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PDWallMech: Harnessing PlasmoDesma Wall Mechanics for plant biotech and biomaterials

Lead Research Organisation: University of Leeds
Department Name: Astbury Centre

Abstract

Plant cells communicate with each other despite the rigid cell wall surrounding them. Communication is essential to coordinate development and responses to environmental inputs perceived locally or in distant organs. Some small molecules can move freely between cells using cell specific transport machineries. Cell walls limit diffusion of larger molecules, such as proteins and RNAs, however these can move via small channels that connect the insides of neighboring cells known as Plasmodesmata (singular, plasmodesma). Plasmodesmata function impacts all aspects of plant growth and development, including spreading of diseases, capacity to exploit soils resources, adaptation and survival to climatic changes. Despite their fundamental importance to all forms of plant life, we know very little about plasmodesmata and consequently this is one of the most promising but least exploited targets when developing new strategies to improve crop growth and resilience to climate change. The work that will be carried out in this project will fill key knowledge gaps on plasmodesmata, such as how different components in the surrounding cell walls affects plasmodesmata structural organization and function in different plants, cells and tissues. The mechanical properties of cell wall components affecting plasmodesmata function will be analysed to identify genes that can be targeted to modify intercellular communication, plant growth and environmental resilience. I will develop plant-type specific platforms that allow exploitation of plasmodesmata knowledge for the improvement of desirable crop traits, thus addressing their untapped potential to modify root branching (to improve access to water and nutrients uptake in depleted soils), resistance to viruses (plasmodesmata serve as a conduit for virus spreading) or the response to toxic metals and other abiotic stress conditions, through modulating intercellular signalling. At the end of the program the goal is to have novel, accessible tools to modify plasmodesmata in a targeted and specific manner that allow the design of strategies to mitigate the effects of climate change on plant growth, thus agricultural sustainability and food security, in a wide range of plant species including food crops such as wheat and tomato. Complementary to the fundamental work, the properties of cell walls controlling plasmodesmata will be exploited in the design of new products, such as novel biomaterials. The project, which integrates plant biomechanics, biotechnology and material engineering, has a wide range of outputs and impacts, thus offering maximal societal and economic benefits. The Fellowship will deliver crucial knowledge for the development of novel applications in the biopolymer and bioplastic sector and in crop biotechnology strengthening the UK's leading position worldwide in industrial biotechnology. Knowledge translation also addresses global priorities to ensure food security for a growing global population and to discover new resources to manufacture products with green credentials for sustainable living.

Planned Impact

The project will generate new strategies to improve plant growth and new biomaterials derived from cell wall polymers. It will advance knowledge on plasmodesmata (PD) and unravel factors affecting PD function in coordinating responses to developmental and environmental cues. It will impact plant biotechnologists, breeders and synthetic engineers which can use the information in the design of strategies for improvement of crop growth, responses to adverse environments and to engineer the production of high value plant biopolymers. Translation of knowledge from this Fellowship will in the longer-term support growth in UK agriculture which currently produces ~60% of food needs and underpin progress on BBSRC strategic priority on 'Food security'. Increased understanding on the physics of biopolymers will reveal information for industrial application as bioplastics and biomaterials responding to RC calls for valorisation of natural resources and also to the grand challenge area 'Understanding the physics of life' and 'manufacturing the future'. In the UK alone over eight million tonnes of unused agricultural residues are generated which can be a valuable source for biopolymers. New applications for plant biopolymers will support the UK manufacturing sector which contributes £6.7 trillion to the global economy (themanufacturer.com) and support growth in the biopolymer/ bioplastic sector which is predicted to contribute £1.92 billion to the UK economy in the next decade (biomebioplastics.com). Innovations of this nature will attract considerable international interest, industrial investments and strengthen the UK's leader position in industrial biotechnology. In brief, in the short term (4 years) major beneficiaries are:
- The UK workforce, through developing highly skilled people in multidisciplinary and translational research. Interdisciplinarity at the Bioscience-Physic interface is highlighted as strategically important and vulnerable area in the latest BBSRC/MRC report. The project targets this skill area, increasing the employability of the staff involved and their transferrable skills.
- The UK economy and international industrial scientific community by identifying new factors affecting plant growth and new biopolymers for novel biomaterials. UK rain fed crops, such as wheat, are at risk because the greater inter-annual variability in climate. New diseases (such as the tomato chlorosis virus) have also negative impacts on the UK economy. The project will identify new genes to target PD (a path for signaling and virus spreading) in wheat and tomato, providing new strategies for crop improvement through breeding and/or biotechnology. New biomaterials will sustain development and innovations in a variety of industries using cellulose and other plant polymers as, for example, scaffolds for tissue engineering and drug delivery, textiles and packaging products. Such advancements in plant research will provide opportunities to reduce costs and environmental damage (carbon footprint) associated with biomaterial production (e.g. by enabling use of agricultural waste).
- Policy influencers (e.g. public bodies within DEFRA) by gathering evidence on gene editing (relevant on the GMO agenda) and its impact on crop improvement and biomaterial design. The project will deliver new applications for 'rare' plant polymers which may be relevant in the context of government research priorities and funding to promote innovations in, for example, bioplastic research.
- The general public through greater understanding of plant structural biology and biomechanics and on the importance of plant cell walls for providing sustainable food and natural products. In the long term the global population will benefit from the research as it will support innovations on key food crops (e.g. wheat and tomato) addressing concerns on food security and the development of plant-biomaterials that are biodegradable and more environmentally sustainable.

