Arabidopsis Research Roundup: August 8th

This weeks Arabidopsis Roundup contains a wide breadth of UK research. Firstly the lab of Jurriaan Ton undertakes a global analysis into the role of methylation in the immune response. Jurriaan kindly provides a short audio description of this work. Secondly Dame Caroline Dean’s lab further add to our understanding of the vernalisation response in Arabidopsis. Thirdly is work from Rothamstead that evaluates the fatty acid composition of the seed aleurone while fourthly is a study from Durham and Oxford Brookes that introduces a novel regulator of autophagy. Finally is a study that adds clarity to the phenotypic effects resulting from ascorbic acid deficiency.

López Sánchez A, H M Stassen J, Furci L, Smith LM, Ton J (2016) The role of DNA (de)methylation in immune responsiveness of Arabidopsis Plant Journal http://dx.doi.org/10.1111/tpj.13252 Open Access

Jurriaan Ton is the corresponding for study from the University of Sheffield that looks into the role of reversible methylation on the Arabidopsis immune response. Methylation is a well known regulator of gene expression and in this research the authors attempt to interrogate its effect on the immune response. Hypo-methylated mutants are more resistant, whilst hyper-methylated mutants are more suspectible to the biotrophic pathogen Hyaloperonospora arabidopsidis (Hpa). Downstream gene expression changes in these methylation mutants focus at the level of cell-wall modification and salicylic acid (SA)-responses. Oppositely the hypo-methylated mutant nrpe1 is more suspective to the necrotrophic pathogen Plectosphaerella cucumerina whilst the hyper-methylated ros1 mutant is resistant to this organism. The Ton-lab has been involved in the discovery of the exciting phenomon of transgenerational acquired resistance, and both nrpe1 and ros1 fail to develop this response against Hpa. Global gene expression shows that either NRPE1 or ROS1 influence about 50% of the gene expression changes that occur following Hpa infection. Finally since less than 15% of genes with altered gene expression reside close to NRPE1 or ROS1, the authors are able to propose that much of this regulation is due to methylation effects that act in trans- throughout the genome.

Jurriaan kindly provides a comprehensive description of this work:


Qüesta JI, Song J, Geraldo N, An H, Dean C (2016) Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization Science. 353(6298):485-8 http://dx.doi.org/10.1126/science.aaf7354

VAL_pic
From http://science.sciencemag.org/content/353/6298/485

Dame Caroline Dean (John Innes Centre) is the lead author of this manuscript that builds upon the portfolio of work from her lab aimed at characterising the vernalization response. This work again uses the FLOWERING LOCUS C (FLC) gene as a model to study the factors that allow gene-silencing mediated by Polycomb silencing complexes. The authors find that a single intragenic point mutation prevents nucleation of the homeodomain-Polycomb repressive complex 2 (PHD-PRC2) to this region, a process that involves the transcriptional repressor VAL1. In the wildtype FLC locus the localisation of VAL1 promotes transcriptional silencing through histone deacylation through interaction with the conserved apoptosis- and splicing-associated protein (ASAP) complex. This study adds an additional layer of molecular complexity to the process of regulating the FLC locus and provides insight into the important role for primary sequence-specific targeting during gene silencing.

Bryant F, Munoz-Azcarate O, Kelly AA, Beaudoin F, Kurup S, Eastmond PJ (2016) Acyl carrier protein DESATURASE 2 and 3 are responsible for making omega-7 fatty acids in the aleurone Plant Physiology http://dx.doi.org/10.1104/pp.16.00836 Open Access

Peter Eastmond (Rothamstead) leads this work that investigates the components that determine seed fatty acid content. Specifically Omega-7 monounsaturated fatty acids (ω-7s) are enriched in the aleurone of Arabidopsis seeds so this study used a Multiparent Advanced Generation Inter-Cross population to identify a QTL linked to ω-7 content that includes the ACYL-ACYL CARRIER PROTEIN DESATURASE1 (AAD1) and AAD3 genes. AAD family members possess both stearoyl- and palmitoyl-ACP Δ9 desaturase activity and aad3 mutants show a significant reduction in ω-7 content, which is common with mutants in other AAD family members. In addition the authors show that the FATTY ACID ELONGASE1 protein is required for accumulation of long-chain ω-7s in the aleurone. Overall this research provides new insight into the pathway that produces ω-7s in the aleurone, indicating that these genes might represent a target for future strategies to alter seed fatty acid content.

