Welcome to the Mukhopadhyay group site! 


Some news from lab..

Interested in working with us? Contact Aindrila!

Dec 7th 2023









Group Lunch with the whole team to mark the end of a great year!

Oct 10-12th 2023

JBEI Annual meeting in Santa Rosa! It was a really great annual meeting. Deepanwita got the commendation for best research contribution and Jing got one for best publication!

Sept 26th 2023

Our ensemble approach for growth-coupled production from aromatics is out in Cell Reports! Congratulations to Thomas and Deepanwita for leading this study

Jul 31st 2023


The SIMB 2023 Annual Meeting took place in Minneapolis, Minnesota!  Aindrila served as Chair and Thomas convened the session on Domesticating and Engineering Non-model Organisms. Aparajitha presented a slam talk and poster. There was great representation from JBEI and other BRCs! Here is the recap!

June 3rd 2023

Jing Huang’s brilliant study in Nature! Complete integration of carbene-transfer chemistry into biosynthesis. Image credit from this C&EN article

Jan 31st 2023


Aindrila is among six LBNL researchers elected into the 2022 class of the American Association for the Advancement of Science!! A great honor for our team!







November 1st – 3rd, 2022

JBEI annual meeting 2022
This year, JBEI held its annual retreat in Monterey, California. On the coast of the bay, we could learn more about the excellent work and updates of each division and the other Bioenergy Research Centers.

It was a very participative week for the group! Aindrila presented the Biofuels and Bioproducts Division talk session highlighting the objectives of FY23, Aparajitha talked about her work modifying bacteria for the production of Isoprenol and other products such as Tetramethylpyrazine using plant biomass, Shawn presented a poster about his work designing and optimizing a synthetic Isoprenol biosensor, and Deepanwita and Javier presented a poster about their work developing growth-coupling strategies for the production of the bio-pigment Indigoidine.

It was a great time to meet new people and to better understand the synergy of our work. Congratulations to the JBEI team for making it possible to enter phase 4!

October 28th, 2022

Farewell, Nico!
Today we say goodbye to a great researcher, Nicolas Gurdo! He visited us for 4 months from the Denmark Technical University where he is completing his PhD, and it has been a pleasure sharing lab, knowledge, and research with him. We hope you have a good trip back and that you will visit us soon!!

September 22nd, 2022

In the Science SLAM – Congratulations, Aparajitha Srinivasan!
Aparajitha has placed third in the 2022 Berkeley Lab Research SLAM. With a metaphor about how Google recalculates the estimated time of arrival, Aparajitha explained how her work in computational models is helping her to engineer microbes to produce sustainable products in the most efficient way.

If you want to know more, Checkout the Youtube link to the event recording. Sarah Gleeson (1st place), Mohammed Ombadi (2nd place), and Aparajitha will advance to the regional Bay Area Research SLAM!


M-group annual meeting 2022

To celebrate this year’s annual retreat, we decided to spend the day at Charles Lee Tilden Regional Park. We hiked the mountain with the smell of eucalyptus trees and views of the bay in the morning and finished with a picnic with a mix of international foods. It was a great way to spend the day as a team outside the lab and get some fresh air on the last day of summer, we will definitely do it again!


August 2022

It’s raining Science at SFO

M-group members had a great time at the SIMB annual meeting (SIMBAM 2022). It was great to see our peers and collaborators in person after a long time. From co-chairing sessions to presenting posters and giving SLAM talks, we had a great time at SFO! Looking forward to m
ore in-person conferences, enlightening discussions, and exchange of cool
scientific ideas







Farewell, Nahtalee!

