September 18th, 2017

I come from Chile




Population: 17 million

Spanish colony 500 years ago (so language is Spanish)

Independent Republic 200 years ago

First Latin American country to recognize Turkish republic

OECD member, same as Turkey

Everyday life very similar to Turkey

Chilean Exports 2015

Chilean Economy: Exports


1st world producer of copper

2nd world producer of salmon

Fruits: peaches, grapes, apples, avocado

Wine: exported worldwide

Biotechnology can improve all these industries

Official data for 2014. Banco Central de Chile

Bioinformatics to understand biotechnological process

  • Peach:
    • response to cold stress
  • Grapefruit:
    • development related to seed and grape size (Sultaniye)
  • Wine:
    • quality control on exported wine,
    • avoid secondary fermentation

Even in the main industries

  • Salmon:
    • effect of diet on metabolism,
    • selection of stress tolerant families.
    • Whole genome sequencing
      • 10M dollars project,
      • harder than human genome
      • Chile, Canada and Norway
  • Mining:
    • copper extraction helped by bacteria

Mining Industry

Copper is heated and melt

to separate it from other compounds

This is
very expensive

… and contaminant

(this smoke is sulphuric acid)

Solution: Bioleaching

The use of bacteria to extract elements from ore

Bioleaching is much better that melting copper

  • Reduced contamination
  • Cheaper

The goal is to understand and improve the involved bacteria so this technology can be used extensively

Enables building new mines

It is like discovering petrol reserves for the country

Bioleaching bacteria

We had a research contract with the main mining company

State owned, big enough to pay for long term research

We focused mainly on 2 questions:

  • Monitoring the microbial community in the mine
  • Understanding how these bacteria do “mining”

Monitoring Microbial Communities

Diversity of microorganisms

Microorganisms can live in extreme environments

  • They produce proteins that can have industrial application
  • We want to identify these proteins
  • We want to monitor and control their presence

Microorganisms are essential to human life

  • 90% of the cells in your body are not “human”
  • Most of them are essential to our health
  • Our digestion depends on them

They are the foundation of all ecosystems


Genomic of the ecosystem

Microorganism live in the most diverse environments.
They are the key to:

  • develop new biotechnology
  • manage our natural resources
  • improve our health
  • understand our past

But only ~5% of them can be grown in the lab

Approach 1: Probe based detectors

If we know the DNA sequence for each relevant organism

  • We can determine a “fingerprint” for each organism DNA
  • That is, a short DNA sequence that is “unique” to each organism
  • Length about 20 nucleotides
    • qPCR primers
    • microarray oligonucleotides

Ideally the primer probably binds to the organism DNA, and probably do not bind to others organisms.


N.Ehrenfeld, A. Aravena, A. Reyes-Jara, N. Barreto, R. Assar, A. Maass, P. Parada, Design and use of oligonucleotide microarrays for identification of Biomining microorganisms. Advanced Materials Research 71-73 (2009) 155-158.


  • Method for the design of oligonucleotides for molecular biology techniques.
    • Australia, Mexico, South Africa, USA
  • DNA fragments array from biomining microorganisms and method for detection of them.
    • Argentina, Australia, Mexico, Peru, South Africa, USA
  • Array of nucleotidic sequences for the detection and identification of genes that codify proteins with activities relevant in biotechnology present in a microbiological sample, and method for using this array.
    • Australia, Chile, China, Mexico, Peru, South Africa, USA

Patents (2)

  • Method and array for detection and identification of microorganisms present in a sample by using genomic regions coding for different tRNA-synthetases.
    • Argentina, Australia, Chile, Mexico
  • Method for the identification and quantification of microorganisms useful in biomining processes.
    • Australia, Chile, Mexico, South Africa, USA

Approach 2: Big Data in Biology

Since most microbes cannot be isolated, and given current technology, the modern approach is:

  • Sample all DNA from the environment
  • Determine the sequence of each fragment
  • Cluster similar sequences together

Of course the clusters depend on the distance we choose

Discovering unknown organisms

Most of the sequences from environmental samples are unique

That is, they do not correspond to any known organism

The question is, given a DNA read, which are the “nearest” known organisms?

Here “closest” is in the phylogenetic sense


Istanbul University

Currently we use this approach to explore archeological data

  • What did our ancestors eat?
  • Which diseases they had?
  • What was the weather then?

“Dry Lab”

  • Genomics and bioinformatics
  • Metagenomic analysis of ancient DNA
    • Collaboration with METU, U. Sweden and U. Bordeaux

Technology changes fast

In 2001, the cost of sequencing the first human genome was USD 108

Today you can have your own genome for 1000 USD

The problem is no longer how to do the experiment

Instead is how do we make sense of the results


why this course is different

Full Semester Project

Your own metagenomics

Idea of DNA Sequencing

Sequencing genomes

Current technology allows us to read DNA in runs of ~100-600 letters. Imagine a book of 1000 pages:

  • several copies of the book are cut randomly in one million pieces
  • different pieces may overlap
  • half of the pieces are lost
  • the remaining half is splashed with ink in the middle

The problem is to reconstruct the original book

Shotgun DNA Sequencing

Shotgun DNA Sequencing (2)