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.