The summer is almost over and that means it’s time for our Summer Bridge Fellow, Nahtalee Lomeli to get back to the Delcassian lab at UC, Berkeley! We hope you had fun trying out some cool microbiological techniques!  We will miss you and so will all the 62 strains of P. putida that you helped build 😉


July 2022

More the merrier

We welcome Nahtalee Lomeli and Nicolas Gurdo to mgroup! Nahtalee, currently a bioengineering grad student at UC Berkeley is joining as a Summer Bridge fellow. She will work on establishing a computational workflow for the visualization of DAP-seq data and learn some cool microbiology techniques with Anne Kakouridis. Nico, a visiting graduate researcher from Pablo Ivan Nikel’s group at DTU will be working on integrative multi-omics analysis of Pseudomonas putida on multiple carbon sources.


A modeler in every sense Research Scientist, Deepanwita Banerjee talks about her passion for modeling not just genomes but also miniature houses in this “Behind the Breakthrough” series of Berkeley Lab. Dee takes a trip down memory lane giving us a glimpse of her childhood spent in India and how it inspired her research career. We are in love with the cool doll-house she built from recycled items. Are you?


This month’s Midday Science Cafe menu – CRISPR, Blue dyes, and Biofuels

Deputy director of host engineering, Thomas Eng whips up a cool talk  on “Systems Biology Approaches For Renewable Bioproducts” organized by the SCIENCEatCal team. Checkout this video where Thomas explains a sustainable approach to make eco-friendly blue pigments with some great analogies.


June 2022

What happens when you heterologously express response regulators from one bacteria in another? How does the post-translational phosphorylation change? Is it even important to characterize the phosphorylation states upon heterologous expression? Read the full research article here. Congrats to Megan Garber, Anne Kakouridis and other collaborators on this publication!


April 28th, 2022

Congratulations to Kevin Lam, Angela Wei and Kevin Chen-Xiao!! It was great having undergraduate students with us at the lab again! On 4/28/22 they presented the work they had done in the lab in the last months, and as you can see in the picture, their mentors couldn’t be prouder! We hope you have a great well-deserved summer!


March 31st, 2022

It was a pleasure having Silvia Rossbach with us at JBEI! We have enjoyed working and exchanging ideas with her and learning more about her work at Western Michigan University. We hope you have a safe flight and a beautiful spring in Michigan!


March 15th, 2022

New study co-authored by Maren, Megan and Aindrila demonstrating a droplet-based microfluidic system for high throughput strain engineering in collaboration with colleagues from the JBEI’s Technology division is out in Microsystems and Nanoengineering. Congratulations!


Feb 15th, 2022

Undergrad researchers Angela Wei, Kevin Lam and Kevin Chen-Xiao (or Kevin^2 as their mentors call them) from UC, Berkeley joined the group. Welcome and as we get back to normalcy, here’s hoping you have a great time in the lab!


Jan 21st, 2022

Space traveling Cyanobacteria

Aindrila: Hey, What are you up to these days?
Random researcher in the group (RRIG) : Hi Aindrila! I am sending my samples for sequencing today.
Anne Kakouridis: I am sending my samples to SPACE.
RRIG : Wait, what?
Yup, you heard that right!
Anne and Aindrila, in collaboration with Rhodium Scientific and NASA are figuring out ways to transport DNA to space using Cyanobacteria as the model host. Cyanobacteria are fascinating organisms with valuable natural functions such as photosynthesis and viability under extreme conditions. Anne and Aindrila are using these features of cyanobacteria already present in nature to figure out ways to transport DNA to space more easily and reliably.
“In the first part of the project, we transformed simple plasmids into Nostoc punctiforme, desiccated the cultures, and transported them to the International Space Station (ISS) and back. In the second part of the project, we will attempt to revive the cyanobacteria and retrieve the plasmids we placed into them. We will then evaluate if there are any mutations or defects in the DNA to determine if conditions such as desiccation, microgravity, and radiation affected the DNA in situ. Our hope is that the DNA was preserved intact during desiccation and space travel. If this works – these cyanobacteria may become the carrier for DNA for space travel!”, says Anne.

Read the highlights of this work in the biosciences area news and on the ISS national lab website.


