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Hellos! In Adelaide, we’ve welcomed Ryan Edwards as a Ph.D. student (who will be co-supervised by A/Prof Matt Tucker). He’ll be developing duckweed strains optimised for human nutrition. We’ve also welcomed Matt Morgan as a Ph.D student (primary supervisor will be Prof. Matt Gilliham), who’ll be working on in planta pharmaceutical production. All the Matts. In Emeryville, we’ve loved hosting two undergraduate students from UC Berkeley during the last semester (Nikita Gounder and Shirlyne Ong) who’ve been working with EcoFABs as part of the m-CAFEs project with Hsiao-Han. We’ve also recently welcomed undergrad Dylan Chin for a summer research project, also working with Hsiao-Han. Other than that, we’ve been busy working on grant proposals and renewals (including for JBEI and m-CAFEs), so fingers crossed!
OK, so it seems that updates have been worse than usual – a pretty good indication of how busy we have been. So, a few quick summaries:
Hellos! In Adelaide, we’ve welcomed Dr. Fleur Dolman and Dr. Daniel McKay as postdocs, to work on projects characterizing cell wall glycosyltranferases and duckweed synthetic biology and salinity tolerance. respectively. We’ve also welcome two undergraduate summer research students, Natalie Chan and Malcom Hang, who will be testing different markers in duckweed. In Emeryville, we’ve welcomed Nick Downs, who joins us an RA, joint with the Scheller group.
Goodbyes: In Emeryville, we’ve said farewell to Dr. Kavitha Satish Kumar (off for a well deserved break!), Dr. Xiaoxian Liu (who is now a Staff Scientist at the Moffett Cancer Centre in FL), Dr Tallyta Silva (who is now a postdoc at Federal University of Lavras, Brazil) and Dr. Rebecca Dewhirst (who is now a Staff Scientist at Living Carbon in CA). We’re really going to miss them all, but I’m so excited to see their achievements (and to see some excellent papers that will be out soon).
Papers: Despite the really tough past 18 months, we’ve somehow managed to keep up momentum of paper publications, thanks to the immense fortitude of the team. Highlight papers include Tallyta’s fantastic “how to guide” for sorghum as a crop for the emerging bioeconomy (Silva et al, 2021, Journal of Experimental Botany), and her collaborative review on how nanotechnology can enhance CRISPR-mediated gene editing in plants (Demirer et al. 2021, Nature Nanotech), the publication (FINALLY) of Beibei’s beautiful paper describing the function of the GDP-Man transporter, GONST2 , Rebecca’s two papers looking at the role of acetic acid/methanol VOCs in tree drought responses (Dewhirst et al. 2021a, ACS Earth Space Chemistry, and Dewhirst 2021b, Plants), and many papers which we’ve contributed to, which have been led by our fanstastic collaborators including the Scheller group (Moore et al. 2021, Current Biology), the Mongrand group (Cassim et al. 2021, JBC), and the Murray group (Munson et al. 2021, Frontiers in Plant Sciences). For more information, see our publication page.
Patents: New section! Our patent on using a bio-derived ionic liquid as a herbicide was awarded. This idea came out of a collaboration with the Mukhopadhyay lab, and the co-inventors include former lab member Robin Herbert.
After 2 weeks in hotel quarantine in Sydney, I arrived in Adelaide on the 17th January, and after 3 more COVID tests, I have started my new job as Associate Professor of Plant Synthetic Biology at the University of Adelaide, in the School of Agriculture, Food and Wine. Based on the stunning Waite campus, just a few kms south of the CBD, it is the full Australian experience, complete with kangaroos outside my office window on my first day. Over the next few weeks I’ll be updating this website to reflect the dual lab locations and research projects. In the meantime, any questions you can reach me on jenny.mortimer @ adelaide.edu.au or on my LBL email address, which will continue to work.
Dec 2020 Farewells
In December I bid a (virtual) farewell to my friends and colleagues in California. I am very fortunate that I will remain as an Affiliate Staff Scientist at Berkeley Lab for some years to come, as I continue to manage my projects (particularly those part of JBEI and m-CAFEs) and supervise my group (with the help of my lovely colleagues, Henrik and Aymerick). My group have been immensely understanding throughout this whole process. They also gave me the most wonderful leaving gift – the beautiful image below as a poster for my new office (featuring, amongst other things, the lab mascot Eddie Lizard). I couldn’t ask for a smarter or kinder team of people to science with.
