Directed Evolution and Synthetic Biology Interest Group

New Interest Group!

After some drift, we are restarting our Directed Evolution and Synthetic Biology Interest Group. We encourage everyone in the community - professors, postdocs, grad students, undergrads, and research staff - to participate.

If you are interested in direct evolution, experimental evolution, synthetic biology, and/or genetic engineering, please contact Dr. Chang Liu to be added to the email list.

Date and Time: Friday, October 14th, 2016 from 4-5PM

Location: Natural Sciences 2, Room 3201

Speaker: Professor John Chaput - He will be speaking on in vitro RNA and TNA evolution.

We plan on having a meeting once per month, (on the 2nd Friday) and after Professor Chaput, the talks will be primarily from postdocs and graduate students. We'll describe logistical details at our October 14th meeting.

Prokaryotic Interest Group

New Interest Group!

The Prokaryotic Meeting cover topics on bacteria and phage from an inter-disciplinary perspective, including approaches from Biology, Chemistry, Engineering, Physics, Quantitative Biology, and Systems Biology. 


Date and Time: Friday, October 7th, 2016 at 4:00PM

Location: McGaugh Hall, Room 1246

Speaker: Anerudh Kannan (Siryaporn Lab)

Title: Anerudh will present the following journal article: "Exposing the Three-Dmensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling" (DePas et al., mBio, 2016).


Date and Time: Friday, September 2nd, 2016 at 10:00AM

Location: McGaugh Hall, Room 1246

Speaker: Siavash Ahrar (Siryaporn Lab)

Title: "Towards dynamic monitoring of mechanical signaling in Pseudomonas aeruginosa during virulence and biofilm formation"


Date and Time: Friday, August 5th, 2016 at 10:00AM

Location: McGaugh Hall, Room 1246

Speaker: Nicole Ing (Hochbaum Lab)

Title: "Electronic conduction in Geobacter sulfurreducens pili"


Date and Time: Friday, July 1st, 2016 at 10:00AM

Location: McGaugh Hall, Room 1246

Speaker: Joann Phan (Whiteson Lab)

Title: " Stable isotope profiles reveal active production of VOCs from human-associated microbes"


Date and Time: Friday, June 3rd, 2016 at 2:00PM

Location: McGaugh Hall, Room 1246

Speaker: Anerudh Kannan (Siryaporn Lab)

Title: " Bacterial biofilms, motility, and metabolism in flow environments"


Date and Time: Friday, May 6th, 2016 at 2:00PM

Location: McGaugh Hall, Room 1246

Speaker: Arunima Bhattacharjee (Hochbaum Lab)

Title: " Metabolic Fingerprint of Bacteria by Fluorescence Lifetime Imaging Microscopy"

Drosophila Interest Group

New Interest Group!


Dates are:


-Friday, April 1

Speaker: Abed Alnaif, Lander Lab

"Coordination of patterning and growth in the wing disc"


-Friday, May 6

Speaker: Ceazar Nave, Holmes Lab

“Investigating ‘Social Jetlag’ Using Real-Time Longitudinal Imaging of the Entire Drosophila Circadian Neural Network”


 -Friday, June 3

Speaker: O'Dowd Lab Members

Using CRISPR in Drosophila

-Friday, July 8

Speaker: Mahul Chakraborty, Emerson Lab 

"Beyond the tip of the iceberg: uncovering hidden genetic variants with long molecule sequencing"


11:45 am – 12:00 pm, Come and Chat

12:00 pm – 1:00 pm, Research Talk

Location: Natural Sciences II, Room 4201


The Drosophila Interest Group aims to hold highly interactive meetings that bring together the Drosophila labs across campus. Speakers may present ideas for a new project or grant, data from a project in progress, figures for a paper, etc. 

Come, bring your lunch, listen to and discuss Drosophila research. All are welcome.


For more information, please contact Dr. Zeba Wunderlich at:



Cellular Metabolic Dynamics

New Interest Group!

Join us for engaging discussions and learning on Cellular Metabolic Dynamics.

All are welcome!

