Download MSc in Biochemistry Dissertation Project – 2nd Cycle Student´s

MSc in Biochemistry
Dissertation Project – 2nd Cycle
Student´s Name:
Student email address:
No.
Supervisor(s): Rita Sobral andSusana Gaudêncio
Supervisor(s) email address:[email protected] and [email protected]
Lab/Institution: Lab of Molecular Microbiology of Bacterial Pathogens (Lab333), DCV, UNL and Lab 202,
DQ, UNL
TITLE:A genome-wide approach to understand the diversity of marine bacteria and identify new
producer species
BACKGROUND
Ocean environments constitute a major source of biodiversity, harboring marine life forms capable of
producing a variety of molecules with unique features, unmatched biochemical diversity and structural
complexity. Marine bacteria are an exceptional source of bioactive chemical diversity, especially
actinomycetes, providing a high number of lead-like compounds for drug discovery. Due to the
dramatic increase of infectious diseases and mutiresistant bacteria, the need to discover and develop
new drugs has never been greater.
The sequencing and annotation of the genome of bacteria that are known producers of new chemical
structures will reveal new biosynthetic pathways of secondary metabolism responsible for the
synthesis of such compounds.
S. Gaudêncio has gathered a diverse collection of 400 taxonomically described marine-sedimentderived bacteria, collected from the Madeira Archipelago. Several of these strains have revealed new
phylogeny, exclusive adaptation to sea-life conditions and biological activities (antimicrobial,
antibiofilm, antifouling and proteasome inhibition).
OBJECTIVES
We aim to perform whole-genome sequencing of pre-selected strains of Salinispora genus and
Streptomyces aculeolatus species, that were identified as prolific producers of compounds with
antimicrobial and anti-biofilm activity. Through a genome-based approach we aim to identify new
clusters of genes involved in the production of these new compounds.
Furthermore, results from 16SRNA sequencing suggest that, strains representative of new unidentified
species of Micromonospora, Verrucosispora, Stackebrandtia, Actinocorallia, among others, exist among
our collection. These strains are also producers of compounds with biological activity. We aim to
characterize such strains in order to define them as new species.
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MSc in Biochemistry
Dissertation Project – 2nd Cycle
PROJECT DESCRIPTION
- The genomic DNA of theSalinispora and Streptomyces strains will be extracted through the
CTAB/phenol/chloroform method(Task 1). The yield of the extraction procedure and the integrity of
the DNA will be assessed using Qubit Fluorometer, agarose gel electrophoresis and NanoDrop
Spectrophotometer. Genome sequencing will be performed using the MiSeq (Illumina) platform(Task
2). Preliminary annotation of the sequence will be performed using a reference genome in CLC
Genomics Workbench(Task 3).
- For the characterization of the new species, several phenotypic traits will be explored(Task 4),
including optimum growth conditions, microscopic morphology (SEM), hydrolysis of complex polymers,
metabolic patterns (Biolog), etc. Also the composition of the cell wall and the genome GC content will
be evaluated(Task 5).
TIMELINE(use fill tool for the cells)
Month 1
Month 2
Month 3
Month 4
Month 5
Month 6
Month 7
Month 8
Month 9
Month 10
Task 1
Task 2
Task 3
Task 4
Task 5
Thesis
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