April 2025
There is a lot to celebrate this month!
First of all, a huge congratulations to Nayak Lab graduate student Annelise Goldman for winning the NSF GRFP! Way to go Annelise, very well deserved!
Also, another huge congratulations to Annelise for passing her qualifying exam and advancing to candidacy.
Moreover, Blake Downing presents his finishing talk as one of the last steps before graduation this semester. Congratulations, Blake! It is wonderful to celebrate the amazing science you’ve done during your time in the lab.
Finally, another enthusiastic round of congratulations to Maddie for passing her qualifying exam as well!
We are so proud of our new Ph.D. candidates!
March 2025
Nayak Lab graduate student Blake has a new review out in Trends in Biochemical Sciences! In this review, Blake summarizes our current understanding of electron transport chains of methane-metabolizing archaea. The review highlights modularity in these electron transport chains, as well as the evolutionary innovations that have allowed certain groups of archaea to develop specialized metabolisms. Congratulations, Blake!
February 2025
Lab members Gray, Maddie, and Katie have a new pre-print out on BioRxiV! In this story, Gray, Maddie, and Katie investigate the role of methanogenesis marker metalloprotein 16 in Coenzyme M (CoM) biosynthesis and find that MMP16 is a bona fide CoM synthase (ComF). Their work also reveals that while MMP16 is the main ComF in Methanosarcina acetivorans, backup pathways for CoM biosynthesis exist, and are able to compensate in the absence of MMP16. Congratulations to all authors!
January 2025
Several members of the Nayak lab participate in the MCB BBS retreat this month- Gray gives a talk and Fernando presents during the poster session. Great presentations, Fernando & Gray.
December 2024
We’re so excited to welcome Jin Hee Yoo, from the MCB graduate program, to the lab for her rotation. Glad to have you, Jin Hee!
November 2024
We’re excited that our former postdoc, Gray Chadwick, has transitioned to a role in as an assistant researcher in our lab! Congratulations, Gray, on your new role!
October 2024
Our joint postdoc with the Stolper Lab in EPS, Jonathan, publishes his pre-print on BioRxiV! This story resolves a long-standing conundrum in the field of geobiology by showing how the biochemistry of methanogenesis impacts the isotope composition of biogenic methane! Congratulations to Jonathan and all co-authors!
September 2024
Our lab has its first ever Nayak Lab retreat in the Santa Cruz mountains! We spent time exploring the forests and the beaches, cooking together, refreshing our knowledge of the field with a “Methanogenesis Bootcamp”, and learning about each other’s interests outside of the lab. It was a great way for all of us to connect and build community together.
Dev Desai, from the MCB graduate program, starts his rotation in the lab. Welcome, Dev!
August 2024
Many members of the Nayak Lab attend Gordon Research Symposia & Conferences this month!
Postdocs Jonathan & Gray both give talks at the Organic Geochemistry GRC.
Blake gives a talk at the Molecular Basis of Microbial One-Carbon Metabolism (C1) GRS. He wins best talk and goes on to give his talk to the main conference as well. He is also elected co-chair for the next C1 GRS in 2026. Congratulations Blake!!!
Dipti also gives a talk on the lab’s research at the C1 GRC.
Finally, Gray also moderates the career panel at the C1 GRS.
Overall, it was another great summer of conference participation for our lab!
July 2024
Our newest graduate student Maddie spends two weeks participating in the second annual Archaeal Cell Biology Workshop over at UCSF. Huge thank you to the Mullins lab for once again hosting this workshop.
June 2024
Gray and Gavin’s paper on the physiological and transcriptomic response to MCR limitation is published in Applied and Environmental Microbiology (AEM). Check it out here! Congratulations!
May 2024
May was an exciting month for the lab!
First off, we are so excited to welcome Maddie Williams to the lab as our newest full time graduate student! Maddie joins us from the MCB program. We can’t wait to see the awesome science you do, Maddie!
Next, we’re thrilled to announce that both Maddie and Annelise have been selected as trainees for the GDTP Genetics Training Grant program! Congrats, Maddie and Annelise!
Speaking of awesome accomplishments, we are also so proud of Gavin Dury for passing their qualifying exam this month! Congratulations Ph.D. candidate Gavin!
The lab was very excited to celebrate all of these milestones and accomplishments this month. What a great end to this academic year.