Jan 5th, 2022

A new article with our collaborators Douglas Clark, Jay Keasling and John Hartwig exploring the assembly and evolution of artificial metalloenzymes within E. coli cells for enantioselective and site-selective functionalization of C─H and C═C bonds is out in JACS. Congrats to Jing!


Jan 3rd, 2022

A happy new year indeed with new members in the group! We warmly welcome Shawn Kulakowski and Silvia Rossbach to the group.
Shawn recently graduated with a B.A in Biochemistry and Molecular Biology, B.S in Chemical Biology from UC Berkeley and will work on developing syn bio tools for nitrogen-fixing bacteria to create sustainable alternatives to chemical fertilizers.
Silvia is a visiting scientist from Western Michigan University where she works on microbial ecology, understanding the influence of heavy metals on soil bacteria and how plant-bacteria interactions promote plant growth and bioremediation.


Dec 14th, 2021

Thomas Eng is now Deputy Director of Host Engineering. Congrats, Thomas! Don’t forget to check out this cool video where he talks about his exciting research at the lab.


Dec 3rd, 2021

We are thrilled to announce that Aindrila will assume the role of the BSE Deputy for Science. In this role, she will be involved with directing the S&T programs in the BSE division and be an Ambassador for Science internally and externally to the Lab. Congratulations, Aindrila and we look forward to working under your leadership!


Nov 18th, 2021

Our study on genomics characterization of an engineered Corynebacterium glutamicum grown in bioreactor under ionic liquid stress is out in Frontiers in Bioengineering and Biotechnology. Congratulations to all the authors!




Oct 14th, 2021

Of synthetic chemists, biologists and unnatural biosynthesis..

Check out this supercool study published in Nature Chemistry with our collaborators – Douglas Clark, Jay Keasling and John Hartwig. We demonstrate that marrying synthetic biology with synthetic chemistry can produce molecules that were previously inaccessible to nature, in engineered E. coli cells. Congrats to Jing who led this study! This work was also featured in Chemical and Engineering news  and the Berkeley News.



Sep 26th, 2021

Hearty Congratulations, Dr. Megan Garber! That was an awesome finishing talk with some supercool analogies. Good luck with your postdoctoral fellowship at UCSF!



June 29th, 2021

Ankita’s cool study on the discovery of Viral Genomes from the circular plasmid sequence data is out in mSystems!



June 25th, 2021



A new review in Nature Microbiology Reviews with Jay Keasling and our close collaborators at JBEI and ABPDU. We got a chance to review the modes of toxicity and inhibition during strain engineering for the production of biofuels and approaches to overcome some of them.



May 6th, 2021

Deepanwita and Thomas lead another nice study where we show that a deletion in a response regulator GacA in  P. putida results in greater fitness during bioreactor growth. This mutation also improved the production of Indigoidine from the non-sugar carbon source para-coumarate. Read our OA paper here!


March 11th, 2021

We had our 2021 annual m-group offsite virtually this year. It isn’t the same as spending a day together in person but it’s the next best thing! We had some really great activities! Hearty laughing at impromptu presentations, a great guess-who session, and even some meditation! The best part was welcoming new and yet to join group members who are onboarding during this difficult time.

(Zoom screen! Megan, Aindrila, Javier, Jeff, Shweta, Deepanwita, Jing, Thomas, Anne, Russel. Aparajitha and Alex).



Nov 30th, 2020

The Daily Cal published a great article on our Pseudomonas putida study to require glucose use for indigoidine production!

Read it here Photo: Andrew, Thomas and Deepanwita

And Berkeley Lab IPO now has a link to the technology. See the Technology link here!





Oct 23th 2020

Product Substrate Pairing! This is great a start to what we hope are many more such systems to come. Being able to rewire metabolism to ensure that growth is coupled to the production of target compounds or their precursors allowed us to get the highest levels of indigoidine yet, in P. putida KT2440 from glucose. And the production shifted to an exponential phase. The nice production features held up in fed-batch and higher scales. Another collaboration with the ABPDU and JGI. Congrats to Deepanwita and Thomas for leading this paper, now out in Nat Comm.



