Bristol GARNet/NewPhyt/BCAI Gene editing meeting report

Geraint Parry and I wrote a meeting report on outcomes from the gene editing workshop that we co-organised and held in Bristol earlier in the year that you can read here.

Four new faculty posts @Bristol BioSci

The School of Biological Sciences seeks four new academics at lecturer or senior lecturer level. Successful applicants will be research leaders with proven international track records commensurate with experience. They will drive influential research programmes that span the long-standing research strengths of the School: behavioural ecology and sensory biology, ecology and environmental change, evolutionary biology and plant and agricultural science.

Successful applicants will have strong interdisciplinary research portfolios and evidence of academic leadership along with strong commitment and aptitude for teaching at undergraduate and postgraduate level and roles across the spectrum of academic life. 

A good fit to existing University Research Institutes and the Faculty of Life Sciences would also be an advantage.

For informal enquiries please contact Prof Claire Grierson (headofschool-biology@bristol.ac.uk).

The closing date for applications is 11:59pm on Thursday 14^th February 2019.  It is anticipated that interviews will be held during week commencing 1^st April 2019.

Details listed here.

Fellowship opportunities in plant and agricultural science at Bristol

The Bristol Centre for Agricultural Innovation (BCAI) is offering an additional £50,000 to boost project funding for three individuals that are awarded mid-career independent research fellowships at Bristol (such as BBSRC David Phillips Fellowships, Royal Society University Research Fellowships or UKRI Future Leader Fellowships). Those applying for earlier-career, shorter-term fellowships are eligible for an additional £5,000 of research funding. Proposed research must fall within the remit of BCAI to be eligible for this additional funding.
To be considered for BCAI and departmental support, prospective fellowship candidates are required to submit an expression of interest to helen.harper@bristol.ac.uk by 10th January 2019. Your application should consist of your CV, a covering letter (indicating which fellowships you wish to apply for and confirmation that you are eligible) and a research plan (up to 2 pages). We will select and invite candidates with the potential to visit the department in March.
Please contact Dr Helen Harper for any informal enquiries. We look forward to hearing from you.

FASEB Mechanisms in Plant Development meeting

Ken Birnbaum and I are putting the finishing touches together for next years FASEB Mechanisms in Plant Development meeting in St Bonaventure. The dates are July 28-August 02 2019, and I hope to see lots of you there!

Part-funding for PhD: fundamental requirements for branching in plants

Supervisor: Dr Jill Harrison

Background:

Branching is a key determinant of crop yields because it affects the positioning of organs around stems, and hence light interception and productivity. Identifying the basic mechanisms underlying branching is therefore of considerable relevance to agriculture. Our understanding of mechanisms for branching is limited to flowering plants that have complex shoot development and branching patterns¹. This means that it is not possible to block branching without perturbing many other aspects of plant development. Furthermore, flowering plants have complex genome organisations with many genes affecting the same process².

The only living plants that do not branch are bryophytes such as mosses. Mosses have low genetic complexity, meaning that few genes regulate each developmental process³. My lab has disrupted the function of a single gene in a moss and identified mutants that can branch⁴. The decision to branch or not is binary. This brings exciting potential to identify the fundamental requirements for branching.

My lab has recently demonstrated that this approach of stripping out developmental and genetic complexity can generate fundamental new insights into plant development in general⁵. Findings from this project in moss are therefore likely to be transferable to flowering plants including crops. To understand how the switch from one stem to branching can occur, this proposal aims to determine how changes in PIN gene activity can lead to branching during moss development^4,6.

Your project will involve four experimental approaches:

1. Characterisation of moss development in wild-type and mutant plants

2. PIN gene expression analyses

3. PIN protein localisation analyses

4. Auxin distribution analyses in wild-type and mutant plants.

Training:

The project will provide training at the cutting edge of the plant evolution and development fields. The techniques that you learn will be broadly applicable in the academic biology and biotech sectors. The skills that you learn will be widely transferable to other areas such as science policy and publishing.