April 2024
Dinesh’s paper on the roles of MmcA in methanogenic electron transport is published in Nature Communications. Check it out here! Congratulations to Dinesh & co-authors on this electrifying story.
Several members of the lab present at the PMB graduate student-organized 23rd annual Microbiology Student Symposium! Dinesh and Fernando give talks, while Blake presents a poster. Thank you to Nayak lab graduate student Annelise for helping to organize the symposium.
March 2024
The work study position in our lab has been filled!
Sophie wins an Outstanding GSI award for their teaching in MCB 100B last spring. Congrats, Sophie, we are very proud of you!
February 2024
We are so excited that Dipti has been awarded a 2024 Sloan Research Fellowship! Dipti joins nine other UC Berkeley faculty and a total of 126 incredible early career researchers in receiving this award. We are thankful to the Sloan Foundation for supporting our research!
January 2024
We’re very happy to welcome a new undergraduate researcher, Jessica Kasper, to the lab. Jessica is a senior in MCB and will be working with Sophie! Glad to have you, Jessica.
December 2023
We’re so excited to welcome Annelise Goldman as the newest Nayak Lab graduate student! Annelise is from the GGM and will be starting full-time in January!
We’re also very excited to announce our lab’s newest pre-print, now available on bioRxiv. In this story, postdoc Gray and Ph.D. student Gavin explore the physiological and transcriptomic response to MCR limitation, digging into the question of whether or not MCR is growth rate limiting for Methanosarcina acetivorans under laboratory growth conditions. Congratulations on this very cool work!
November 2023
The Nayak Lab attends the annual MCB retreat at beautiful Asilomar this month. We enjoyed learning about our MCB colleagues’ research and exploring the Monterey Bay Aquarium!
At the retreat, Blake won a best poster award! We’re so proud of your awesome science communication skills, Blake!
October 2023
Jason Avalos and Colin Robinson from the GGM start their rotations in the lab. Welcome Jason & Colin!
Fernando attends the National Diversity in STEM Conference, organized by SACNAS, in Portland, OR. At the conference, he presents his research in a talk titled: “An unknown and widespread signaling pathway that blocks methanogenesis”.
Jonathan attends the 2nd Joint Symposium of the International Societies for Environmental Biogeochemistry & Subsurface Microbiology in Banff, Canada! He presents his research in a talk titled: “Studying the isotopic composition of microbial methane with a genetically-tractable methanogen”.
September 2023
Maddie Williams from MCB starts her rotation in the lab. Welcome Maddie!
Shally Li from PMB starts her rotation a few weeks after Maddie. Welcome Shally!
Our lab excitedly welcomes a new anaerobic chamber for expanded experiments (pictured right).
Fernando wins best talk at the Midwest Geobiology Symposium. Great job Fernando!!
August 2023
Two new undergraduate researchers join our lab. Frank Cai is from Earth and Planetary Science and will be working with Jonathan. Alexandra Harte is from MCB and will be working with Alienor. Welcome Frank and Alexandra!
Gray and Alienor attend the inaugural Archaeal Cell Biology Workshop, hosted by the Mullins Lab at UCSF.
Annelise Goldman from the GGM starts her rotation in the lab. Welcome Annelise!
July 2023
Katie, Blake, Sophie, and Fernando attend the Applied and Environmental Microbiology Gordon Research Conference in Massachusetts. All four group members present posters, and Fernando wins a prize for his poster. Congrats, Fernando!
Dinesh, Alienor, Gray, and Dipti attend the Archaea Gordon Research Conference in Vermont. Alienor and Gray give talks at the GRS and everyone presents posters at the GRC.
We really enjoyed our conferences this summer!
June 2023
The McrD story co-led by our postdoc Gray and Dr. Aaron Joiner is published in PNAS. Check it out!
May 2023
We are incredibly excited to welcome Gavin Dury to the lab as a full time graduate student! Gavin is from the MCB graduate program and will be studying MCR! Welcome Gavin!!!
April 2023
A new pre-print is out from our lab! In this electrifying story, our postdoc Dinesh leads a study on M. acetivorans heptaheme cytochrome MmcA and reveals the roles it plays not only in intracellular electron transport, but in extracellular electron transport as well. Congratulations to Dinesh, as well as co-authors Dr. Keying Chen and Prof. Sean Elliott, both at Boston University.
We’re also very excited to announce that Dinesh has been awarded an NIH F32 to support his research on developing M. acetivorans as a model to study archaeal cytochromes! Congratulations, Dinesh- this is so well deserved!