Wang P, Richardson C, Hawes C, Hussey PJ.(2016) Arabidopsis NAP1 Regulates the Formation of Autophagosomes Current Biology http://dx.doi.org/10.1016/j.cub.2016.06.008

NAP1_pic
From http://www.sciencedirect.com/science/article/pii/S0960982216306200

This is collaborative effort between the labs of Patrick Hussey (Durham) and Chris Hawes (Oxford Brookes) investigates the role of the NAP1 protein, which is a member of the SCAR/WAVE complex, on the formation of autophagosomes. These organelles are induced by certain stress conditions and fewer are produced in nap1 mutants after starvation stress. This also corresponds to wildtype NAP1 localisation. Concomitantly nap1 mutants, as well as mutants of other members of SCAR/WAVE complex, are more suspectible to nitrogen starvation and is less tolerant to salt stress. The best characterised role of the SCAR/WAVE complex is during ARP2/3-mediated actin nucleation yet this study demonstrates an addition function as a regulatory of autophagy.

Lim B, Smirnoff N, Cobbett CS, Golz JF (2016) Ascorbate-Deficient vtc2 Mutants in Arabidopsis Do Not Exhibit Decreased Growth Front Plant Sci. 7:1025

http://dx.doi.org/10.3389/fpls.2016.01025 Open Access

Nick Smirnoff (Exeter) is a co-author on the Australian-led research into Arabidopsis vtc mutants, which have a significant reduction in ascorbate-acid levels. Ascorbate is synthesized via the L-galactose pathway, the first enzyme of which is encoded by the paralogs VITAMIN C2 (VTC2) and VTC5. This study characterises the growth of a vtc2 T-DNA mutant that has a 30% reduction in ascorbate levels. Surprisingly this does not result in any signficant phenotypic and they suggest that a previously characterised growth reduction in other vtc2 mutant alleles is likely due to unknown genetic lesions.

ICAR2016 Meeting Report: William Broad

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Published on: August 5, 2016

Submitted by William Broad (University of Oxford)

I was very grateful to receive a travel bursary from the Gatsby Foundation and GARNet to attend the International Conference on Arabidopsis Research 2016 (ICAR2016), held in the city of Gyeongju, South Korea. The location and number of attendees gave this event a much different atmosphere and made for a unique experience in comparison to the small subject-specific gatherings I have attended in the UK. While even small conferences attract an international audience, due to their locations, they are typically populated by those living just a cheap flight away. Therefore when attending a conference on the other side of the planet, with the vast majority of delegates coming from Korea, China, and Japan, it was amazing to discover the cutting edge research that is occurring in East-Asia.

ICAR2016 offered a great opportunity to delve deeper into my own field of organellar biology, as well as to become acquainted with the areas of research that simply attracted my attention. Indeed, there were many interesting talks and here I will briefly highlight a few memorable speakers.

JenSheenThe conference opened with a key note lecture delivered by Professor Jen Sheen, who began in contrast to the typical fashion of justifying why plant science is important, by displaying some of her own craftsmanship of photography and horticulture, to instead remind us how diverse and beautiful plants really are. Professor Sheen has spent much of her career delving into the world of how sugars, mainly glucose and also nitrates, act as a signalling molecules in plants. Dissecting this process is truly an interesting topic for a cell biologist, these processes are important to organisms at a multitude of levels, and critically they are not static, and are among a tangle of interconnections. Professor Sheen’s description of these processes made for an excellent talk at the cutting edge of molecular biology.

In organellar biology I was excited to meet Dr. Jesse Woodson, who presented the findings of his recent Science paper (Woodson JD, et al. 2015. Science 350:450-4) together with some previously unseen data. Jesse and colleagues from Professor Joanne Chory’s lab, has found that stressed chloroplasts can be selectively degraded by the vacuole, something not previously observed, and that this process is triggered in part by a cytosolic ubiquitin-proteasome system E3 ligase called PUB4. A really cool piece of this talk was the 3-D image of the engulfment process generated by TEM, which offers far more detail and insight than the 2D representation. This work raises interesting questions regarding how the chloroplast can communicate its stressed state externally to the cytosol and how that results in it being specifically selected for degradation by the vacuole.