Reading:

1. Domagalska and Leyser (2011). Nature Reviews in Molecular and Cell Biology 12: 211-21.

2. The Arabidopsis genome initiative (2000). Nature 408: 796-815.

3. Rensing et al. (2008). Science 319: 64-69.

4. Bennett et al. (2014). Current Biology 24: 2776-85.

5. Whitewoods et al. (2018). Current Biology 28: 2365-2376.

6. Bennett et al. (2014). Molecular Biology and Evolution 31: 2042-60.

Applications:

This project is part-funded by the Bristol Centre for Agricultural Innovation, and applicants will need to identify further sources of funds (see info here). The call is open to students from any country. Please apply via the University of Bristol here, and direct informal enquiries to Dr Jill Harrison.

BBSRC SWBio DTP studentship available

Roles for polarity in Marchantia thallus shape determination

Supervisors: Dr Jill Harrison (Bristol) and Dr Martin Homer (Bristol)

Background:

Plant shapes range from tiny string or mat-like forms to massive multilayered upright forms with complex organ systems such as shoots, roots and leaves. Despite these wide differences in shape, many plant gene families are very ancient, predating diversification. We can therefore study the mechanisms for shape determination in simple plants such as liverworts and use the knowledge gained to understand plant shape determination in general.

To this end, my lab has used a combination of live imaging, statistical model fitting, computational modelling and molecular biology to discover mechanisms regulating shape in the liverwort Marchantia polymorpha (Solly et al. (2017): Current Biology).

We found that Marchantia undergoes a stereotypical sequence of shape transitions during development. Key aspects of global plant shape depend on regional growth rate differences specified by the co-ordinated activities of the growing apical notches. Computational modelling showed that a diffusible, growth-promoting cue produced in the notches is likely to pattern regional growth rate differences, and pharmacological experiments suggested that the plant hormone auxin may equate to the model growth-promoting cue.

New models suggest a role for differential oriented growth (anisotropy) in Marchantia shape determination. Anisotropy emerges as an outcome of underlying tissue polarities, and directional auxin transport is one potential mechanism for generating polarity.

 

Your project will build on the prior work above to determine how auxin contributes to plant shape determination in Marchantia.

It will:

1. Predict the effects of different tissue polarities on Marchantia shape by modelling

2. Analyse the auxin distribution in Marchantia in comparison to distributions predicted from modelling

3. Disrupt auxin biosynthesis, directional transport, conjugation and decay and test the effect on growth and shape

4. Use live-imaging, image segmentation and quantitative growth analyses to discover how growth and shape change in plants with different auxin biology.

Training:

By combining computational and wet lab approaches, the project will provide training at the cutting edge of the plant evolution and development fields. The techniques that you learn will be broadly applicable in the academic biology and biotech sectors. The skills that you learn will be widely transferable to other areas such as science policy, publishing and computing.

Reading:

Solly et al (2017).  Regional growth rate differences specified by apical notch activities regulate liverwort thallus shape.  Current Biology 27: 16-26.

Applications:

Applications will be open on the SWBio DTP website  and the closing date is the 3^rd December. Informal enquiries to Dr JillHarrison.

BBSRC SWBio CASE DTP studentship available

Intercepting CLAVATA receptor-like kinase function to engineer ear size in wheat

Supervisors: Dr Jill Harrison (Bristol), Professor Keith Edwards (Bristol) and Dr Chris Burt (RAGT Seeds)

Ensuring continuous global food security will be a major challenge of the 21st century, and wheat contributes approximately 20% of the total calories consumed by humans (FAO, 2017). In cereals like wheat, inflorescence (ear) size determines the number of flowers (florets) and grains produced, and this aspect of plant architecture is regulated by the activity of stem cells in the growing shoot tips. The CLAVATA peptide/ receptor-like kinase signalling pathway maintains the size of the stem cell pool during plant development, and mutants in maize and tomato have increased yields, arising due to an increase in size of the stem cell pool. This project aims to intercept wheat CLAVATA

signalling to engineer ears with more fertile grain sites and increase yield.

The project will involve:

(1) Identification of wheat CLAVATA pathway components

(2) Expression analyses of wheat CLAVATA pathway components

(3) Generation phenotypic analysis of wheat CLAVATA pathway mutants.