March 2023
Gavin Dury from MCB starts their rotation in the lab. Welcome, Gavin!
February 2023
Our fabulous postdoc Gray and co-first author Dr. Aaron Joiner from the Hurley lab here a UCB publish their pre-print on BioRxiV. This work investigates the assembly of the key methanogenesis enzyme Methyl-coenzyme M reductase (MCR) and reveals new insights into how this important complex comes together inside the cell. Other authors include collaborators Sangeetha Ramesh and Prof. Doug Mitchell from the Mitchell lab at UIUC.
January 2023
Blake’s paper is published in Molecular Microbiology! Congratulations, Blake and co-author Dinesh. We are so proud of you; turns out RNF stands for “Really Nice First (publication)”. Check out the online paper here!
The lab belatedly celebrates the holidays with our second annual holiday party and white elephant gift exchange.
November 2022
Theresa Proctor from the GGM starts a rotation in the lab. Welcome, Theresa!
October 2022
Most of the lab attends the MCB department GGED retreat at wonderful Asilomar.
Katie gives an awesome talk at the retreat about her work, titled: The Regulatory Effects of Genetic Code Expansion on Methane Metabolism. Awesome job, Katie!
September 2022
Clare Gill from the MCB graduate program starts her rotation in the lab! Welcome Clare!
Fernando receives the Simons Foundation Postdoctoral Fellowship in Marine Microbial Ecology! Congratulations Fernando on this well deserved award!
Dipti is named a co-PI on a DoE grant titled ‘Ecological and molecular controls of metabolic activity in microbial interactions driving ecosystem‐wide methane cycling’ with Dr. Victoria Orphan, Dr. Christopher Henry, Dr. Ribert Hettich, Dr. Manuel Martinez Garcia, Dr. Mark Ellisman, and Dr. Christof Meile. Congratulations to all recipients!
August 2022
Dinesh, Gray, and Blake attend the Molecular Basis of Microbial One-Carbon Metabolism Gordon Research Conference in Southbridge, MA. They had a wonderful time learning about awesome science from around the world.
Dr. Jonathan Gropp arrives in lab! Welcom Jonathan, we’re so excited to be working with you!
July 2022
Blake publishes his first, first-author pre-print! Blake, Dinesh, and Dipti reveal how multi-heme cytochrome MmcA plays a two roles in the cell, one in conserving energy via the electron transport chain, and another in carbon metabolism. Check out the pre-print here!
Alienor is appointed to the Genetic Dissection of Cells and Organisms NIH Training Program (GDTP). Congrats, Alienor!
June 2022
Our incoming postdoc, Jonathan Gropp is awarded an EMBO fellowship to investigate isotopic signatures of methylotrophic methanogenesis! Congrats, Jonathan!
April 2022
Katie Shalvarjian is awarded the NSF GRFP. Congratulations, Katie!
Dinesh Gupta and Katie Shalvarjian’s paper, An archaea-specific c-type cytochrome maturation machinery is crucial for methanogenesis in Methanosarcina acetivorans, is published in eLife!
Katie Shalvarjian passes her qualifying exam and advances to candidacy! Congrats, Katie!
Sophia Adler passes her qualifying exam and advances to candidacy! Great job, Sophia!
We are so proud of our lab’s new candidates!
March 2022
Nina Abers joins the lab as an undergraduate student! Welcome Nina!
Alienor Baskevitch passes her qualifying exam and advances to candidacy! Congrats, Alienor!
February 2022
Sunnie Kong from the Chemical Biology Graduate Program & Department of Chemistry starts her third rotation in the lab. Welcome Sunnie!
Jonathan Gropp from the Weizmann Institute accepts a joint postdoc offer. Jonathan will be co-advised by Dipti and Dr. Dan Stolper in the department of Earth & Planetary Science, starting in August 2022. We’re looking forward to working with you, Jonathan!
January 2022
The Nayak lab is awarded the CZBiohub Investigator Award!
The newest preprint from our lab, Biogenesis and Function of c-type Cytochromes in the Methanogenic Archaeon, Methanosarcina acetivorans, is out on bioRxiv! Congratulations Dinesh, Katie, and Dipti on this cool story!
The work-study position for our lab has been filled. All undergraduates interested in working in our lab should fill out the interest form on the “Join Us” page instead.