We hope to encourage those researchers interested in cellular metabolism to participate in an open informal meetings regarding:


1) cell metabolism

2) metabolism in cancer

3) metabolism in development

4) metabolism in neurodegenerative diseases

5) fluorescence lifetime imaging  microcopy (FLIM)

6) Seahorse technologies

7) new computational tools to quantify concentrations of NADH

8) new computational tools to obtain indexes of metabolic chances for drug screening, healthy and unhealthy cells

9) advances in auto-fluorescence dynamics (retenoic acid, NADH etc)

Time and Day: 8:30-9:30AM; dates below

Location: Room 3201 Natural Sciences II

Tentative schedule:

Speaker Date Topic Location
Aimee Edinger

April 14th     


Warburg effect and how cancer cells acquire nutrients and respond to nutrient stress and present from FLIM data 3201 Natural Sciences II
Jenu Chacko April 21st 8:30-9:30AM FLIM in tissues 3201 Natural Sciences II
Nik Hedde and Rachel Cinco

May 5th


Application of FLIM to defining Ovarian Follicular Metabolism; NADH Dynamics 3201 Natural Sciences II
Olga V. Razorena

June 16th 8:30-9:30AM CANCELLED

The role of CDCP1 in lipid metabolism in breast cancer cells  3201 Natural Sciences II


If you would like to volunteer to lead a discussion, please send Dr. Michelle Digman an email:

Why is this group formed?

1)  It has come to our attention that many investigators on campus are doing work in investigating changes of cellular metabolism.

  • One method used to measure the redox state of cells is the popular Seahorse technology that uses test kits to measure energy utilization in living cells. In particular this system measures “oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) at intervals of approximately 5-8 minutes. OCR is an indicator of mitochondrial respiration, and ECAR is largely the result of glycolysis” ( ) .
  • While the Seahorse system provide bulk rate measurements some investigators are doing parallel experiments using fluorescence lifetime imaging microcopy (FLIM). The advantage of this method is that researchers have a map of metabolic changes within a cell. Thus single cell analysis can be done more accurately and comparative results can be done to distinguish cell populations at the single cell level without using any fluorescence markers.  That’s right the cells have their fluorescence biomarkers (in particular NADH, a metabolic co-factor) that is predominant in cells. Given that we are mainly exciting NADH with the 2-photon laser with a narrow emission filter between 420-465nm,, their phasor finger printing would be outside the linear phasor trajectory for free and bound NADH.
  • We will discuss topics in metabolism including Cancer, embryo development, advances in FLIM analysis and other research that focus on metabolic changes. We will also discuss other optical imaging technologies that can be used in parallel for FLIM. These include but are not limited to: Second harmonic imaging, third harmonic imaging and CARS.



Visualizing Microbial Chemical Molecular Networks: MIG meeting (June 17, 2015)

We are pleased to annouce Dr. Robert Quinn from the Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, as our invited guest speaker for this month's Metabolomics Interest Group (MIG) meeting.
Dr. Quinn will be speaking on "Visualizing the Chemical World of Mucosal Associated Microbial Communities with Molecular Networks" using examples of microbial metabolomics data from coral reefs and human lung samples, and showcasing the GNPS (Global Natural Products Social Molecular Networking) initiative.
Wednesday, June 17th @ 12:00 -1:00 pm,
BioSci III, Rm 2120 (conference room)
Light refreshments will be served.
Quinn chemnetworksAbstract: Mucosal associated microbial communities exist in all biological environments from coral reefs to human lungs. They are comprised of host epithelial cells coated in mucus and harboring a symbiotic microbial community. These systems are highly diverse and contain myriad competitive and cooperative interactions. Dysbioses is an important phenomenon in these systems, where shifts in the constituent microbial communities are associated with a diseased state. While the taxonomic and functional genetics of these communities has been characterized in a number of studies, the global chemistry of these environments is poorly uncharacterized. Mass spectrometry based metabolomics has lagged behind progress in sequencing based omics because of the paucity of sufficient searchable databases. Since the advent of the novel MS/MS data analysis algorithm ‘molecular networking’ the knowledge gap between sequence and metabolite is beginning to narrow. We have applied mass spectrometry based metabolomics to two very different, mucosal associated microbial communities, the cystic fibrosis lung and the reef building coral. The molecular networking approach has revealed that although separated by 500 million years of evolution and thought of as very different systems, the chemistry and physiology that governs these two environments contains much similarity. This lecture will describe the preliminary findings of our foray into the chemical world of these complex systems. 
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