Publications

10 25 50
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Amsbury S (2022) Immunofluorescence Detection of Callose in Plant Tissue Sections. in Methods in molecular biology (Clifton, N.J.)

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Bayer EM (2024) Plasmodesmata: Channels Under Pressure. in Annual review of plant biology

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Benitez-Alfonso Y (2022) George Washington Carver: A plant scientist's perspective. in Current biology : CB

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Benitez-Alfonso Y (2022) Yoselin Benitez-Alfonso in Current Biology

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Benitez-Alfonso Y (2023) Enhancing climate change resilience in agricultural crops. in Current biology : CB

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Benitez-Alfonso Y (2023) Brassinosteroids en route. in Nature chemical biology

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Benitez-Alfonso Y. (2022) Preface in Methods in Molecular Biology

 
Title Commissioned Artwork by Besiana Sinanaj 
Description Artwork to accompany a review in Curr Biology on Climate resilience crops. The painting is currently held at the University of Leeds 
Type Of Art Artwork 
Year Produced 2023 
Impact Benitez-Alfonso et al., Current Biology, 2023 
URL https://www.cell.com/current-biology/pdf/S0960-9822(23)01429-X.pdf
 
Title Plasmodesmata art figure 
Description Figure created by an artist to represent symplastic intercellular transport 
Type Of Art Artwork 
Year Produced 2024 
Impact The figure was included in a recent review on Plasmodesmata channels under pressure. 
URL https://www.annualreviews.org/doi/10.1146/annurev-arplant-070623-093110
 
Description Research has found cell wall composition and specifically callose regulated in tomato pit fields (complex plasmodesmata) and identified the differential regulation of two antibodies during ripening in fruits. Research also correlated the regulation of callose at plasmodesmata with the response to drought and temperature stress.
The mechanical properties of cell walls around pit fields which are complex plasmodesmata were texted using AFM-nanoindentation. The results suggest some differemces with other cell wall domains.
Moreover when ectopically expressing an enzyme that degrade callsoe, a components at plasmodesmata, cell walls became stiffer.
Exploitation Route the out comes of this funding period could highlight routes for modifications of cell walls in fruits reducing or delaying fruit spoilage and improving shelf life and sugar content.
Translation of knowledge acquired in model plants could be used to enhance drought responses thus plant resilience to environmental stress.
Sectors Agriculture

Food and Drink

 
Description BBSRC panel B core member
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description A cryo-capable electron microscope for the Astbury Biostructure Laboratory
Amount £498,376 (GBP)
Funding ID BB/W019485/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2022 
End 07/2023
 
Description A plasma focused ion beam microscope for Structural Cell Biology at the Astbury Biostructure Laboratory
Amount £1,000,000 (GBP)
Funding ID BB/X019373/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2023 
End 07/2024
 
Description Action in solution: Embedding new technology and new capability in Biomolecular Interactions in the University of Leeds
Amount £256,607 (GBP)
Funding ID BB/Z516053/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2024 
End 07/2025
 
Description Farm2Lab Link Platform
Amount £228,002 (GBP)
Funding ID BB/V019775/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2021 
End 08/2022
 
Description Learning from Plant Cell Walls for Innovations in Material Sciences
Amount £30,000 (GBP)
Funding ID 2619616 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 11/2021 
End 07/2025
 