An unexpected highlight for me was the work presented by Professor Ikuko Hara-Nishimura, whose lab’s research focus is on the directional growth and movement of plants. She presented data regarding a group of regulatory factors of such movement – components of the cytoskeleton, mysosins XIf and XIk, and Actin8. Mutants of these proteins exhibit hyper-bending in response to gravity, the plants therefore seem to overshoot their reorientation as if there is nothing to put the brakes on once bending has been triggered. Curiously, in at least one of these mutants the circadian up and down oscillation of Arabidopsis rosette leaves is absent, a finding punctuated by an enthusiastic attendee sitting behind me booming ‘That is interesting! That’s Really interesting!’.

On the last day of the conference I was able to see a talk by Professor Harvey Millar, which was on plant proteomics. Specifically with regard to how the proteome of the Arabidopsis leaf changes over time during growth, what the turnover rates of individual plant proteins are, and even calculation of the energy cost of protein turnover in different leaves. What could have come across as a mundane stamp-collecting aspect of biology was presented as something much more, the results of which appear to give great insights into how these plants manage this aspect of their economy during growth.

Broad_13599898_10153845726471676_7147785929705411430_nFinally, it is important not to forget the value of meeting fellow researchers, the coffee breaks and evenings spent at the bar were as appreciable as attending the talks. As a young researcher I found attending ICAR2016 to be a formative experience. I was able to see first-hand what my fellow researchers are doing and how they are doing it, put faces to the names atop the papers I’ve been reading, and discuss science with fellow PhD students, post-docs, PIs and long established professors. I was able to gain exposure to new ideas in research and, as I was privileged enough to give a presentation, I received helpful feedback on my own work. My experiences there really turned the competitive publish-or-perish mentality of science on its head and revealed a community of interested people driven by curiosity.

Arabidopsis Research Roundup: July 27th

Each of the papers in this Arabidopsis Research Roundup involves the response to different stimuli. Giles Johnson at Manchester provides an audio description of work that has discovered a novel mechanism of cold sensing whilst Gordon Simpson and John Brown from Dundee are contributors to work that has interrogated the sugar signaling pathway. Finally is a study from Warwick that has identified novel loci involved in ABA signaling and seed vigour.

Dyson BC, Miller MA, Feil R, Rattray N, Bowsher C, Goodacre R, Lunn JE, Johnson GN (2016) FUM2, a cytosolic fumarase, is essential for acclimation to low temperature in Arabidopsis thaliana Plant Physiology http://dx.doi.org/10.1104/pp.16.00852

Open Access

From http://www.plantphysiol.org/content/early/2016/07/20/pp.16.00852.long
From http://www.plantphysiol.org/content/early/2016/07/20/pp.16.00852.long

Giles Johnson (Manchester) is the corresponding author on this UK-German collaboration that looks at the mechanisms by which plants sense the low temperatures that cause significant phenotypic changes. GC-MS showed that fumarate is a key component in the cold tolerance response and that the activity of the FUM2 enzyme is responsible for accumulation of fumaric acid. Plants that lack FUM2 activity show significant alteration in gene expression and metabolite profile following a cold treatment and in particularly are unable to acclimate photosynthesis at lower temperatures. Therefore this study introduces a novel component of the temperature sensing apparatus, which might have broad significance for attempts to develop crops with an improved cold response.

Giles kindly provides an audio description of this work, which includes an overview into cold acclimation of photosynthesis. This includes an excellent ‘stress-ball’ analogy! (Apologies for pen-clicks :/).

 

Carvalho RF, Szakonyi D, Simpson CG, Barbosa IC, Brown JW, Baena-González E, Duque P (2016) The Arabidopsis SR45 Splicing Factor, a Negative Regulator of Sugar Signaling, Modulates SNF1-Related Protein Kinase 1 (SnRK1) Stability The Plant Cell http://dx.doi.org/10.1105/tpc.16.00301

From http://www.plantcell.org/content/early/2016/07/19/tpc.16.00301.abstract
From http://www.plantcell.org/content/early/2016/07/19/tpc.16.00301.abstract

Gordon Simpson and John Brown (James Hutton Institute) are contributors to this Portuguese-led study that investigates the role of the SR45 splicing factor in sugar signaling. In sr45-1 mutants they show that glucose-feeding causes increased levels of the energy-sensing SNF1-Related Protein Kinase 1 (SnRK1) yet without increasing its gene expression. Concomitantly the hypersensitivity of sr45-1 mutants is rescued in plants with reduced levels of SnRK1. The authors discovered that the mechanistic link between these genes involves SR45-1 regulating the alternative splicing of the 5PTase13 gene, which encodes an inositol polyphosphate 5-phosphatase that interacts with SnRK1 in vivo. In wildtype plants 5PTase13 modulates proteasomal-mediated degradation of SnRK1 and therefore a perturbation of this process in sr45-1 explains this defect in sugar-sensing.

