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) - iPSC's
* David Nyer (Research Tech), Daniel Vargas (Biological Design PhD), Stefan Tekel (Biological Design PhD), 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 and transfection of iPS cells to enhance current measurements of pluripotency.
* 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)
* René Daer (Biological Design, PhD), Cassandra Barrett (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.




'''Engineering synthetic chromatin transcription factors'''
'''Synthetic chromatin systems for cell development'''
* Cameron Gardner (FURI, BS)
* David Barclay (Biomedical Eng. BS), Jan Simper (Biomedical Eng. BS), Theodore Kyriacou (Biomedical Eng. BS)
* 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: Designing a single-cell-level fluorescent reporter that tracks changes in epigenetic states in developing cells.




'''Microbial communication with synthetic quorum sensing'''
'''Microbial communication with synthetic quorum sensing'''
* René Davis (Biological Design, PhD), Ryan Muller (SOLUR, BS)
* René Daer (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 Ben]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/RNA-seq_of_PcTF_Transfected_U2OS_%26_SK-N-SH_cell_lines Ben - RNA-seq of PcTF transfected cell lines]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/HPK-CFP_insertion_into_Gal4EED/Luc_using_CRISPR Ben - HPK-CFP insertion into Gal4EED/Luc using CRISPR]
* [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/MPeterson_Cloning_Bootcamp Mara Peterson]
* [http://openwetware.org/wiki/User:Rene_M_Davis/Notebook Rene]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Lab_Traning_-_Pradyumna_Kadambi#Pradyumna_Kadambi.2FUndergraduate_Lab_Traning Prad]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook:Shared/Cloning_Bootcamp SHARED: Cloning Bootcamp]
* [http://openwetware.org/wiki/User:Rene_M_Davis/Notebooks René - Quorum Sensing]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/Short_Projects SHARED: Short Projects]
* [http://openwetware.org/wiki/Haynes_Lab:Notebook/CRISPR_Editing René - CRISPR Editing]
* [http://openwetware.org/wiki/User:Stefan_J._Tekel/Notebook/Pc-TF_Engineering Stefan Tekel]
* [http://openwetware.org/wiki/User:Brendan_F._Fries/Notebook/Brendan_Fries Brendan]
* [http://openwetware.org/wiki/User:Mara_Peterson/Notebook/Mara_Peterson Mara Peterson]
* [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]

Latest revision as of 10:44, 7 January 2016


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), Daniel Vargas (Biological Design PhD), Stefan Tekel (Biological Design PhD), 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

  • René Daer (Biological Design, PhD), Cassandra Barrett (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.


Microbial communication with synthetic quorum sensing

  • René Daer (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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