Farewell to Kavitha!! She is off for new adventures in Canada. We wish her the best of luck and we will miss her kindness and fun in the lab. We also have no idea how we’ll keep the HPAEC-PAD running! We managed to have a goodbye party/virtual holiday party to wave her off. It seems many of us were calling in from the Four Seasons in Philly….
Farewell also to our SULI student Chris, who completed his internship. Completing this in a 100% virtual environment was not easy, and we had to learn and adjust as we went. However, Chris did a great job contributing to the design and architectre of the sorghum CAZy database.
Yu’s paper on the sorghum cell wall architcture is out in Nature Communications. He did an amazing job putting this together, and it was a very successful collaboration with Andy Lipton at EMSL and Dylan Murray and Yuuki Wittmer at UC Davis. We show that the majority of xylan in the sorghum cell wall is in the three-fold conformation (contrasting with Arabidopsis), and that the xylan tightly associates with the amorphous regions of cellulose. LBNL/PNNL wrote a sumary of the paper here.
Our comment on our lack of success in using magenetofection for monocots was published in Nature Plants. This was led by John Fowler at the University of Oregon, and was the result of a conversation that began on Twitter!
Plus, we have some lovely collaborative papers published which include: two papers characterizing secondary cell wall transcription factors in poplar with Prof. Chiaki Hori at the University of Hokkaido, Japan (Sci Reports and Plant Biotechnology), a collaboration with Prof. Bob Henry at UQ to look at sugar cane cell wall composition (Biotechnol. Biofuels), and characterizatio of the wheat CslA12 as a manan synthase with former JBEI-er Yves Verhertbruggen (Plant Science).
We are really happy to welcome Dr. Destiny Davis to the lab! Destiny recently completed her PhD in the lab of Prof. Georgia Drakakaki at UC Davis, and brings cell wall and confocal expertise to the LDRD project.
Yu Gao’s book chapter describing our 13C growth chamber for growing plants for multi-dimensional solid state NMR is out! If you don’t have access, let me know and I’ll send you a pdf. Look our for his first paper describing sorghum cell walls coming soon….
A paper from the LEAD division at JBEI on which we collaborated was just published in ACS Sus Chem Eng. Here, we looked at the potential of using ensiled biomass sorghum as a feedstock for lignocellulosic biofuel production. This has a lot of advantages – reduced fire risk for long-term storage, no need to dry down material, gets chopped in the field, and we found in many scenarios this made it cheaper and lower C-emitting than using dry biomass!
At the end of last month, we were sad to say farewell to Dr. Wenjia Wang. She’s only been with us a short time (much under COVID shelter in place conditions), but she will be much missed. We’re really excited for her next adventure back in China (more on that soon I hope), and wish her a huge amount of luck traveling back to China mid-pandemic. Enjoy some much deserved time with your family!
We welcome Chris Aboujudom to the lab! Chris is an undergraduate at UC Berkeley and joins us as part of the SULI program. He is our first ever remote intern, and he will be working with Dr. Xiaoxian Liu to develop user interfaces for some of our sorghum bioinformatic tools.
Amid global pandemics, visa restrictions etc, we are excited, relieved, and excited to welcome Dr. Hsiao-Han Lin to the lab! She starts as a postdoc on the mCAFEs SFA. She recently completed her PhD in the labs of Dr Erh-Min Lai and Dr Chi-Te Liu at Academica Sinica and National Taiwan University, where she looked at Type VI secretion systems in plant-associated bacteria. You can find her on Twitter @HsiaoHanLin1.
Another Paper alert! Paper accepted in Frontiers in Microbiology. This work, led by Thomas Eng, was a collaboration with the lab of Aindrila Mukhopadhyay is the final paper from our LDRD funding. In it, we explored ways to understand how root-associated bacteria interact with each other, and what might be drivers of these interactions.
Paper alert! Our second TiPS paper of the year – this time laying out our ideas behind the PECTIN project. Congratulations Becca!
[Open Access in TiPS is monumentally expensive, so we’ve broken the lab rule. If you want a copy then please email one of us].