Morris K, Barker GC, Walley PG, Lynn JR, Finch-Savage WE (2016) Trait to gene analysis reveals that allelic variation in three genes determines seed vigour. New Phytol. http://dx.doi.org/10.1111/nph.14102 Open Access

Bill Finch-Savage is the corresponding author on this study from the Warwick University that uses Brassica oleracea natural variation to identify novel loci involved in seed vigour. The discovered QTL was termed Speed of Germination (SOG1) and contained two genes, BoLCVIG2, a homologue of the alternative-splicing regulator (AtPTB1) and BoLCVIG1, which has unknown function. Transfer of these alleles into Arabdopsis causes alterations in seed germination, which is also observed in mutants of the equivalent Arabidopsis genes (At3g01060, At3g01150). Furthermore an additional discovered QTL encodes the Reduced ABscisic Acid 1 (RABA1) gene, which influences ABA content and seed vigour. Therefore this mapping strategy has discovered three genes that promote seed vigour resulting from alterations in ABA content and sensitivity.

ICAR2016 Student Perspective: Marie Bruser

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Published on: July 26, 2016

Thanks to Marie Bruser for putting together her thoughts from the ICAR2016 meeting.

The annual Arabidopsis conference was held in GyeongJu in South Korea this year. I was fortunate to go, thanks for some extra funding from the Gatsby Foundation and GARNet.

HICO_Bruser
Going to the conference I of course looked forward to my own supervisor Lars Østergaard’s talk. But I also had some other sessions and speakers I was really excited about. And they did not disappoint. Sabrina Sabatini wonderfully explained her elegant model of auxin and cytokinin distribution in the root, Dolf Weijers showed some stunning images of the Arabidopsis embryo which were only rivalled by Minako Ueda with her live-cell imaging of cell divisions, microtubule arrangement and mitochondria in the zygote. There was also Annika Weimer from the Bergmann lab who told the story of how formative divisions occur in the root and the stomata, followed by a great description of the sepal cellular arrangements by Adrienne Roeder. She outlined the effect of ATML1 levels on cells division versus endoreduplication.

Tom Beeckman’s talk was also great where he presented his Science paper, published in January, on a cyclical auxin signal coupled to cell death which determines lateral root formation. I had read his paper and discussed it in a journal club but it was brilliant to hear the story told by the person most excited and motivated about it! One of the most important things I learned from these sessions was not to dismiss Domains of Unknown Function (DUFs). Hunting down a DUF, Dolf Weijers and his lab found a protein beautifully localized in the corner of cells, playing a role in determining the cell division plane. And who wouldn’t want to name a protein!?

I also want to highlight two talks from the transporter session, a topic not directly relevant to what I do. Yi-Fang Tsay neatly described her research on nitrogen transporters. She identified one that was involved in transporting N from old to new plant parts in times of low N (NRT1.7) and others that transported nitrogen in high N conditions (NRT1.11 and NRT1.12). The other talk, by José A Féijo, showed that transport in the plant can be a lot more complex, with a large network of genes involved in calcium transport in the pollen tube.

But for me the best talk came from a very relaxed and confident John Bowman in the session on shoot development. His theory that leaves are modified shoots has led him to attempt to modify leaves in a way that they revert back to the indeterminate growth of shoots. And he has succeeded, producing Arabidopsis leaves that are crinkled, a little like kale, and grow indeterminately. His talk was delivered in a very clear manner and kept me fascinated all the way through, even though he was the last of his session. And even though it was my favourite talk, it was one I took the fewest notes on and I believe that is because I was so captivated by his story that I just sat back and listened and simply forgot about notetaking!
PIN_BruserAnd there is one more thing I really got to appreciate at this, my first large conference: that the talks are just one part of the event. The few hours you get around the talks; during coffee and lunch times, dinner, poster sessions and drinks, are the times that probably matter just as much. They give you the chance to talk to the people you have just seen present. They give you the chance to meet people you admire and talk to them on a first name basis. They allow you to meet scientists from all over the world, from all career stages. They make you realise that everyone else, same as you, is there to have a great time talking science and experiencing a different country. And most of all, it makes you appreciate that in the end, no matter what stage of your career you are, you are part of a community that is interested in a common topic, driven by curiosity and a thirst for knowledge.
Mix_Bruser

ICAR2016 Perspective from Jue Lan.