August 13th 2020

Our paper on using the yeast Bar-seq library to study population dynamics during bioreactor cultivation is published. Congrats to  Maren, Mitch, and Deepanwita. Great collaboration with the ABPDU. Check out the OA paper.


July 2nd 2020

Our paper on microbe-microbe interactions is out in Frontiers. We found iron to play an important role in antagonistic interactions, by using P. putida as a proxy microbe. Congrats to Thomas and Robin and collaboration with Jenny Mortimer!





March 24th 2020

Our first paper in Stay-at-Home life. A review on methods to study response regulators of  Two component signaling systems. The paper is Open Access. We highlight the DAP-seq and DAP-chip methods developed in our group.




March 14th 2020

The day we left our labs for the shelter-in-place and then the stricter stay-at-home, as a response to COVID19. Many papers and proposals to write. And lots to pick up when we return.





Feb 24th 2020

Our study on a genome scale approach and implementation to engineer a P. putida strain that show high production reliably across scales in on BioRxiv

Feb 13th 2020

Our 2020 annual m-group offsite. At the Cal Faculty Club again. A fantastic day of discussing science, careers, kindness, building clay objects and failing at unentangling human knots!!










Jan 11th 2020

Megan gives a beautiful talk on swapped domains in response regulators at the GRS for Sensory Transduction in Microorganisms at Ventura Beach, CA





Nov 21 2019

Thomas Eng and Yusuke Sasaki showed that ceratin variation in the heterologous  isopentenol production pathway lead to the production of tetramethyl pyrazine – solely and upto 5g/L. TMP is famous for its use as a coffee flavoring! Open source in Metabolic Engineering Communications!









Nov 21 2019

Kudos to Ankita Kothari for showing that a putative mercury resistance operon present on an abundant 8-kbp native plasmid found in Oakridge ground waters encodes functional genes and that this plasmid can be taken up via natural competence by a range of isolates from this site! The paper is open access on mSystems.





Nov 21 2019

A very special day for our group. THREE papers accepted. One: Deepanwita and Aindrila co-authored a review led by Yan Chen and Chris Petzold on Systems biology methods and that’s accepted in Current Opinions in Biotechnology ! Thanks also to Deepanwita for supporting JBEI in our outreach activities (Nov 11th Biotechnology Celebration event on Saturday!)






Summer 2019: Conference season


We had a great summer of conferences! Thomas presented at the ECI conference, Ankita at the SEED conference Maren at the SIMB conference , Aindrila at Pseudomonas2019!  We heard some great talks, got awesome feedback and came back to the lab inspired!

May 29th 2019

We engineered a fungal host, R. toruloides and optimized production condition to get high titer production of a blue pigment Indigoidine. This compound is a non-ribosomal peptide. We are now exploring if R. toruloides is a good host for other NRPs – a large group of compounds ranging from commodity to fine chemicals. All this and sustainability!! Read Maren’s  open access paper here!






May 15th 2019

Our first paper on examining the impact of “JBEI” chemicals on biological systems is out! Robin and Thomas make a great team and we have fantastic cross-disciplinary contributors this story from across LBNL and also from external collaborators. We found that microbial presence does impact how plants respond to exposure to many chemicals. Check out the paper! More studies to follow and all in collaboration with the Mortimer group!!








May 3rd 2019

Very cool video of Ankita discussing Mercury as part of the #MyFavElement Series by Berkeley Lab! Check out the video here!



April 9th 2019

Lara’s paper is accepted! We have known since 2011 when we published our genome wide DAP-chip paperthat the Lur Regulon in Desulfovibrio vulgaris is targeted by several two component systems. We now show how LurR regulates this operon. Rajeev et al 2019

April 5th 2019

We got a chance to present our Host Engineering thoughts, ideas and stories at the DOE JGI User meeting in San Francisco! What an amazing group of speakers to be part of!