June 10th. I’ve been considering publishing a Lab Values/Lab Guide page for a while, in part encouraged by other scientists on Twitter (e.g. Prof. Ben Britton at Imperial), but somehow I never got around to actually *doing* it. The STEM Black Lives Matter movement #shutdownstem and #strike4blacklives today made me think that this could be a useful task to do as I take part. So here it is. It is of course a draft. I expect this to be a living, evolving document as I and the team learn. But it’s a start. I’m especially grateful to all the scicommers out there, especially black scientists (e.g. @ibjiyongi, Dr Rubidium, @seismatters, @BerondaM, @DNLee5 and many more), who share their experiences and thoughts via public channels, and have undertaken the hard work to educate us all (usually unpaid, and often at the risk of becoming a target). Being able to listen to those conversations has been incredibly valuable to me.
June 1st. So, since March 16th, we’ve been sheltered in place in the bay area, with the lab completely closed. This has been hard for many reasons but as a team we’ve been finding our way forwards. The good news is that from today, LBNL has started Pilot 1, in which a limited number of people are allowed back. What this means in practice is that most folks in the group get 1 or 2 days in the lab a fortnight. We’re hoping that COVID numbers continue to move in the right direction, and that we can move to Pilot 2, with more people in the lab shortly. It’s been a real team effort to maximize what gets done in the lab, as well as working on data analysis and papers while at home. I couldn’t be prouder!
Other BIG news – Jenny has accepted a position as an Associate Professor at the University of Adelaide, Australia, in the Waite Research Institute. She will start January 2021, but will continue to manage the group at LBNL for 18 months – 2 years while projects wrap up. Press Release here: https://sciences.adelaide.edu.au/news/list/2020/05/01/new-top-talent-appointment-to-lead-plant-synthetic-biology-research
Paper Updates Feb – June
We’ve been busy again, and I’ve been slow to post here. So what’s new.
Our first paper in collaboration with the Jardine group as part of the PECTIN project is out in PLoS One, led by postdoc Dr. Rebecca Dewhirst. There was a nice write up from DOE here. In it, we start to explore the proposed link between the plant volatile organic compounds (VOCs) acetic acid and methanol, and the cell wall. Since these VOCs increase under drought, and contribute to the carbon cycle, understanding their source and how they might change under future climate cycles is important.
Henrik and I wrote a TiPS forum piece on our favorite topic – GIPC glycosylation. We’ll convert you all to enthusiasts! Unusally for us, it’s not open access (it was pretty expensive), so e-mail me if you want the pdf.
Our collaboration with our LBNL colleagues Corinne Scown and Patrick Shih, led by Scown lab postdoc Dr. Minliang Yang is out in PNAS. We explored the economics around in planta production of high-value chemicals, and how these can be used to help produce economically viable advanced biofuels. We hope this is a useful model for plant metabolic engineering in future bioenergy crops.
This year feels like it’s only just getting started but it’s been BUSY! First, I’m delighted to say that our paper on transient gene expression in sorghum leaves, led by Dr. Rita Sharma, who joined us on a sabbatical from Jawaharlal Nehru University, India is finally out in BMC research notes! Congratulations to Rita, Yan, Ramana and Mi Yeon. This method has been already useful in the lab, particularly for screening sgRNAs.
I gave a seminar in the Department of Plant & Microbial Biology at UC Berkeley on our sphingolipid work. It was a lot of fun meeting my scientific neighbors, and hearing about the research up the road. Certainly some new avenues for potential collaboration! A trip to Washington DC for the DoE BER Genomic Sciences PI meeting rounded out the month, including a workshop that I hosted with Trent Northern on fabricated mesocosms.
Happy New Year! We welcomed Dr. Wenjia Wang (who just completed her graduate work at MSU) to the lab to work on our new LDRD project, Roots2.0. She’ll be using EcoFABs to investigate how root architecture and biochemistry modulate plant-microbe interactions. We also had the lab shinnenkai (新年会) party at my house… looks like everyone survived my cooking!
I am also excited to announce that I am now an editor for Plant & Cell Physiology, which is the society journal for the Japanese Society of Plant Physiologists. I’m really happy to be involved in a journal that supports our plant science community, and I look forward to getting involved. If you’d like to know more about the journal, or have feedback about publishing with us, then get in touch.