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Published on: July 18, 2016

Guest Post: Jue Lan, Hetherington lab, University of Bristol

This summer, from 29th June to 3th July, I had the honour to attend and give a talk about my research at the International Conference of Arabidopsis Research 2016 at Gyeongju, Korea. The venue for the conference, HICO, was in the green mountains next to a peaceful reservoir. All this gave the conference a romantic and scenario touch.

The conference started promptly with the keynote from Prof Jen Sheen of Harvard University. She gave three nice examples of how her group looking for missing links in signalling pathways using genetic tools. It was particular useful to know that an ultrasensitive Calcium sensor is available out there. In the rest of the whole conferences, there are more talks with these highlights of technology, giving me useful updates of the cutting edge techniques in science research today.

In the five days of conference progression, I enjoyed Youngsook Lee’s nice overview of ABC transporters, Annika Weimer’s fascinating claim that cyclin dependant protein kinase controls the expression of meristemoid lineage gene SPCH, Doris Wagner’s outstanding epigenetic approach to increase plant water use efficiency by the brm gene.

Most importantly, it was the first time for me to give a talk on such a big platform and to such a big audience. The talk went very well and I received some constructive questions and suggestions, as well as some toughening grilling. Throughout the process I got to know some very talented researchers from all over the world, giving me information both on scientific projects and other relevant information.Jue_Lan

This leads to the social part of the conference. Meeting new people is always one of my favourite part of academic conferences. It is always encouraging to know there are so many bright minds and great people out there, doing great things and willing to support each other in the community. I myself managed to reconnect to a couple of old friends in America, and to know a few more friends from UK and all over the world. Besides, there was one fresh experience this time. As the conference was held in Asia, I was able to talk to many fellow Chinese people, have some great chats and get a better idea of the current picture of plant science in China. Some of them, due to the language barrier or other issues, did not make international contacts despite high quality research outputs. This is truly a shame for the whole community and hope things can change a little bit in the future.

If there were some lessons to be learnt, I certainly hope, in the future, before attending such a big meeting, I would sit down and go through all the poster abstracts and prioritise the ones I would like to see most. When there were over 500 posters in the same room, there was hardly enough time to see them all and discuss with their authors properly.

DvonWangenheim_PosterPhoto from @DvonWangenheim

In conclusion, I thoroughly enjoyed the meeting and grateful to GARNet and Gatsby foundation to support me to go there. It was great to be immersed in such an international ambience and absorb knowledges and ideas from different aspects. And as I said in my talk, science should be all about open and collaboration, and carry this globalism spirit forward whatsoever.

How to be a Plant Science Consultant…

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Published on: July 15, 2016

The annual American Society of Plant Biologists (ASPB) conference was recently held in Austin, Texas. For a summary of this event please check out the ASPB blog.

As part of the Career Chat Workshop at the meeting, Bethany Huot from the Michigan State University took notes from a general discussion with Michael Gonzalez who works as a Plant Biology Consultant. Her summary of this discussion was published on the excellent Plantae resource but given its unusual subject matter I thought it would be good to re-post here on the GARNet blog.

Bethany also launched and curates the the PubClubHub website, which has a range of other awesome articles surrounding careers, outreach and other advice. Please check it out.

From Plantae:

At the 2016 Plant Biology conference in Austin, Texas, we had the opportunity to sit down with Michael Gonzalez to get tips on pursuing a career as a Plant Biology Consultant.  Here are some of the tips and suggestions Michael shared with us.

Getting Started:

The first step towards establishing yourself as an independent consultant is to identify what skills you have to offer and how you can market those skills.  Some areas of expertise that Michael has seen used successfully in this way are computational, educational or in plant breeding! As a self-employed person, some basic skills you will need to develop are time and money management, as these are the most critical factors for your short and long term success.  Some specifics on these and other necessary skills are detailed below.

Building your clientele:

The first step towards making your new business successful is to start building your clientele.  The key here is Networking and to make the most of each conversation, you will need to be prepared.  Michael suggests writing down a mission statement based on what you do well and practicing it as a sales pitch. This way you will be sure to hit on every key element of what you have to offer during any particular conversation.  One thing to keep in mind is to provide enough information to gain interest, but not so much that you enable your potential client to take your ideas and run with them on their own.

