Haynes Lab: Difference between revisions

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CURRENT SYNTHETIC BIOMEDICAL ENGINEERING PROJECTS<br>
CURRENT SYNTHETIC BIOMEDICAL ENGINEERING PROJECTS<br>


'''Synthetic chromatin for cell differentiation'''
'''Synthetic chromatin for cancer research'''
* David Barclay (FURI & SynBERC, BS) - pancreas, Jan Simper (FURI, BS) - cardiac
* David Nyer (Research Tech), David Tze (Biomed Eng. BS)
* Description: Testing the "PcTF" synthetic chromatin protein/transcription activator described in [http://www.ncbi.nlm.nih.gov/pubmed/21669865 Haynes & Silver 2011] to determine its ability to alter the phenotypes of healthy cells, such as cell fate switching from alpha cells to beta cells in the pancreas to treat diabetes or the growing of programmable "organoids" from iPS cells.
* Description: Using the "PcTF" synthetic chromatin protein/ transcription activator described in [http://www.ncbi.nlm.nih.gov/pubmed/21669865 Haynes & Silver 2011] to regulate genes in cancer cells. Building and testing re-engineered versions of PcTF.




'''Editing synthetic genes using CRISPR'''
'''Opening silenced chromatin'''
* René Davis (Biological Design, PhD)
* Daniel Vargas (Biological Design PhD)
* Description: Characterizing chromatin/CRISPR interactions. Re-engineering synthetic gene circuits in human cells using CRISPR.
* Description: Using synthetic chromatin proteins to induce a permanently re-opened state at epigenetically silenced genes.
 
 
'''Synthetic chromatin systems for cell development'''
* David Barclay (Biomedical Eng. BS), Jan Simper (Biomedical Eng. BS), Theodore Kyriacou (Biomedical Eng. BS)
* Description: Designing a single-cell-level fluorescent reporter that tracks changes in epigenetic states in developing cells.




'''Engineering synthetic chromatin transcription factors'''
'''Editing synthetic genes using CRISPR'''
* Cameron Gardner (FURI, BS)
* René Davis (Biological Design PhD)
* Description: Building and testing re-engineered versions of the "PcTF" synthetic chromatin protein/ transcription activator described in [http://www.ncbi.nlm.nih.gov/pubmed/21669865 Haynes & Silver 2011].
* Description: Characterizing chromatin/CRISPR interactions.




'''Microbial communication with synthetic quorum sensing'''
'''Microbial communication with synthetic quorum sensing'''
* René Davis (Biological Design, PhD), Ryan Muller (SOLUR, BS)
* René Davis (Biological Design, PhD), Ryan Muller (Biochem. BS), Jiaqi Wu (Biomedical Eng. BS)
* Description: Characterizing cross-talk between decoupled cell-cell communication systems from bacteria.
* Description: Characterizing cross-talk between decoupled cell-cell communication systems from bacteria.


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'''Lab Notebooks - Active''' {{hide|
'''Lab Notebooks - Active''' {{hide|
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/SynBERC_Scholars_2013 Alfonso & Zazu]
* [http://openwetware.org/wiki/User:David_Benjamin_Nyer/Notebook Ben]
* [http://openwetware.org/wiki/User:Behzad_Damadzadeh/Notebook/PcTF_Subcloning_in_E-coli Behzad]
* [http://openwetware.org/wiki/User:Daniel_A._Vargas/Notebook/General_lab_notebook Daniel]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/RNA-seq_of_PcTF_Transfected_U2OS_%26_SK-N-SH_cell_lines Ben]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Engineering_PC-TFs Cameron]
* [http://openwetware.org/wiki/User:David_Barclay/Notebook David Barclay]
* [http://openwetware.org/wiki/User:David_Barclay/Notebook David Barclay]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Heathers_Lab_Notebook Heather]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Synthetic_Chromatin_for_Cancer_Research David Tze]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Jan Jan]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Jan Jan]
* [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook Karmella]
* [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook Karmella]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Lab_Traning_-_Pradyumna_Kadambi#Pradyumna_Kadambi.2FUndergraduate_Lab_Traning Prad]
* [http://openwetware.org/wiki/User:Rene_M_Davis/Notebook Rene]
* [http://openwetware.org/wiki/User:Rene_M_Davis/Notebooks René - Quorum Sensing]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook:Shared/Cloning_Bootcamp SHARED: Cloning Bootcamp]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/CRISPR_Editing René - CRISPR Editing]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Short_Projects SHARED: Short Projects]
* [http://openwetware.org/wiki/User:Brendan_F._Fries/Notebook/Brendan_Fries Brendan]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook:Shared/Cloning_Bootcamp Cloning Bootcamp]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Short_Projects Short Projects]
}}
}}
'''Lab Notebooks - Archived''' {{hide|
'''Lab Notebooks - Archived''' {{hide|
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Chimera_Biosensor_%28C.R.SYS%29 Abhi]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Chimera_Biosensor_%28C.R.SYS%29 Abhi]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/SynBERC_Scholars_2013 Alfonso & Zazu]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Inteins Amanda]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Inteins Amanda]
* [http://openwetware.org/wiki/User:Behzad_Damadzadeh/Notebook/PcTF_Subcloning_in_E-coli Behzad]
* [http://openwetware.org/wiki/User:Brendan_F._Fries/Notebook/Brendan_Fries Brendan]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Engineering_PC-TFs Cameron]
* [http://openwetware.org/wiki/Carly's_Lab_Notebook Carly]
* [http://openwetware.org/wiki/Carly's_Lab_Notebook Carly]
* [http://openwetware.org/wiki/User:David_Dreher/Notebook/Chromatin_controlled_cell_pattern David Dreher]
* [http://openwetware.org/wiki/User:David_Dreher/Notebook/Chromatin_controlled_cell_pattern David Dreher]

Revision as of 10:19, 26 June 2015


Our group uses synthetic, systems, and quantitative biology to engineer useful gene and protein-based biological devices and to deepen our understanding of molecular cell biology. We operate biological devices primarily in human/ mammalian cells. Accelerating the pace of therapeutic technologies (such as tissue regeneration and customizable protein-based drugs) via modular design is the grand challenge that shapes our research plans.

CURRENT SYNTHETIC BIOMEDICAL ENGINEERING PROJECTS

Synthetic chromatin for cancer research

  • David Nyer (Research Tech), David Tze (Biomed Eng. BS)
  • Description: Using the "PcTF" synthetic chromatin protein/ transcription activator described in Haynes & Silver 2011 to regulate genes in cancer cells. Building and testing re-engineered versions of PcTF.


Opening silenced chromatin

  • Daniel Vargas (Biological Design PhD)
  • Description: Using synthetic chromatin proteins to induce a permanently re-opened state at epigenetically silenced genes.


Synthetic chromatin systems for cell development

  • David Barclay (Biomedical Eng. BS), Jan Simper (Biomedical Eng. BS), Theodore Kyriacou (Biomedical Eng. BS)
  • Description: Designing a single-cell-level fluorescent reporter that tracks changes in epigenetic states in developing cells.


Editing synthetic genes using CRISPR

  • René Davis (Biological Design PhD)
  • Description: Characterizing chromatin/CRISPR interactions.


Microbial communication with synthetic quorum sensing

  • René Davis (Biological Design, PhD), Ryan Muller (Biochem. BS), Jiaqi Wu (Biomedical Eng. BS)
  • Description: Characterizing cross-talk between decoupled cell-cell communication systems from bacteria.

Lab Notebooks - Active

Lab Notebooks - Archived

Benchling
Trello Boards

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