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

• 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

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”

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

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

• 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

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

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

• Find providers for DNA sequencing
• Determine a sample you are interested
  • https://www.scientificamerican.com/article/dirty-money/
• Extract DNA
• Send to sequencing
• Analyze
• Report

• ARDİ Medikal Araştırma http://www.ardimed.com/
• Anatolya Geneworks http://www.anatoliageneworks.com/
• Accura Science http://www.accurascience.com/
• Illumina https://www.illumina.com/
• BaseSpace https://basespace.illumina.com/home/index
• Genomics Powered by Google Cloud Platform https://www.blog.google/products/google-cloud/our-genes-how-google-cloud-helps-broad-institute-slash-cost-research/
• BioCoder (O’Reilly books)

• NCBI https://www.ncbi.nlm.nih.gov/
• DNA Data Bank of Japan https://www.ddbj.nig.ac.jp/
• EMBL-EBI https://www.ebi.ac.uk/
• ENSEMBL https://www.ensembl.org/

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