Another critical element is developing a Marketing strategy.  To maximize your networking opportunities, you will want to increase your visibility.  In addition to the traditional business cards, Michael also recommends using online tools, like setting up your own website and blogging on sites frequented by potential clients. Bare in mind however that the best marketing tool is face-to-face interaction!  Michael’s advice for this is to be prepared with that sales pitch and, above all, sound professional.  Michael repeated this tip multiple times, emphasizing that the extent to which you are prepared and sound professional will go a long way towards closing the deal.  The best way to prepare for each meeting is to not only rehearse what you have to offer, but to also research the person with whom you are interacting, what it is they do and what specifically you have to offer them in their research.  Michael says potential clients are looking for someone who can come in and get the job done, not another graduate student they will need to manage. [Also remember that any random conversation could lead to something in the future so always maintain your professionalism- GARNet note]

Finally, while having clients is obviously critical to establishing a solid business, you will want to be selective about the clients with whom you agree to work.  Entering into contracts with the wrong people can be more trouble than its worth, and may potentially put your business at risk.  Remember that building a solid reputation is an essential element of establishing a sustainable business, and the people with whom you do business reflect on you as well.

Negotiating your contract:

Two of the main tips here are to develop your negotiation skills and to get your contract in writing.  No matter how nice or honest a client appears, you do not want to take the risk of someone “forgetting” the deal to which you both agreed prior to you doing the work.

This brings us to the delicate issue of setting a consulting fee.  Of course you do not want to over price yourself, but you also need to be able to pay your bills and have some money left over for savings and spending. Michael shared with us that one of the mistakes he made as a new consultant was failing to account for having to pay his own taxes, healthcare and retirement savings. In general, he advised estimating ~30% above what your salary would be if you were employed by a company. If you aren’t sure what average salaries are for people employed in your area of expertise, you can find out by using online sources, such as PayScale, Glassdoor, Monster and many others. When doing this, use more than one source and be mindful of the job location to be sure the number is reasonably accurate.

The key here is to be sure how much your time is worth before entering into a contract fee negotiation. Michael also advised to keep in mind who your client is and adjust up or down based on what they can afford. It is also fine to ask for more and negotiate down, but know your lower limit. Of course, with each kind of client there come different challenges. One specific example Michael provided was that when working for academic clients, one issue in getting your desired fee could be that it is higher than the salary of the PI who is hiring you, which would be difficult for them to justify. In this case he suggests compensating for the lower salary by asking for additional money to cover travel or equipment, which will be tax deductible business expenditures.

Determining which jobs to take and which to decline is a balancing act between the amount of time and effort you will need and want to devote to a project and how much money they want to pay you to get the job done. Another thing to consider in negotiating your contract is whether to set your fee based on the project or by the hour. If by the project, you should have a reasonable estimation of how much time it will take you to complete so you do not end up shorting yourself.

Finally, Michael also advised keeping your long-term goals in mind when setting your contract parameters. While you may be excited to be self-employed, you may not want to remain so forever. In the event you do decide to return to work for someone else, whether in academia or industry, you will want a publication record – including posters, papers and patents – to which you contributed.  Along this line, when you agree to do work for someone at a company or a University, be sure you are clear on what you are agreeing to give them. Michael cautioned us to verify the contract distinguishes between using your intellectual property for someone and developing intellectual property for them. The difference is in who owns your work when you are done! One thing to avoid is accepting equipment, such as a work computer or email address, from a client as any work done using this equipment, including emails, will belong to them. Michael again emphasized the need to know what you want and to what you are agreeing when negotiating your contracts.

Formalizing your business:

Be sure to know the different types of business before committing to one.  Michael recommends going with a LLC (limited liability company) over a sole proprietor option.  The main reason?  Going with sole proprietor makes all of your personal assets vulnerable if a client decides you did not fulfill your contract obligation and sues you.  With an LLC, you open a separate bank account to use for all business expenses, and only the money and assets associated with this account are at risk in a lawsuit. (For more information on this, click here.)  Michael also recommends using Legal Zoom, as it is a user friendly, affordable tool for getting the appropriate paperwork together for your business.

In Summary:

Overall, Michael provided us with some valuable advice regarding a career option many of us may have overlooked or been too intimidated to consider.  Even if you prefer to work for someone else, these tips can help you be more attractive as an applicant.  Thanks, Michael, for taking your time to share your expertise.