Title Additional file 1 of A comparative meta-proteomic pipeline for the identification of plasmodesmata proteins and regulatory conditions in diverse plant species 
Description Additional file 1: Table S1. Arabidopsis thaliana proteins reported to localize at PD. Table S2. Plant species compatible with PIP1. List of plant species listed in both PANTHER16 and Ensembl Plant databases at the time of publication. Table S3. PANTHER16 subfamilies represented in experimental proteomes. Table S4. in silico PD proteome for poplar generated with PIP. Table S5. in silico PD proteome for A. thaliana generated with PIP1. Table S6. Genes identified in clusters 87 and 100 of the callose interactome shown in Fig. 3d. Table S7. Description of the microarrays used in this study. Table S8. in silico PD proteome for Medicago truncatula using PIP1. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_1_of_A_comparative_meta-proteom...
 
Title PIP1: Plasmodesmata in silico Proteome 
Description R pipeline for generating and classifying plasmodesmata (PD) candidates based on proteomics and feature prediction. 
Type Of Material Computer model/algorithm 
Year Produced 2022 
Provided To Others? Yes  
Impact researchers have reported using this pipeline successfully, A research paper was published and linked to it: Kirk et al., 2022 
URL https://github.com/PhilPlantMan/PIP1
 
Description Anther development in Rice 
Organisation Graduate University for Advanced Studies (SOKENDAI), Okazaki
Country Japan 
Sector Academic/University 
PI Contribution I have contributed to the writing, interpretation of results and publication of a paper based on this collaboration
Collaborator Contribution Somashekar H, did all the experimental work related with this paper as part of his PhD Ken-Ichi Nonomura, supervised the student and prepare and edit the paper.
Impact Ann Bot. 2024 Dec 31;134(6):1013-1026. doi: 10.1093/aob/mcae137.
Start Year 2023
 
Description Mathematical simulation 
Organisation University of Dublin
Country Ireland 
Sector Academic/University 
PI Contribution My research team (Pallavi kumari, Postdoctoral) teamed up with Pietro Ballone from University of Dublin, to develop a simulation of callose-cellulose hydrogels which led to a publication in the journal Biomacromolecules. Myself and the team drafted, review and answered to reviewers comments during the preparation of this publication
Collaborator Contribution Pietro Ballone is a mathematician thus the simulation and access to supercomputer clusters were managed by him. Candelas Paniagua (University of Malaga) completed analysis of hydrogels (water content and dye loading experiments) to validate the simulation
Impact research paper: Kumari P, Ballone P, Paniagua C, Abou-Saleh R, Benitez-Alfonso Y, (2024). Cellulose-Callose Hydrogels: Computational Exploration of Their Nanostructure and Mechanical Properties.. Biomacromolecules, 25 (3), pp. 1989-2006 This is a multidisciplinary collaboration: Mathematics and physics and Biology
Start Year 2023
 
Description Mathematical simulation 
Organisation University of Malaga
Country Spain 
Sector Academic/University 
PI Contribution My research team (Pallavi kumari, Postdoctoral) teamed up with Pietro Ballone from University of Dublin, to develop a simulation of callose-cellulose hydrogels which led to a publication in the journal Biomacromolecules. Myself and the team drafted, review and answered to reviewers comments during the preparation of this publication
Collaborator Contribution Pietro Ballone is a mathematician thus the simulation and access to supercomputer clusters were managed by him. Candelas Paniagua (University of Malaga) completed analysis of hydrogels (water content and dye loading experiments) to validate the simulation
Impact research paper: Kumari P, Ballone P, Paniagua C, Abou-Saleh R, Benitez-Alfonso Y, (2024). Cellulose-Callose Hydrogels: Computational Exploration of Their Nanostructure and Mechanical Properties.. Biomacromolecules, 25 (3), pp. 1989-2006 This is a multidisciplinary collaboration: Mathematics and physics and Biology
Start Year 2023
 
Description Plasmodesmata 
Organisation University of Bordeaux
Country France 
Sector Academic/University 
PI Contribution collected data, made figures and drafted and edited the review
Collaborator Contribution Emmanuelle Bayer contributed with figures and drafted and edited the review
Impact Bayer E, Benitez-Alfonso Y, (2024). Plasmodesmata: Channels Under Pressure.. Annual review of plant biology, 75 (1), pp. 291-317
Start Year 2023
 