December 2021
Gray gives a fantastic talk about the physiological and transcriptional response to the repression of methanogenesis at this year’s virtual West Coast Bacterial Physiologists conference!
The Nayak lab annual holiday celebration returns after a pandemic-induced hiatus!
November 2021
Eleanor Wang from the GGM starts a rotation in the Nayak lab. Welcome Eleanor!
October 2021
The Nayak lab attends MCB’s GGD retreat in Tilden Park!
At the retreat, Blake gives an excellent talk on his current research, and several members of the lab present posters.
The Nayak lab wins best group costume contest in the PMB Halloween costume competition!
September 2021
Xylina Rusit from the MCB graduate program starts a rotation in the lab. Welcome Xylina!
Dipti’s second iBiology video, Mysteries of the Methanogens, premiers online.
Dipti receives an honorable mention for the 2022 Rosalind Franklin Young Investigator Award from the Genetics Society of America & The Gruber Foundation.
August 2021
The lab has its second annual Winogradsky column making day. We went to a local park to collect mud, then came back to the lab to assemble our columns.
For more photos of our Winogradsky column adventures, check out our lab photos page!
If you would like to make your own Winogradsky columns, check out this protocol from Project MICROBE at University of Illinois.
July 2021
Sophia is appointed to the Genetic Dissection of Cells and Organisms NIH Training Program (GDTP). Congratulations, Sophia!
The lab is awarded a grant to synthesize sgRNA libraries for methanogenic archaea through the Functional Genomics Community Science Program at the Joint Genome Institute (JGI).
June 2021
Dipti presents the lab’s research at a session titled ‘New Frontiers in Microbial Metabolism and Metabolic Engineering‘ at the World Microbe Forum.
May 2021
The lab welcomes three new graduate students: Alienor Baskevitch (GGM), Katie Shalvarjian (GGM), and Sophia Adler (MCB)!!! We are beyond thrilled to welcome Sophia, Katie and Alienor to the lab.
Blake passes his qualifying exam and becomes the lab’s first PhD candidate. Congratulations, Blake!
April 2021
Dipti is named a 2021 Simons Early Career Investigator in Marine Microbial Ecology and Evolution.
March 2021
Dr. Fernando Medina Ferrer joins the lab as a postdoctoral fellow. Prior to joining the lab, Fernando was a graduate student in the Bailey lab at U. Minnesota where he developed antibody-based assays to detect biomarkers in the rock record and studied the role of microbial enzymes in the formation of tufas. We are thrilled to welcome Fernando to the lab and are excited for some fieldwork in the near future!
The lab receives a grant from the Shurl and Kay Curci Foundation.
February 2021
Katie Shalvarjian and Alienor Baskevitch from the GGM start a rotation in the Nayak lab.
Welcome Katie and Alienor.
January 2021
Katie’s review on transcriptional regulation of methanogenic metabolism in archaea is accepted to Current Opinion in Microbiology.
December 2020
Dr. Dinesh Gupta joins the lab as a postdoctoral fellow. Prior to joining the lab, Dinesh was a graduate student in the Bose lab at WUSTL where he studied extracellular electron uptake in phototrophic bacteria including the model photoferrotroph, Rhodopseudomonas palustris TIE-1. We are absolutely electrified to have Dinesh as a lab member.
November 2020
Allison Hung from the MCB graduate program starts a rotation in the Nayak lab.
Welcome Allison.
October 2020
Dipti gives a talk at the Department of Biochemistry seminar series at Montana State University.
Dipti gives a talk at the Innovative Genomics Institute (IGI).
Dipti receives the Packard Fellowship for Science and Engineering.
The lab attends the virtual screening of the iBiology video on Archaea and the Tree of life at the Bay Area Science Festival.
September 2020
Dipti gives a talk at the Microbial Sciences Initiative (MSI) seminar series at Harvard University.
Sophia Adler and Alena Bishop from the MCB graduate program start a rotation in the Nayak lab.
Welcome Sophia and Alena.
August 2020
Dr. Grayson Chadwick joins the lab as a Miller postdoctoral fellow. Prior to joining the lab, Gray was a graduate student in the Orphan lab where he identified the genomic basis of methanotrophy in archaea and so much more. We are beyond thrilled to have Gray as a part of the team!
We bid a fond farewell to Katie Shalvarjian who will be joining the Graduate group in Microbiology in the PMB department at UC Berkeley.