 

The amazing QQS!

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Published on: July 13, 2016

On the final morning of the recent ICAR2016 meeting attendance was rather low, seemingly after a heavy karaoke-filled night! However those that got out of bed had to pleasure of attending the excellent ‘Plant Biotechnology’ session, which provided great insights into the process of developing and bringing plant products to the market.

However for me it was a more ‘conventional’ presentation that was a real eye-opener. Li Ling from Iowa State University introduced the QQS gene that is an orphan gene only present in Arabidopsis. This small loci has no previously characterised domains and was identified during expression analysis of genes that are upregulated in a strach synthase mutant. Although it is small and mysterious, the QQS gene appears to play a remarkably role in the control of plant carbon-nitrogen balance. Arabidopsis plants that overexpress QQS show a significant decrease in leaf starch content and an associated increase in overall leaf protein content. This occurs without any phenotypic change or yield penalty.

Li Ling subsequently overexpressed QQS in soybean and also showed, even though plants were again morphologically identical to wildtype, an increase in seed protein and only a slight decline in seed oil content. Remarkably this is occuring in plants that have been previously ‘seen’ the QQS gene and this effect occurs independent of growth location (greenhouse, field) or soil nitrogen content. Similar results have been also found when QQS is overexpressed in maize and rice.

N change in Soybean QQS OX. From: http://onlinelibrary.wiley.com/doi/10.1111/pbi.12238/abstract
N change in Soybean QQS OX. From: http://onlinelibrary.wiley.com/doi/10.1111/pbi.12238/abstract

In more recent experiments Ling and co-workers discovered that QQS acts upstream of the AtNF-YC4 gene in Arabidopsis and that overexpression of AtNF-YC4 also causes an increase in protein content and a decrease in starch. Soybean, maize and rice each contain orthologs of AtNF-YC4, demonstrating that the signalling module is preserved in these distantly related crops. Li mentioned that attempts to modify the expression NF-YC4 in crop plants using gene-editing techniques are at an advanced stage, which will hopefully lead to the generation of transgene-free plants that have increased protein content. Furthermore Li reported that the QQS:NF-Y4 module influences multiple aspects of the response to pathogens, work which will be published soon and further demonstrates the pleiotropic nature of QQS function.

From http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664325/
From http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664325/

Overall the QQS gene has remarkably potential for use in experiments that aim to generate plants with altered C/N balance. It seems that even though Arabidopsis, soybean, maize and rice are evolutionarily divergent, they each retain the ability to respond to the QQS protein via the NF-YC4 signaling module.

As the authors state, the yield-altering effects of this response pathway have broad societal importance and hopefully can be used in the generation of crops with different nutritional attributes.

On a smaller scale, this work with an orphan gene should also offer encouragement to researchers who have identified a gene with ‘no known function’ from their particular mutant screen! If you persevere, you never know where it might lead!

 

Arabidopsis Research Roundup: July 11th

After a conference break the Arabidopsis Research Roundup returns with an outstanding selection of papers from UK (and mostly Scotland-based) researchers. Firstly Levi Yant provides an audio description of work that has identified important loci for adaption to harsh environments. Secondly John Doonan leads a multi-national group investigating the role of eiF4A phosphorylation within proliferating cells. Next two Scottish-based studies both investigate aspects of light signalling on different scales: a Glasgow-based consortium dissects the UVR8 signaling module while the role of phytochrome on global carbon allocation is studied by Karen Halliday’s group in Edinburgh. The final paper also involves significant Scottish involvement with Piers Hemsley at Dundee together with Simon Turner at Manchester investigating the role of s-acylation in the activity of the cellulose synthase complex.

Arnold BJ, Lahner B, DaCosta JM, Weisman CM, Hollister JD, Salt DE, Bomblies K, Yant L (2016) Borrowed alleles and convergence in serpentine adaptation. PNAS http://dx.doi.org/10.1073/pnas.1600405113 Open Access

New investigator at the John Innes Centre, Levi Yant, is the corresponding author on this study that also includes contributions from the labs of Kristen Bomblies and current GARNet Chairman David Salt. This investigation uses GWAS techniques to identify loci in Arabidopsis Arenosa that are important for growth on serpentine barrens, which are characterised by drought, mineral paucity and high levels of heavy metals. They showed that polygenic multi-trait genomic locations are important for serpentine adaptation. The authors reassessed previous independent datasets and showed that 11 loci have been identified across these studies and are therefore good candidates as drivers of convergent evolution. This study provides evidence that certain A.arenosa alleles have been introgressed from A.lyrata and that these may facilitate adaptation to a multi-hazard environment.