Description SLCU 
Organisation University of Cambridge
Department The Sainsbury Laboratory
Country United Kingdom 
Sector Academic/University 
PI Contribution We are collaborating to understand how callose accumulation affects cell walls and associated uses as wood for raw materials. We have provided detailed analysis of changes in cell wall composition using soft polymer physics and biochemistry approaches as a results of inducing callose using transgenic constructs in Arabidopsis and Poplar.
Collaborator Contribution the collaborators (Helariutta lab) has generated and contributed to the analysis of the transgenic material
Impact one Publication produced. This collaboration is multidisciplinary involving biochemical, cell biology approaches, genetics and soft polymer physics. Bourdon M, Lyczakowski JJ, Cresswell R, Amsbury S, Vilaplana F, Le Guen MJ, Follain N... Helariutta Y. (2023). Ectopic callose deposition into woody biomass modulates the nano-architecture of macrofibrils.. Nature plants, 9 (9), pp. 1530-1546
Start Year 2016
 
Description Thomas Greb at the University of Heidelberg 
Organisation Heidelberg University
Country Germany 
Sector Academic/University 
PI Contribution I visited the University for a week and learned about Brioullin microscopy.
Collaborator Contribution the group of Thomas Greb paid for my stay and also provided all consumables and access to instrumentation required for this experimental work. Furthermore they dedicated a Msc student to complete the work which now provided new data.
Impact n/a yet
Start Year 2021
 
Description Underrepresentation of Black and Asian students in UK plant science 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution I Analyzed data and highlighted relevant action plan to address the issues of underrepresentation in plant sciences
Collaborator Contribution Katherine Hubbard was the initiator of this action, collecting all data and analyzing them and prepare the draft paper. Nicola Patron and Jade Bleau together with me Analyzed data and highlighted relevant action plan
Impact paper published . 2024 Sep;10(9):1272-1275. doi: 10.1038/s41477-024-01778-w.
Start Year 2024
 
Description Underrepresentation of Black and Asian students in UK plant science 
Organisation University of Dundee
Country United Kingdom 
Sector Academic/University 
PI Contribution I Analyzed data and highlighted relevant action plan to address the issues of underrepresentation in plant sciences
Collaborator Contribution Katherine Hubbard was the initiator of this action, collecting all data and analyzing them and prepare the draft paper. Nicola Patron and Jade Bleau together with me Analyzed data and highlighted relevant action plan
Impact paper published . 2024 Sep;10(9):1272-1275. doi: 10.1038/s41477-024-01778-w.
Start Year 2024
 
Description Underrepresentation of Black and Asian students in UK plant science 
Organisation University of Hull
Country United Kingdom 
Sector Academic/University 
PI Contribution I Analyzed data and highlighted relevant action plan to address the issues of underrepresentation in plant sciences
Collaborator Contribution Katherine Hubbard was the initiator of this action, collecting all data and analyzing them and prepare the draft paper. Nicola Patron and Jade Bleau together with me Analyzed data and highlighted relevant action plan
Impact paper published . 2024 Sep;10(9):1272-1275. doi: 10.1038/s41477-024-01778-w.
Start Year 2024
 
Description : Be Curious. Stall at for engagement with schools 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Stall as part of the bigger event at the University to showcase science for the wider public. Be curious 2023 (attended by over 1,600 visitors)
Year(s) Of Engagement Activity 2023
URL https://biologicalsciences.leeds.ac.uk/biological-sciences/news/article/374/inspiring-the-next-gener...
 
Description Black In plant science network (conference) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact 80 attended.The BiPS Conference 2024 serves as a response to one of the many recommendations made by the members of our community that attended the Community Network Event in March 2024. With activities ranging from keynote talks to creative workshops, you can expect fruitful discussions and time dedicated to connection, celebration, and cultivation of the next generation.