March 12th 2019

Aindrila presents the Plasmidome story in the IGI Seminar series and answers some cool questions for Mira Cheng’s blog. Mentions of the awesome Esther Lederberg and Mary-Dell Chilton were very well received! We also presented this work at the Technology Mini Colloquia at the the DOE Annual meeting in San Francisco on April 2nd!






Feb 27th 2019


We engineered  Corynebactrium glutamicum to produce a pretty tidy level of isopentenol – a biofuel and a platform chemical. Great work by Yusuke Sasaki and Thomas Eng and the rest of the JBEI team! The paper is online and open access



Feb 26th 2019

Our discovery of large plasmids from the Oak Ridge FRC, spanning many incompatibility groups and many interesting functions is ONLINE!! Congratulations to Ankita Kothari and the team. Really pleased to have this out as it sets the stage for a lot more on this topic!






Feb 25th 2019

Our review on what we view to be challenges in engineering robust strains for large scale applications, and how Systems + Synthetic Biology can address them. Kudos to Maren for taking the lead on this! Read Online!!

Jan 17th 2019

2018 ended well for our team. We started the new year with an M-group annual offsite at the UC Faculty Club. It was a really fun day with interesting discussions on science, careers and some very fun team activities!









Dec 14th 2018

We published Maren’s study in characterizing the correct conditions required to produce the blue pigment Indigoidine in yeast. Also the first demonstration of this NRPS in Saccharomyces cerevisiae! Check out the paper

Dec 7th 2018

Congratulations to Jadie and Albert and their mentors Maren and Ankita for winning the  best poster and best presentation competition. A special thanks to Drishti for her very cool poster also! And a shout out to the JBEI and ENIGMA projects!!


Oct 13th 2018

Our paper examining the role of an essential gene in improving not only tolerance but also restoring production levels in the presence of biomass pretreatment reagents is out in Microbial Cell Factories!! Check out the Open access paper here!

Jul 11th 2018

Proud of these two bright researchers going off to grad school this fall. Congratulations to Jess and Robin on their acceptance to Riverside and Cal!

Jan 17th 2018

Our study on two component signaling cross-regulation is out in Molecular Microbiology! We used the DAP-seq method that Megan has developed and presented at the recent Gordon Research Conference. Congratulations to Megan and the whole team!

Dec 8th 2017

Read Maren’s interview with BD Biosciences about the Accuri!

Nov 9th 2017

Our one pot jet-fuel research got a mention in a popular science book! Woo hoo! Thanks to Kelly Weinersmith!

Oct 30th 2017

We published our paper in developing a synthetic transcriptional factor – hybrid promoter library for use in S. cerevisiae strain engineering.

Oct 12th 2017

Our study on improving membrane protein expression using genome wide edits is out in Scientific Reports!

July 17th 2017

DOE announces funding for JBEI other BRCs! Looking forward to many more years of research with a great team!


April 28th 2017

Duy presented her undergraduate work at the JBEI undergraduate Seminar! We loved having her in our group, and her research with Lara and Megan focused on understanding copper responsive systems in denitrifying Pseudomonads. She is a master of RNAseq preps! Congratulations on a great talk Duy!!


March 8th 2017

Ankita’s study on native plasmids from the Oakridge FRC is now online at BioRxiv!


Jan 19th 2017

Aindrila’s perspective on the future of microbial biofuel production in Biofuels International

Jan 5th 2017

Victor’s paper on Engineering glucose metabolism of Escherichia coli under nitrogen starvation is out in Nature Systems Biology and application.


November 27th 2016

Our Cas9 toolkit for yeast is now published online. Read about it on Today at Berkeley Lab. All the plasmids are available from Addgene!



May 10th 2016

Marijke’s paper on combining Ionic Liquid tolerance with biojet-fuel production is our in Green Chemistry and has a great write-up on Today at Berkeley Lab!




We lost a year of m-group news updates to grant writing…we may or may not be able to catch-up. But research was good and we published a lot!