Levi kindly provides a short audio description of this work, that also touches on ionomics and data reuse!

Bush MS, Pierrat O, Nibau C, Mikitova V, Zheng T, Corke FM, Vlachonasios K, Mayberry LK, Browning KS, Doonan JH (2016) eIF4A RNA Helicase Associates with Cyclin-Dependent Protein Kinase A in Proliferating Cells and is Modulated by Phosphorylation Plant Physiol. http://dx.doi.org/10.1104/pp.16.00435 Open Access

eif4apic
Growth of phospho-null or phospho-mimetic mutants of eif4a1

John Doonan (Aberystwyth) is the leader of this wide collaboration of UK, US, Czech, Greek and Chinese researchers that investigate the interaction of the eIF4A RNA helicase with cyclin-dependent protein kinase A (CDKA). This interaction only occurs in proliferating cells where CDKA acts by phosphorylating specific amino acids on eIF4A. Throughout in vivo and in vitro experiments using phospho-null and phosphor-mimetic version of eIF4A, the authors show that phosphorylation acts to downregulate eIF4A activity, subsequently altering the efficacy of translation.

 

Heilmann M, Velanis CN, Cloix C, Smith BO, Christie JM, Jenkins GI (2016) Dimer/monomer status and in vivo function of salt-bridge mutants of the plant UV-B photoreceptor UVR8. Plant J http://dx.doi.org/10.1111/tpj.13260 Open Access

This exclusively University of Glasgow study is led by John Christie and Gareth Jenkins. Dimeric UVR8 is a UV photoreceptor that after UV-B interaction dissociates into monomers, which interact with COP1 to begin signal transduction. The UVR8 dimer develops through the formation of salt-bridges between individual UVR8 proteins. In this study the details of the dimerization are dissected, showing that several salt-bridge amino acids are necessary for the multiple functions of both the UVR8 dimer and monomer. Interestingly the authors show that UVR8 with conservative mutations of Asp96 and Asp107 to Asn96 and Asn107 are unable to form dimers yet retain wildtype responses to UV-B. This shows that monomeric UVR8 has the ability to normally initiate a signal transduction pathway and complicates our understanding of the in vivo role of the UVR8 dimer.

Fresh_Weight
Phy mutants have reduced biomass. Taken from: http://www.pnas.org/content/113/27/7667.abstract

Yang D, Seaton DD, Krahmer J, Halliday KJ (2016) Photoreceptor effects on plant biomass, resource allocation, and metabolic state. PNAS 113(27):7667-72 http://dx.doi.org/10.1073/pnas.1601309113

Karen Halliday (Edinburgh) is the corresponding author on this investigation into the broader impact of Arabidopsis phytochromes on carbon allocation and biomass production. Even though phytochrome mutants have reduced CO2 uptake they overaccumulate resources into sucrose and starch and show altered day:night growth rates. Overall this leads to reduced growth coincident with reduced expression of CELLULOSE SYNTHASE-LIKE genes. The authors demonstrate that phytochromes play a significant role in the control of biomass allocation and that they additionally differentially respond to external stresses. Evolutionarily this indicates that modification of phytochrome expression might be an important mechanism for responding to changing environments.

Kumar M, Wightman R, Atanassov I, Gupta A, Hurst CH, Hemsley PA, Turner S (2016) S-Acylation of the cellulose synthase complex is essential for its plasma membrane localization. Science. 353(6295):166-9 http://dx.doi.org/10.1126/science.aaf4009

Simon Turner (Manchester) and Piers Hemsley (James Hutton Institute, University of Dundee) lead this research which amalgamates the work from their individual labs and assesses the role of S-acylation on the activity of cellulose synthase complex (CSC). They show that core subunits of the CSC, cellulose synthase A (CESA) proteins, require s-acylation for their localisation to the plasma membrane, which is necessary for their in vivo activity. The authors estimate that a CSC might contain over 100 S-acyl groups, which could significantly alter its hydrophobicity and its interactions within the membrane environment.

CESpic
CES localisation: Taken from http://science.sciencemag.org/content/353/6295/166.full.pdf+html
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