As part of ongoing efforts to say no to things, I decided to resign as an Assistant Editor for Plant Methods. I enjoyed learning about “the other side” of publishing, and I particularly thank Prof. Ute Roessner (EIC) for the opportunity.
In all the business of this year, I somehow forgot to update the papers and grants bit. But we had a pretty good year, with 12 papers published and 3 grants awarded! We’re thankful to all involved, especially our collaborators, which meant that we can keep doing great science.
Lab Outing to the Exploratorium After Dark as part of our Thanksgiving Celebrations. Appropriately, the topic was “Matters of Fact” which explored biases and what it means to do good science. The Exploratorium is an amazing hand-on science museum, and their evening events allow you to play with all the exhibits without feeling guilty about not letting kids play…all with a cocktail in hand.
We said farewell to Eliot with a few beers and some serious games of Jenga. He’s been a great team member, involved in everything from planting the switchgrass to coaxing the HPAEC-PAD into behaving.
We welcome Dr Yuan Zhang, who completed her PhD at Rutgers University, where she was supervised by Prof. Dismukes. First job – out to the field to visit our field trials with Kavitha to help with sampling! We also hosted visitors from all over the world including Prof. Taku Demura (NAIST, Japan), Dr. Sebastien Mongrand (CNRS, France), and Prof. Fayna Garcia-Martni (Hokkaido University, Japan).
We welcome a visiting masters student this summer, Eliot Magnin, from Polytech Clermont Ferrand who will work with Kavitha to analyze our 2018 switchgrass harvest.
We welcomed a new postdoc to the lab! Dr Xiaoxian Liu, who completed her PhD at the University of Florida, where she was supervised by Profs. Pam and Doug Soltis…
…and Sophie Tran has graduated and is now working at SeqMatic. Congratulations on your new job, but we will miss you!
It’s been a busy few months…
We welcomed Dr. Kavitha Satish Kumar and Dr. Yu Gao to the lab. Kavitha joined us from the lab of Prof. Chandrashekhar Joshi at Michigan Technical University, where she worked on the biosynthesis of lignin in poplar trees. Yu joins us from the lab of Prof. Marcus Foston as Washington University in St. Louis, where he focused on the catalytic reductive depolymerization of lignin.
Julien and Soe’s paper on the function of GGLT1 (the Arabidopsis GDP-L-galactose transporter) was accepted in The Plant Journal. Thanks to our great collaborators at the CCRC and Stanford for all their help!
Sophie returned to the lab for her final semester before graduation, after a successful internship at Dupont.
Welcome to Delphine Khuu and Pablo Bouchez, visiting Masters students from Polytech Clermont Ferrand.
Congratulations to Sophie on graduating from UCB Chemistry and on her summer internship with Dupont!
Also, big congratulations to Lin, Emilie, Julien, Jingwei and Beibei, as well as our fantastic collaborators Toshiki Ishikawa (Saitama), Will and Henrik (JBEI) and Ed Cahoon (Nebraska) on getting the Arabidopsis GINT1 paper accepted in Plant Physiology Great team work!
Welcome to Jade Pezard, a Masters student who is visiting us from AgroParisTech to work on sorghum GIPCs.
Welcome also to Dr. Rita Sharma, who’s visiting JBEI on sabbatical from Jawaharlal Nehru University, India, to work on gene editing in sorghum. Rita was a postdoc with JBEI in the Ronald Lab at UC Davis, so it’s especially great to have her back.
Congratulations to alumni Vy Ngo, on her new job with Zymergen.
JOBS available here in the Feedstocks division, two of which are postdocs with me.
Congratulations Lin on getting an Asst. Prof position at the CAS botanic gardens in Guangzhou!
JBEI phase III is go! Watch this space for job adverts
Farewell and congratulations to Julien as he leaves us to start his Agreenskills fellowship at IJPB in Versailles, France. Also farewell and congratulations to Sow Htwe who leaves us to take a position at Resilience Science, a start up in San Francisco (also staffed by ex JBEI-ers). She’s also hoping to find time to work as a part-time pastry chef, and we’re looking forward to trying the results.
Oops, it seems that we’ve been so busy that I forgot to update the News section.
Highlights of the last few months have included:
Vy winning the Grace Fimognari prize for outstanding graduating senior in MCB!
