0.05 to $0.15
Potential for high
sequence yield,
depending upon
sequencer model and
desired application.
Equipment can be very
expensive. Requires high
concentrations of DNA.
Sequencing by
ligation (SOLiD
sequencing)
50+35 or 50+50 bp 100 % 1.2 to 1.4 billion 1 to 2 weeks $13 Low cost per base.
Slower than other
methods. Has issues
sequencing palindromic
sequences
Chain termination
(Sanger
sequencing)
400 to 900 bp 100 % N/A 20 minutes to 3 hours $2400
Long individual
reads. Useful for
many applications.
More expensive and
impractical for larger
sequencing projects. This
method also requires the
time consuming step of
plasmid cloning or PCR.
Comparision of next generation sequencing methods

31. First vs. Next genera1on
sequencing
Jay Shendure & Hanlee Ji, Nature Biotechnology 26, 1135 - 1145 (2008)
(a)High-throughput shotgun Sanger sequencing
1. genomic DNA is fragmented
2. cloned to a plasmid vector and used to transform
E. coli. For each sequencing reaction, a single
bacterial colony is picked and plasmid DNA
isolated.
3. Each cycle sequencing reaction takes place
within a microliter-scale volume, generating a
ladder of ddNTP-terminated, dye-labeled
products, which are subjected to high-resolution
electrophoretic separation within one of 96 or 384
capillaries in one run of a sequencing instrument.
4. As fluorescently labeled fragments of discrete
sizes pass a detector, the four-channel emission
spectrum is used to generate a sequencing trace.

32. First vs. Next genera1on
sequencing
Jay Shendure & Hanlee Ji, Nature Biotechnology 26, 1135 - 1145 (2008)
(b) Shotgun sequencing with cyclic-array methods
1. DNA fragmentation.
2. Common adaptors are ligated to fragmented genomic
DNA,
3. Then subjected to one of several protocols that results in
an array of millions of spatially immobilized PCR colonies
or 'polonies'15. Each polony consists of many copies of a
single shotgun library fragment. As all polonies are
tethered to a planar array, a single microliter-scale reagent
volume (e.g., for primer hybridization and then for
enzymatic extension reactions) can be applied to
manipulate all array features in parallel.
4. Similarly, imaging-based detection of fluorescent labels
incorporated with each extension can be used to acquire
sequencing data on all features in parallel. Successive
iterations of enzymatic interrogation and imaging are used
to build up a contiguous sequencing read for each array
feature.

33. Applications of Next-Generation Sequencing
Jay Shendure & Hanlee Ji, Nature Biotechnology 26, 1135 - 1145 (2008)
Category Examples of applications
Complete genome resequencing Discovery of infectious and commensal flora
Reduced representation sequencing
Quantification of gene expression and alternative splicing; transcript
annotation; discovery of transcribed SNPs or somatic mutations microRNA
profiling
Targeted genomic resequencing microRNA profiling
Paired end sequencing Determining patterns of cytosine methylation in genomic DNA
Metagenomic sequencing Discovery of infectious and commensal flora
Transcriptomics sequencing
Quantification of gene expression and alternative splicing; transcript
annotation; discovery of transcribed SNPs or somatic mutations microRNA
profiling.
Small RNA sequencing microRNA profiling
Sequencing of bisulfite-treated DNA Determining patterns of cytosine methylation in genomic DNA
Chromatin immunoprecipitation-sequencing
(ChiP-Seq)
Genome-wide mapping of protein-DNA interactions
Nuclease fragmentation and sequencing Nuleosome positioning
Molecular barcoding Multiplex sequencing of samples from multiple individuals.