July 2020
Research operations resume albeit at limited capacity. Nonetheless, it’s great to be back in lab again and see each other in person.
Dipti is a course speaker for the ‘Share Your Research: How to Give a Good Talk’ course offered through iBiology. This five-week course is a fabulous (free!) resource for creating and delivering a good research talk. We highly recommend it!
June 2020
Blake is appointed to the Genetic Dissection of Cells and Organisms NIH Training Program (GDTP). Congrats, Blake!
Dipti receives the Arnold and Mabel Beckman Young Investigator (BYI) award.
Dipti receives the Rose Hills Innovator Grant.
May 2020
Blake Downing joins the lab as our first graduate student! We are thrilled to have Blake on-board!
Dipti is named a 2020 Searle Scholar.
April 2020
The lab invites fellow microbiologists for virtual seminars at our group meetings. We are immensely grateful to Dr. Aaron Puri, Dr. Ranjani Murali, Dr. Sampriti Mukherjee, Dr. Olga Sokolovskaya, Dr. Jose de la Torre, Dr. David Booth, Dr. James Hemp, and Dr. Morgan Price for taking the time and presenting their fascinating work to us.
The lab is awarded a Moore Symbiosis in Aquatic Systems Initiative collaborative grant with Dr. Victoria Orphan at Caltech to develop new tools for advancing model systems in aquatic symbiosis. We are so thrilled to be working with the Orphan lab on this collaborative project!
Katie will be joining the PMB department at UC Berkeley as a graduate student in Fall 2020. Great news. Congrats, Katie!
March 2020
All on-going experiments are put on hold as the lab temporarily suspends operations due to the COVID-19 pandemic.
February 2020
Dipti gives a talk at the Joint BioEnergy Institute (JBEI) in Emeryville, CA.
Nick Campbell-Kruger from the MCB graduate program starts a rotation in the Nayak lab.
Rebecca Tarnapol and Leah Gulyas from the GGM start a rotation in the Nayak lab.
Welcome Nick, Rebecca, and Leah!
Dipti is the lead author on a paper published in PLoS Biology.
January 2020
Nathaniel Freuler, a sophomore at UC Berkeley majoring in Molecular and Cell Biology, joins the lab as an undergraduate researcher. Welcome, Nathan!
December 2019
Grayson Chadwick is awarded the Miller Postdoctoral Fellowship. Huge congratulations, Gray! Gray will be joining the lab after completing his graduate work in the Orphan lab in 2020.
The lab attends the West Coast Bacterial Physiologists (WCBP) meeting in Asilomar. Katie give a *great* talk about her ongoing research efforts in the lab.
The first lab holiday party is held at the Fieldwork Brewing taproom in West Berkeley.
November 2019
Victoria Innocent joins the lab as a staff research associate. Prior to joining the lab, Victoria worked in the Taga lab at UC Berkeley to study the transport of corrinoids in bacteria.
Josean Reyes-Rivera from the MCB graduate program starts a rotation in the Nayak lab.
Blake Downing and Sunnyjoy Dupuis from the GGM start a rotation in the Nayak lab.
Welcome Victoria, Josean, Blake and Sunnyjoy!
October 2019
Our first experiments are underway.
Wildfires and power outages disrupt life and research for weeks. The only silver lining – all crucial pieces of equipment in the lab have been connected to a backup power generator.
Dipti gives a talk at the Genetics, Genomics and Development division retreat at Asilomar.
Dipti’s PhD advisor, Dr. Chris Marx, visits the lab!
September 2019
Katie Shalvarjian joins the lab as a staff research associate. Prior to joining the lab, Katie worked with Dr. Tiffany Lowe-Power (now an assistant professor at UC Davis) in the Lindow lab at UC Berkeley to build a Rb-Tnseq library for plant pathogenic Ralstonia spp.
Dimitrios Camacho from the MCB graduate program starts a rotation in the Nayak lab!
Athira Vinod, a sophomore at UC Berkeley majoring in Molecular and Cell Biology, joins the lab as an undergraduate researcher.
Welcome Katie, Dimitrios and Athira
August 2019
Lab renovations near completion. The anaerobic chambers and gassing station have been installed. Biosafety permits have been issued. We are gearing up to start research very, very soon!
Dipti gives a talk at the Plant and Microbial Biology (PMB) department seminar series at UC Berkeley.
July 2019
Hello world! ☺
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