Expertise:

Dr Harrison’s group has recently published gene trees for CLAVATA pathway components from a range of land plants (Whitewoods et al. (2018)), and she has experience of analysing gene expression patterns and function in a wide range of plant species. Professor Edwards and colleagues from the Bristol Centre for Agricultural Innovation have extensive experience with wheat having sequenced the genome (Brenchley et al. (2012)), identified many mutants from the exome sequenced Cadenza TILLING mutant population (Krasileva et al. (2017)) and established engineering procedures using CRISPR/Cas9. The CASE partnership with RAGT seeds will bring an opportunity for the student to directly experience wheat breeding and exchange knowledges and finding with wheat growers.

By combining computational and wet lab approaches, your project work will provide training at the cutting edge of the plant development field. You will benefit from further formal teaching and internships included in the SWBioDTP programme. The skills and techniques you learn will be broadly applicable in the academic biology and biotech sectors and widely transferable amongst areas such as science policy, publishing and computing.

Reading:

Brenchley et al. (2012). Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491: 705-710. Food and Agriculture Organization of the United Nations, FAOSTAT statistics database, Food balance sheets (2017); www.fao.org/faostat/en/#data/FBS.

Krasileva et al. (2017). Uncovering hidden variation in polyploid wheat. PNAS 114: E913-E921.

Whitewoods et al. 2018. CLAVATA was a genetic novelty for the morphological innovation of 3D growth in land plants. Current Biology 28: 2365-2376.

Applications:

Applications will be open on the SWBio DTP website  and the closing date is the 3^rd December. Informal enquiries to Dr JillHarrison.

Part-time bioinformatics post-doc position open

Applications are invited from post-doctoral researchers with bioinformatics expertise to join my lab to work on a Leverhulme Trust- funded project to look at the mechanisms regulating branching in Selaginella kraussiana. I would like to use a candidate gene approach looking at Selaginella PIN and TCP function. I have written a bit about the project here, and you can apply here.

Post-doctoral position open: the innovation of branching in plants

Very excited to invite applications from post-doctoral researchers to join my lab to work on a Leverhulme Trust- funded project to look at the mechanisms regulating branching in Selaginella kraussiana. I would like to use a candidate gene approach looking at Selaginella PIN and TCP function. I have written a bit about the project here, and you can apply here.

Grant awarded from The Leverhulme Trust: the innovation of branching in plants

The earliest land floras looked something like the tiny fungi, freshwater algae and lichen crusts that we can see today growing on a roof, tree trunk or wall. Plants originated from algae growing in such crusts around 470 million years ago, and the first land plants resembled modern mosses, each having a tiny simple stem with a swollen reproductive tip. In contrast, the vast majority of today’s land plants are large with elaborate branching shoots that make leaves and flowers from proliferative shoot tips. I am interested in how the switch from simple to elaborate plant forms occurred during evolution and would like to answer questions such as how did branching first arise, how did plants learn to make proliferative shoot tips and how did they later learn to make leaves? These steps were all pivotal in enabling plant life as we know it to conquer the land, and as animals depend on plants for oxygen and food, they ultimately underpinned the radiation of life on Earth.

Over the last decade, newly discovered fossils, genetic techniques and model systems have unlocked the door to answering my fundamental questions about plant evolution. I aim to build on these advances to identify the genes that were responsible for the origin of branching. Most of our knowledge about branching comes from flowering plants, which have a recent evolutionary origin. With my Leverhulme Trust Project Grant I will use a relative of coal swamp plants whose branching form has changed little during the past 300 million years to study the genes involved in branching. This spike moss is called Selaginella kraussiana, and it shows an ancient pattern of branching in which the proliferative shoot tips split in two as the plant grows to give the plant a forking overall structure, rather than the bushy structure of flowering plants. The project will identify any similarities and differences in branching mechanisms between spike mosses and flowering plants and will thereby reveal the route by which branching forms evolved.

Blog for The Node on our recent paper on moss CLAVATA function

Testing Zimmermann’s Telome Theory.