34. Microarrays
https://youtu.be/UgL1Pq2sk3M

35. Microarrays
https://youtu.be/UgL1Pq2sk3M

36. • DNA microarrays, such as cDNA microarrays,
oligonucleotide microarrays, BAC microarrays and
SNP microarrays
• MMChips, for surveillance of microRNA populations
• Protein microarrays
• Peptide microarrays, for detailed analyses or
optimization of protein-protein interactions
• Tissue microarrays
• Cellular microarrays (also called transfection
microarrays)
• Chemical compound microarrays
• Antibody microarrays
• Carbohydrate arrays (glycoarrays)
• Phenotype microarrays
• Reverse Phase Protein Microarrays, microarrays of
lysates or serum
• interferometric reflectance imaging sensor (IRIS)
Types of microarrays

37. ChIP-Seq
Hongkai Ji et al. Nature Biotechnology 26: 1293-1300. 2008
ChIP-sequencing, also known as ChIP-seq, is a
method used to analyze protein interactions with DNA.
ChIP-seq combines chromatin immunoprecipitation
(ChIP) with massively parallel DNA sequencing to
identify the binding sites of DNA-associated proteins. https://youtu.be/4oFdS9EN9Pk

38. ChIP-Seq
Hongkai Ji et al. Nature Biotechnology 26: 1293-1300. 2008
ChIP-sequencing, also known as ChIP-seq, is a
method used to analyze protein interactions with DNA.
ChIP-seq combines chromatin immunoprecipitation
(ChIP) with massively parallel DNA sequencing to
identify the binding sites of DNA-associated proteins. https://youtu.be/4oFdS9EN9Pk

40. Restriction
enzymes

41. Restriction enzymes
• Are enzyme that cuts DNA at
or near specific recognition
nucleotide sequences
known as restriction sites
• To cut DNA, all restriction
enzymes make two
incisions, once through each
sugar-phosphate backbone
(i.e. each strand) of the DNA
double helix.
https://youtu.be/lWXryzgRces

42. Restriction enzymes
• Are enzyme that cuts DNA at
or near specific recognition
nucleotide sequences
known as restriction sites
• To cut DNA, all restriction
enzymes make two
incisions, once through each
sugar-phosphate backbone
(i.e. each strand) of the DNA
double helix.
https://youtu.be/lWXryzgRces

44. Polymerase Chain
Reaction PCR

45. PCR
The polymerase chain reaction (PCR) is a
technology in molecular biology used to amplify
a single copy or a few copies of a piece of DNA
across several orders of magnitude, generating
thousands to millions of copies of a particular
DNA sequence.
1993
Kary Mullis, &
Michael Smith
https://youtu.be/2KoLnIwoZKU

46. PCR
The polymerase chain reaction (PCR) is a
technology in molecular biology used to amplify
a single copy or a few copies of a piece of DNA
across several orders of magnitude, generating
thousands to millions of copies of a particular
DNA sequence.
1993
Kary Mullis, &
Michael Smith
https://youtu.be/2KoLnIwoZKU

47. Genome Editing

48. Decemberer 11, 1968
Jennifer Anne Doudna
February 19, 1941
2015
Princess of Asturias
Award
CRISPR/cas9
Dr. Paul Janssen
Award for Biomedical
Research
2014
2015
Gruber Prize in
GeneticsEmmanuelle Charpentier 2014

49. CRISPR/cas9
Is a prokaryotic immune system
that confers resistance to foreign
genetic elements such as
plasmids and phages, and
provides a form of acquired
immunity.
CRISPR spacers recognize and
cut these exogenous genetic
elements in a manner analogous
to RNA interference in eukaryotic
organisms.
CRISPRs are found in
approximately 40% of sequenced
bacteria genomes and 90% of
sequenced archaea.
https://www.youtube.com/watch?v=2pp17E4E-O8

50. CRISPR/cas9
Is a prokaryotic immune system
that confers resistance to foreign
genetic elements such as
plasmids and phages, and
provides a form of acquired
immunity.
CRISPR spacers recognize and
cut these exogenous genetic
elements in a manner analogous
to RNA interference in eukaryotic
organisms.
CRISPRs are found in
approximately 40% of sequenced
bacteria genomes and 90% of
sequenced archaea.
https://www.youtube.com/watch?v=2pp17E4E-O8

51. -omics

52. http://omics.org/index.php/Omes_and_Omics
“The word omics refers to a field of study in biology ending in
the suffix -omics such as genomics, interactomics, or proteomics.
The related ome addresses the objects of study of such
fields, such as the genome, interactome, or proteome
respectively.
Users of the suffix “-om-” frequently take it as referring to
totality of some sort and complex networks within the omes.”

