MARINE GENOMICS
Understanding biological importance by evolutionary analyses of genomes, gene expression, and genetic divergence
2014 - S U M M E R B R I D G E - R E U
Congratulations to the 2014 REU students for achiving the 2nd Place in the Miami Dade College STEM FYE summer bridge research exposition.
The summer bridge/REU in organismic and evolutionary biology is a colaboration between the STEM FYE program and the laboratory of marine genomics. It was an intensive six-week program designed to provide first-time-in-college students a comprehensive research experience in the field of organismic and evolutionary biology. The project encompassed the four main components of modern biological research: theoretical discussion, fieldwork, bench (laboratory) work and bioinformatics.
As a result of their participation in the summer bridge/REU students achieved:
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Worked as a team to complete the proposed project
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Learned basic laboratory methods to conduct scientific research
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Learned basic techniques to perform DNA extraction, quantification and processing
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Learned basic to use basic bioinformatics tool to analyze DNA data
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Produced a written research summary and a research poster
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Presented their research in the annual Miami Dade College STEM FYE summer bridge research exposition
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Won Second Place in the Miami Dade College STEM FYE summer bridge research exposition
The REU Students joint by the STEM FYE Staff and members of the labortory of Marine Genomics. Left to right: Joaquin Nunez (T.A.), Monica Minchala (STEM FYE Director), Maxime Desse (STEM FYE Coordinator), Jordan L. Parra, Margie Oleksiak (Marine Genomics P.I.), Andrea Olivera, Doug Crawford (Marine Genomics P.I.), Alinord Mezinord, and Martin Cordero.
The 2014 Summer REU group: Jordan L. Parra, Martin Cordero, Andrea Olivera, T.A. J. Nunez and Alinord Mezinord
The 2014 Summer REU group: Jordan L. Parra, P.I. Doug Crawford, Martin Cordero, P.I. Margie Oleksiak, Andrea Olivera, and Alinord Mezinord
REU Calendar
June 16 2015 - 9:00 am
Introduction/Field Collection
Introduction and expectations of the REU/Summer Bridge. Field collection of specimens in Virginia Beach and surrounding areas.
Computation:
R - Introduction
Documents
TBD - 9:00 a.m
DNA Extraction
DNA will be extracted from the collected samples. QC Gel will be run. HW 1 & 2 Due
Documents
Session Presentation
-Done by:
-Topic: Summary of Pipetting trials and Collection activities and Summary of Organism under study
TBD
Project Report 1 Draft
A draft proposal/report must be submitted to the Peer Leader before 6 p.m.
The draft must contain Objective, Goals, Model Organims info, Brief mention of methods and expected results
TBD
DNA processing and PCR reactions
DNA will be amplified via PCR rxns and will be prepared for sequencing. PCR part of HW 3 Due
Documents
-Reading: DNA primers for amplification of mitochondrial cytochrome c oxidase. (O. Folmer el al. 1994)
Session Presentation
-Done by:
-Topic: Summary of Collection activities, Summary of Organism under study and DNA extraction
TBD
DNA sequencing Preparation
QC gel of PCR products. Preparation of samples for sequencing.
Documents
-HW 4 Due
-Reading: DNA sequencing (D. Hudson 2010). Read: 10.1, 10.2, 10.6, 10.7 and 10.8.
-PowerPoint on Sanger Sequencing
Session Presentation
-Done by:
-Topic: Summary of Organism under study, Summary of DNA extraction, Summary of PCR reaction
July 17
Scientific Manuscript as Progress report
The Scientific manuscript must contain a fully developed introduction, explained methods and a more elaborated view of the expected results. This is basically the corrected version of HW4
TBD
Data Analysis
Sequences will be aligned and analized using bioinfomatic tools. HW 5 Due.
Documents
-Reading: Conservation genetics of the extinct dusky seaside sparrow Ammodramus maritimus nigrescens (R. Zink & H. Kale 1994 )
-Identification Websites: nBlast, Bold
-Bioinformatics: Finch TV, Mega X, DNAs
-Online Tools: Clustal W
Session Presentation
-Done by:
-Topic: Summary of Organism under study, Summary of DNA extraction, Summary of PCR, Summary of Sequencing
NOTE: The tasks to be completed this session are relatively time comsuming; aditionally, the poster must be finished. Consider staying overtime for this particular session.
July 23
Poster Submission
Poster must be submitted for printing.
Poster must be crafted as indicated in the template. Information for results ans discussion will be displayed as bullet points.
July 29 - Time 9:00 a.m.
Discussion
Final discussion on results preparation for final presentation. HW 6 Due.
What is due:
-Draft of Manuscript of conducted research: Simply put together all the material produced in this
REU. Do it in the following order: Introduction, Methods (we will provide you with the methods), Results, Discussion.
This session we will:
-Elect group representatives for Final presentation
-Finish poster and research manuscript.
-Rehearse the Final Presentation
July 30, 2014, 10:30 am - 1:00 pm
Summer Bridge Presentation
Room: 3208