(Published with photos on The Node here)

Jill Harrison

A perspective on our recent paper ‘CLAVATA was a genetic novelty for the morphological innovation of 3D growth in land plants’¹.

In the 1950’s, the German botanist Walter Zimmermann (photo here) hypothesized a series of developmental transitions enabling plant forms to radiate during evolution². Zimmermann’s so-called Telome Theory has received much attention from those interested in leaf evolution as it incorporates suggested steps by which early leafless plants such as Cooksonia were modified by processes of overtopping, webbing and planation to form shoots with leaves². Less attention has been given to his ideas about earlier steps in plant evolution, namely how cell division planes translate directly into plant form in aquatic algal relatives of land plants, and how a capacity to rotate stem cell divisions through multiple planes was a key innovation of land plants, enabling them to orient growth along multiple axes².

In mosses, a developmental transition recapitulates Zimmermann’s evolutionary transition when a shoot with multiple growth axes (3D growth) initiates from a filamentous precursor tissue (2D growth) that resembles some algal relatives of land plants. During my post-doctoral work, I collaborated with Dr Adrienne Roeder and Professor Elliot Meyerowitz at Caltech to characterize this 2D to 3D growth transition by confocal live-imaging, and showed how cell division planes start to flip around to establish an apical stem cell with tetrahedral shape during shoot initiation³. We found that new shoots and filaments can initiate right next to each other from a parent cell and concluded that local cues and asymmetric divisions were important in shoot initiation².

When my first PhD student (Dr Chris Whitewoods, né Mr Chris White) joined my lab in Cambridge to work on moss CLAVATA function, we did not know that CLAVATA would act locally to pattern asymmetric divisions in moss shoots, but this is what we found.

CLAVATA signaling involves the production and perception of small mobile peptides, and these two functions are spatially separated^1,4. Mr Joe Cammarata joined my lab and subsequently moved to Cornell to work with Prof. Mike Scanlon and Assoc. Prof. Adrienne Roeder, and showed that disruption of either function results in problems with cell division plane orientation as shoots initiate. We also discovered that CLAVATA genes are only present in land plants, leading us to conclude that these genes contributed to a key, land plant specific innovation during evolution¹.

Moving forwards, I would really like to build on our work to find out how CLAVATA specifies cell division plane orientation during moss shoot initiation, and whether CLAVATA contributed to the origin of indefinitely proliferative shoot growth in vascular plants. Answers to these questions will give fundamental new insights into plant developmental patterning and plants’ conquest of land respectively^5,6.

Whilst Zimmermann’s Telome Theory ideas have been critiqued (e.g.⁷), phylogenetic and molecular genetic advances in a range of plant model systems mean that they are now open to experimental interrogation. I am excited about the possibility of further research to test his ideas and think that our investigation of moss CLAVATA function illustrates one way to do this.

Further reading:
1     Whitewoods et al. (2018). CLAVATA Was a Genetic Novelty for the Morphological Innovation of 3D Growth in Land Plants. Current Biology, here.
2     Zimmermann (1952). Main results of the ‘Telome Theory’. The Palaeobotanist 1, here.
3     Harrison,et al. (2009). Local cues and asymmetric cell divisions underpin body plan transitions in the moss Physcomitrella patens. Current Biology 19, here.
4     Bowman and Eshed (2000). Formation and maintenance of the shoot apical meristem. Trends Plant Sci 5, here.
5     Harrison (2017). Development and genetics in the evolution of land plant body plans. Phil. Trans. R. Soc. B 372, here.
6     Harrison and Morris (2018). The origin and early evolution of vascular plant shoots and leaves. Phil. Trans. R. Soc. B 373, here.
7     Beerling and Fleming (2007). Zimmermann’s telome theory of megaphyll leaf evolution: a molecular and cellular critique. Current Opinion in Plant Biology 10, here.

Paper on plants' conquest of land out

Cell divisions rotate in a spiral pattern at the top of a moss shoot.

Many thanks to those who have commented generously on our latest offering to Current Biology, online here. 