This conference was welcome to all plant enthusiasts where there will also be sessions specially designed to provide safe spaces for Black communities to interact and build networks.
Year(s) Of Engagement Activity 2024
URL https://blackinplantscience.org/bips-conference-2024/
 
Description Black in plant science engagement event 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact - https://blackinplantscience.org/ website, survey, media launched for connecting, celebrating, and cultivating UK-based Black Scientists (Funded by the Gatsby Foundation, £65K). Committee membership and number of activities launched including Research Award excellence, travel awards, publication of profiles as role models, raising awareness via Twitter and Linkedin account etc.
Year(s) Of Engagement Activity 2023
URL https://blackinplantscience.org
 
Description Gatsby Summer school 2021 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact About 60 UG students from all around the country are selected to take part in this summer schools which occur every year. I have serve as tutor for a group of students in these session. Tutorials take place for three consecutive days with a set of 8-10 students from different Universities. Togatheer we attend seminars from leaders in the field of Plant Sciences and then together we discuss the seminar and formulate questions for teh students to ask the speaker. this is a very nteractive sessions where the stduents get to know of my area of research and bond with each other. They gain confidence in using their rational critical thinking.
Year(s) Of Engagement Activity 2019,2020,2021,2022
URL https://www.gatsby.org.uk/plant-science/programmes/gatsby-plant-science-summer-school
 
Description International Women Day. Panel online hosted by BFAN/ Black Female academic network and Panel in person hosted by Nubian Noire 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact panel discussion about the challenges of being black women in academia/ professor journey and to engage next generation in a career in research
Year(s) Of Engagement Activity 2024
 
Description Interview for Women in Crop Sciences 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Interview for Women in Crop Sciences published.
Year(s) Of Engagement Activity 2023
URL https://womenincropscience.org/yoselin-benitez-alfonso/
 
Description Making sustainable biomaterials from plants 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Gatsby Plant Science Education Programme @GPSEP1.28K subscribers, https://www.youtube.com/watch?v=p5HQhwz9_Pc&t=5s (68 views)
Year(s) Of Engagement Activity 2023
URL https://www.youtube.com/watch?v=p5HQhwz9_Pc&t=5s
 
Description National History museum Explorer talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact This is for the Explorers Conference 2023
When: Friday 24th November 2023 10 AM - 7 PM
Where: Natural History Museum, South Kensington
I shared my career journey with attendees
Year(s) Of Engagement Activity 2023
URL https://www.eventbrite.co.uk/e/the-explorers-conference-2023-tickets-731938867857
 
Description Organizer/chair AAB meeting on Food waste valorisation. (KE with industry) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact This was an event designed to link academic researchers with industry practitioners that are using innovative technologies in the valorization of food waste..
Year(s) Of Engagement Activity 2023
URL https://www.aab.org.uk/event/plant-food-waste-valorisation-opportunities-and-challenges/
 
Description Outreach activity in the Bracken Edge Primary School. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Outreach activity in the Bracken Edge Primary School. . interactive workshop with Year 4 kids themed with photosynthesis and plant anatomy.
Year(s) Of Engagement Activity 2023
 
Description Panel speaker at 2019- 2023 7th BME national conference 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Panel speaking event at the 2023 7th BME national conference.
Year(s) Of Engagement Activity 2023
 
Description Plenary speaker presentation at "Let the research speak for itself" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Plenary speaker presentation at "Let the research speak for itself" event organised by the Black Female Academics' Network hosted online by the University of the West Indies and UWITV.
Year(s) Of Engagement Activity 2023
URL https://www.facebook.com/UWITV/videos/let-the-research-speak/107007395676484
 
Description Talk in Schools GSA 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact I delivered a webinar organized by the Girl school association:
@GSAUK
www.gsa.uk.com
we have 30 schools signed up.
I've had some wonderful feedback already, which I've put below

"it was brilliant! What an inspiring woman, I would love to be taught by her"

"Thank you so much - what an amazing career. Thank you for sharing, providing insight and inspiring students to think about plant science as a future pathway."
Year(s) Of Engagement Activity 2025
 
Description Twitter account and website 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact I frequently tweets directions of rseearch and outcomes of our group area of research via twitter @benitez_lab and in our lab website. We currently have more than 2000 followers and this has also give a good influence by multiple audiences.
Recently i have also established a personal account where I engage in Equality and Inclusion issues thata re close to my heart, iming to improve academia but also bussinesses. this had made again huge impact
Year(s) Of Engagement Activity 2017,2018,2019,2020,2021,2022
URL https://benitezalfonso.wordpress.com
 
Description publication George W. Carver 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact I was invited by Current Biology to write an article about the life of George Washington Carver. This was printed in January 2022 and led to positive reactions by academics and other members of the public. The article portrait the contributions of this black African American to research.
Year(s) Of Engagement Activity 2021
URL https://www.cell.com/current-biology/fulltext/S0960-9822(21)01644-4