August 17, 2015


Lara’s paper out in JBact. We described the role of a two component system in nitrite stress in the obligate anaerobe Desulfovibrio vulgaris. 


July 3, 2015

Left to Right; Daniel, Luisa, Rob, Marijke, Victor, Jack, Marimikel, Heather, Megan, Amanda, Whitney, Ankita, Christa, Chuhui and Lara
Left to Right; Daniel, Luisa, Rob, Marijke, Victor, Jack, Marimikel, Heather, Megan, Amanda, Whitney, Ankita, Christa, Chuhui and Lara

The whole group at Bucci’s with all our visiting scientists and students (and the Bucci dog).


May 1, 2015


Victor’s study on a Limonene tolerant AhpC mutant is out in AEM. A good explanation for why Limonene is so much more toxic than other similar monoterpenes. Congratulations to Victor, Florence and the rest our team!!


April 17, 2015


Michela was part of our team that published two studies on D. vulgaris last year, one on motility genes and the other on cyclic-di-GMP signalling. Proud of Michela Catena who is going to travel to India this fall on a Fullbright Scholarship!! Congratulations Michela!


Jan 20, 2015

The Total efflux pump team: Angelique, Melissa, Florence, Aindrila and Camille (Missing Kat and Eric)
The Total efflux pump team: Angelique, Melissa, Florence, Aindrila and Camille (Missing Kat and Eric)

Flo’s paper is out in Biotechnology and Bioengineering A heroic effort in generating an improved pump for a volatile organic compound. We will look to the metabolic engineering community for a hexene production strain to implement this discovery.


Nov 4, 2014

Jensen, Foo et al 2014 gets a nice write up by Lynn Yarris and was featured on the front page of the DOE webpage!

We published our study on improving Isopentenol tolerance and production in the mBio journal. mBio featured it in their blog. We have gotten many more mentions (RDmag, Science Daily, Green car congress…). Congratulations to Heather, Jee Loon and the rest of the team!!


Feb 26, 2014


KQED QUEST Career spotlight video


June 6, 2013


Lara’s Microcoleus Desert soil crust paper in online in the ISME Journal! And we get a wonderful article in TABL by Lynn Yarris.


May 13, 2013


We get a chance to talk about our research at the Berkeley Rep at the Science at the theater organized by Friends of the Berkeley Lab!


March 19, 2013


We get a mention in the Department Of Energy feature on STEM profiles.


Oct 1, 2012

Left to Right: Kavya, Melissa, Nhat-Tan, Lara, Marijke, Camille, Florence, Jee-Loon, Aindrila, Eric, Heather, Zain and Amanda
Left to Right: Kavya, Melissa, Nhat-Tan, Lara, Marijke, Camille, Florence, Jee-Loon, Aindrila, Eric, Heather, Zain and Amanda

The whole group at the Can’t Fail cafe. We have new members in the group – Amanda Reider Appel and Nhat Than Vuong!


Feb 14, 2012


Science Today, a UC Berkeley Radio channel, features comments on our study of the D. vulgaris two component system regulator network.


Nov 9, 2011


Lara and Eric’s Response Regulator Map paper gets written about in Berkeley Lab’s TABL site.


Oct 15, 2011

Lara at the Soil crust display at the Berkeley Lab open house
Lara at the Soil crust display at the Berkeley Lab open house

Lara and Eric’s D. vulgaris Response Regulator map paper is out in Genome Biology.


Sept 27, 2011

Photo by Roy Kaltschmidt

Mario (in the blue lab coat) features in the Berkeley Lab news letter TABL for his important contribution in developing Bisabolene production in yeast. Here is a link to Pamela and TaekSoon’s Nature Communications paper


August 22, 2011


Zain, Heather and Aindrila feature on the cover of the Biorefining magazine. Here is the article.


July 1, 2011


Our efflux pump paper gets a mention in the Microbe magazine. Other mentions of our study are in eureka alert, techblog, science daily, microbeworld, Materials Today to list a few!

Let us know what you think.