In our paper we identify the genetic basis of a defining feature of land plants, namely the capacity to rotate cell divisions through multiple planes. This innovation was important in land plant evolution because plant cells cannot move, and growth and cell division planes pattern overall plant form.  Multiple cell division planes translate directly into multiple growth axes, accounting for the elaboration of land plant forms relative to their algal ancestors. The genes involved encode a small protein that can move, and its receptors, and a major future challenge will be to discover how these act to set the cell division planes.

My team now wishes to address this challenge and to work out how changes in gene activity contributed to the radiation of diverse plant forms during evolution.

I am very grateful to my students, colleagues and collaborators for making this project so enjoyable, and especially to Chris né White for taking a punt when we started the work.

Thanks to Bioballers

Thanks to Nick Franke and others for organising a memorable evening at the museum yesterday. I loved your version of wonderwall, it was great! Good luck to all of you in the next steps.

Paper on Physcomitrella MAX2 function out

Many congrats to first and lead co-authors on bringing a project on Physcomitrella MAX2 function to fruition, and thanks for including me and Yoan! The paper is online in New Phytologist today here, and it shows that the stigolactone signalling pathway operates distinctly in Physcomitrella and flowering plants.

Visit to Pisa

Zoe and I are in Pisa visiting Francesco Licausi and got to see Europe's oldest botanic garden today. Interesting generic beds and beds to showcase individual plants below.

Thanks for the invitation Francesco, it was fun to meet your lab!

FASEB mechanisms in plant development meeting 2019

Very pleased to say that FASEB have given the go ahead for the 'mechanisms in plant development' meeting to be held in 2019 in St Bonaventure, New York.

Please block out July 29- August 2 in your diaries and spread the word!

Ken Birnbaum and I are co-organising the meeting and hope to announce confirmed speakers soon.

Hiring a lab manager @BristolPlantSci

The vibrant Plant Science grouping at Bristol is looking to recruit to an open ended lab manager post in plant molecular and cell biology. The role will be varied involving an ability to work independently and proactively to high technical, academic and interpersonal standards. 

The job advert and particulars are online here, and I look forward to meeting some of you who apply.

Method for working with sterile moss mutants out

Laura Moody's recent paper on 3D growth in Physcomitrella used somatic hybridization to get round the problem that 3D growth-defective mutants don't make gametophores or gametes. The technique she developed used a fluorescent marker line that I started to generate during my post-doctoral work and Yoan Coudert finished making in my lab, and the paper is online today at the New Phytologist- you can read it here.

New opportunities for international students to study at Bristol

Bristol has launched a new international scholarship scheme for partners in countries listed below. The closing dates are in summer 2018- please get in touch if you are interested in joining my lab.

If you have the talent and ability to succeed, concerns about funding should not stop you from applying to come to University. We have several scholarships which might be able to help you fund your studies.

University of Bristol scholarships

In 2018 we are investing £500,000 to help the brightest and best international students come to the University of Bristol.

• Think Big Undergraduate Scholarship 
• Think Big Postgraduate Scholarship 

Partner scholarships

With our prestigious external partners, we offer a range of scholarships for students from specific regions.

Undergraduate

• Aviva Scholarships: for students from China, Hong Kong, Indonesia, Singapore, Taiwan and Vietnam
• Beacon Scholarship: for students from Kenya, Tanzania and Uganda
• Karta Initiative Scholarships: for students from India

Postgraduate taught

• Aviva Scholarships: for students from China, Hong Kong, Indonesia, Singapore, Taiwan and Vietnam 
• Commonwealth Scholarships: for students from developing Commonwealth countries
• GREAT Scholarship 2018: China: for students from China
• GREAT Scholarship 2018: India: for students from India
• Santander Scholarship: for students from Latin America
• Said Foundation Scholarships: for students from Jordan, Lebanon, Palestine or Syria

Other scholarship opportunities

Search our full list of funding to find more scholarships offered by the University of Bristol and external organisations.
Before you apply for a scholarship, check the application deadline and whether you are eligible.

New Shores in Plant Evolution EMBO workshop taking applications

Please come and join us to talk about land plant evolution in Lisbon in June.
You can apply here.