53. Genomics
Transcriptomics
Proteomics
Metabolomics
Nutriomics
Interactomics

54. Biology
Molecular
Biology
Genetic
Engineering
NGS
CRISPR/
Cas9
Read
Write
Synthetic
Biology

55. Genetic engineering

56. Genetic engineering
1. Bacteriophage - virus that infect
bacteria.
2. Cosmids - hybrid vector that (part
phage, part bacteria), used to clone
larger genes or fragments of DNA.
3. Bacterial Artificial Chromosome - is
an engineered DNA molecule used to
clone DNA sequences in bacterial cells
(ex: E.coli).
4. Yeast Artificial Chromosome - is a
human engineered DNA molecule used
to clone DNA sequences in yeast cells.
5. Expression vector - used to
introduce a specific gene into a target
cell.

57. Genetic engineering
1. Bacteriophage - virus that infect
bacteria.
2. Cosmids - hybrid vector that (part
phage, part bacteria), used to clone
larger genes or fragments of DNA.
3. Bacterial Artificial Chromosome - is
an engineered DNA molecule used to
clone DNA sequences in bacterial cells
(ex: E.coli).
4. Yeast Artificial Chromosome - is a
human engineered DNA molecule used
to clone DNA sequences in yeast cells.
5. Expression vector - used to
introduce a specific gene into a target
cell.
… but: too much genetics
and…
almost nothing about
engineering

58. Synthetic
Biology

62. Biopunk & Hacking Culture

63. Bipounk
https://vimeo.com/18201825
Meredith Patterson
https://diybio.org/

64. Biotechnology Market

65. Global Biotechnology Market
Revenue
$336bn
Annual Growth 11-16
4.6%
Employment ('000)
580
Businesses
7,076
http://www.ibisworld.com/industry/global/global-biotechnology.html

66. Global Biotechnology Market
Annual Growth 12-17
11.6%
http://www.prnewswire.com/news-releases/global-biotechnology-market-to-value-usd-4145-billion-2017-transparency-market-
research-276915571.html
• Biotechnology Market by
Application: Biopharmacy,
Bioservices, Bioagri, Bioindustrial
• ByTechnology: Fermentation,
Tissue Regeneration, PCR,
Nanobiotechnology, DNA
Sequencing & Others Revenue 17
$414.5bn
Revenue 11
$216.5bn

67. Forecast 2020
• By Technology: Fermentation,
Tissue Engineering, PCR
Technology, Nanobiotechnology,
Chromatography, DNA Sequencing,
Cell-based Assay
• By Application:
Biopharmaceuticals, Bioservices,
Bioagriculture, Bioindustry
Bioinformatics & Computational
Biology
Blue Biotech: Aquatic applications
Green Biotech: Agricultural
processes
Red Biotech: Medical processes
White Biotech: Industrial
biotechnology
http://www.grandviewresearch.com/industry-analysis/biotechnology-market

68. Forecast 2020
Was valued at USD 270.5 GUSD in
2013 and is expected to grow at 12.3%
owing to the increasing demand
for diagnostics and therapeutics
solutions such as recombinant
technology, red biotechnology, and
DNA sequencing.
And prevalence of diseases such
as cancer, hepatitis B, and other
orphan disorders is expected to serve
as a high-impact rendering driver for
this industry.
Increasing demand for agricultural and
food products such as wheat, rice,
sugarcane, and beans owing to growing
population base in countries is another major
factor positively impacting growth of the
industry.
Factors such as limited availability of
agricultural land, shortage of water, low yield
of crops, and pest attacks are encouraging
researchers to develop innovative agricultural
technologies via extensive R&D activities.
Application of biotechnological processes
such as Genetic Modification (GM) and
genetic engineering on agricultural products is
a major driver for growth of this industry.

69. The U.S. biotechnology market revenue by application, 2012-2020,
USD Million

70. Thanks!!!!
Carlos Manuel Estévez -Bretón
LISI - Universidad Nacional de Colombia
Laboratorio de investigación
en sistemas inteligentes
@karelman