The arrival of Lily, taking the lab baby count to 3 so far – congratulations Lin!
Ramana and Amir had a paper accepted in the Journal of Visual Experimentation (JoVE) where they will be demonstrating using PACE to analyze mannan structure. Coming to a screen near you soon…
I got to visit the impressive new AgriBio building at La Trobe University, Australia, where I was lecturing on their Systems Biology workshop. Impressive science and good wine.
I also traveled to Dalian, China, to the World Economic Forum summer meeting, the Annual Meeting of New Champions. This was my second visit as part of the “Young Scientist” cohort, and it really was a privilege to attend. I hosted a session on Green Chemistry, with fellow Young Scientist Ning Yan, from the National University of Singapore. I also took part in a WEF press briefing on the fun and challenges of being a young scientist in the current climate, with fellow Young Scientists Michael Bowen and Kellie Charles from the University of Sydney.
We’ve also said very sad farewells to Thea, Amir and Vy over the past few months. Thea has returned to Germany to a postdoc with Andreas Weber, Amir has returned to Sweden (where his wife has just started her PhD) and Vy is staying in Berkeley as she will start as a Junior Specialist in the Schaffer lab at UCB.
We’re excited to welcome two new people to the lab:
Robin Herbert will join us on a joint project with Aindrila Mukhopadhyay’s group at JBEI where he will be developing an eco-toxicity platform to look at the effects of various JBEI-developed compound on plant growth and plant-mircrobe interactions.
Sophie Tran, an undergraduate student from UCB’s Chemistry department, will be joining us to work for credit on the topology of the CSLA proteins with Amir.
Happy New Year!
Our book chapter describing xylan analysis using PACE is out! It is published in Xylem: methods and protocols, edited by M de Lucas and JP Etchells. This method was developed in Paul Dupree’s lab at Cambridge University (e.g. Goubet et al. 2002), where I did my postdoctoral research. We use it regularly here in my group at JBEI. The method is simple to set up, cheap to perform, and gives detailed polysaccharide structural information. Watch out for a JOVE video on the method, coming in the next few months…
We’re also very sad to wave goodbye to Gosia Murawska. She’s been a great addition to the lab, first as a Masters student, and then as a Research Assistant. She’s a very enthusiastic chemist, but I think we’ve convinced her of the joys of plants! We all wish her a lot of luck with her PhD studies at the University of Basel in the group of Prof. Dennis Gillingham.
Very happy to report that our paper describing the function of GMT1, a putative Arabidopsis glycosyltransferase, in sphingolipid biosynthesis has been accepted in The Plant Cell! Lin led this study, with big contributions from many people at JBEI. This work wouldn’t have been possible without our fantastic collaborators, especially Toshiki Ishikawa at Saitama University in Japan.
Happy Thanksgiving All!
Jenny, in collaboration with our collaborator Prof. Igor Cesarino at the University of São Paulo, has been selected by The Plant Cell to develop a Plant Cell Wall Teaching Tool http://blog.aspb.org/2016/09/22/winning-entries-of-the-august-2016-teaching-tools-proposal-competition/, which will form part of their series of tools to support undergraduate plant science teaching.
Vy Ngo is back, joining us from UC Berkeley MCB department as an honors student. Welcome back Vy!
Sadly, we’ve had to say goodbye to Fekadu Anderbehan. We wish Fekadu a lot of luck with her future career, and look forward to her returning for a visit with her science-enthusiast nephews.
Dominik Bodi, our Biotech Partners high-school student, did an excellent job of presenting his poster describing his research at the BRAVO! event. He was a great addition to our group over the summer, and we wish him all the best for his future career in STEM!
Vy Ngo, our SULI undergraduate researcher this summer also presented her fantastic work at the LBL intern poster day. She is off on a well earned vacation now, but we can’t wait to see her back as a student researcher in the Fall Semester.
We have also welcomed back Gosia Murawska! She initially joined us as part of her Masters studies at Groeningen in the Netherlands. She will now return as a research assistant to continue her development of GIPC analytical techniques.
Lab BBQ in Golden Gate Park, San Francisco
Thea, Amir, and I, along with some other JBEIers attended the ASPB annual meeting in Austin Texas. We particularly enjoyed Plantae‘s “selfie station” at the poster session…