We’ve had some queries about why we follow who we do on Twitter, as we follow quite a few people. We also occasionally get asked by some people why we’re not following them. So here’s some explanation.

There a couple of reasons why we follow people on Twitter. One is to keep track of the zeitgeist. We track what is getting shared on Twitter to see what matters in botany. When n people share the same paper or news item a scanner sends a ping to us. That way we don’t have to be awake if a story catches some people’s eye when we’re asleep. Making that sample as bigger rather than smaller means that a small interest group isn’t going to skew what we find.

Who we follow

People who tweet links to news stories with some botany interest, or links to plant science papers. First though, we have to know that these people exist. The way we tend to find these people is they follow us. If we get a notification abc123 is following you, then we’ll look to see what abc123 is interested in, and if we see some botany links near the top of the profile we’ll follow them.

Another way to catch our attention is to retweet something we’ve posted. It doesn’t have to be one of our tweets. It could be something we’ve retweeted. That’s a little less likely to catch our attention, but it happens.

Who we don’t follow

People whose tweets are mainly politics. We actually think it’s a good thing for scientists to be politically engaged, so socially tweeting politics is good. However, Twitter is a tool for botany for us, so filling the scanner with political tweets is just going to make finding the botany more difficult.

Another kind of account we don’t follow from @botanyone is an account that mainly tweets photos of plants someone has seen. Again, that’s not supplying links into the system. On the other hand, we would follow an account like that on Instagram, where we have the handle @botany_too. If you think we should be following your Instagram account, then leave a comment below — or on one of our images on Instagram.

Finally, we tend not to follow gardening accounts. We like gardening and think more gardeners would be good thing — but gardening tends to be quite local interest. For example, I have a friend in Arizona who is interested in xeriscaping, to avoid using additional irrigation. In a Welsh garden often the problem is an excess of water instead of a lack. We probably don’t have much in common in the garden. However, a lot of gardeners have an interest in plants beyond their own patch, so being a gardener doesn’t you out from our follow list. It just doesn’t automatically put you on it either.

If you’re not followed, please don’t take it personally. @botanyone doesn’t follow either of my personal accounts because I’m far more likely to tweet about Formula E, or Welsh politics than botany on them.

What do we do with these links?

Not as much as we should. When I’m not busy and paying attention to the windows in the background, I’ll retweet things that are becoming popular. I’ll try to find the original tweeter to retweet when I see that.

We also compile the most popular links into our weekly email, The Week in Botany. On a Monday morning, I send out what we’ve posted to Botany One, the most popular news links, and paper links in an email. If you’ve seen an alert about an email list on the site, that’s what it’s about. Somewhere on my to-do list is find a way of getting breaking twitter news on to the site in a timely way. That’s not a small task.

The second reason is that by choosing the people we do, if I’m having a lousy day then I don’t have to look far in the @botanyone stream before I find someone who’s doing something interesting.

There are many ways of using Twitter. If we’re not following you, it’s not that we think you’re using Twitter the wrong way, just that we’re using it in a different way to you. Of course if you think we’re using Twitter the wrong way, you’re welcome to leave a comment below or tweet us.

Originally published at Botany One.

Why are/aren’t we following you on Twitter? was originally published in Alun Salt on Medium, where people are continuing the conversation by highlighting and responding to this story.

Every so often you find a new site, and then discover everyone else has known about it for years. For once, this is a site I’ve known about for ages — but it seems not everyone else has. So for those of you who don’t know — if you’re interested in science blogging, you should be following ScienceSeeker.

ScienceSeeker is a site that’s been going since 2011 and the first Science Blogging conferences. It’s not a science blog itself. It’s a site that aggregates science blogging. For example here’s the Plant Science bundle, which is a bit patchy as some sites are a bit generalist, but it does help keep an eye on what’s happening. From the Biology bundle, I found this post on the Hereford Pomona, at the Biodiversity Heritage Library. If you’re looking for new sites to visit, then this curated collection of sites is an excellent place to start.

However, if you’re a blogger — or a plant podcaster — then I think you should also be looking at this as a place to get listed. We tend not to get too many visits from these bundles. But when we’ve been one of the picks of the week on the blog, there has been a measurable uptick in traffic.

You can follow ScienceSeeker via their mailing list, Facebook or Twitter. If you’re looking for general science reading it’s an excellent place to start.

Sadly the other site that used to aggregate science blogging, ResearchBlogging.org, remains inactive.

Originally published at Botany One.

Seeking Science? See ScienceSeeker was originally published in Alun Salt on Medium, where people are continuing the conversation by highlighting and responding to this story.

Not all honey is equal. New research by Clearwater and colleagues has been looking how mānuka nectar, an essential ingredient of mānuka honey, is affected by various factors such as temperature, drought and even the genes of mānuka (Leptospermum scoparium, Myrtaceae) plants.

Understanding the composition of the nectar is important because of how bees make honey. They take nectar from flowers and store in their crop, specialised foregut. Here, it’s partially digested. When a bees arrives back in the hive, she passes on the nectar by regurgitating it, and the next bee passes it along and so on, until the fluid is eventually stored in a honeycomb. It’s then fanned to evaporate the excess water from it to become honey. The qualities of the honey therefore depend on the qualities of the nectar. For example, eating a lot of rhododendron honey is a Very Bad Idea.

In contrast, there is a lot of demand for mānuka honey. New Zealand produces 1700 tons of mānuka honey a year, of which 1800 tons is consumed by the UK alone. The driver for this fraud is the possible health benefits of mānuka honey. While the science is not conclusive, there are reasons to think that mānuka honey could have health benefits as an antibiotic treatment.

The non-peroxide antibacterial activity of mānuka honey originates from dihydroxyacetone, a saccharide, present in the floral nectar. When the nectar becomes honey the dihydroxyacetone becomes methylglyoxal — and this is the antibacterial agent. The causes of variation in nectar composition and the origin of the dihydroxyacetone are unknown. Clearwater and colleagues examined how the nectar yield and composition of mānuka varied with temperature, among genotypes, and as flowers develop because of differential secretion and reabsorption of the various nectar components.

Different varieties of mānuka have different genes, so the scientists started by selecting six mānuka genotypes. They planted the plants and grew them without nectar-feeding insects. They measured how the flowers developed and the composition of the nectar in the flowers at various stages of development. They also stressed some of the plants by restricting water and compared them with their better-watered neighbours to see how this affected the nectar.

What they found was that there was nectar almost as soon as the flowers opened until the petals started falling off the flowers. There wasn’t always the same amount of sugars in the nectar though — which suggests that some of the plants reabsorbed some of their nectar when no insects came for it. They also found that the ratio of sugars to dihydroxyacetone varied according to the genotype of the mānuka plant, so it would seem that not all plants are as good for the honey. They also found that the stage of flower development was important too, meaning that for the best yields you’d want to catch the right plants at the right time. It’s not surprise there are problems with cowboy apiarists roaming New Zealand.

As for the magic ingredient, Clearwater and his team found the amount of dihydroxyacetone per flower only weakly correlated with the amount of other sugars. The authors think this means that the dihydroxyacetone probably has a different source in the flower to the other sugars.

For now mānuka isn’t giving up all its secrets.

Originally published at Botany One.

What is it that gives mānuka floral nectar its unique composition? was originally published in Alun Salt on Medium, where people are continuing the conversation by highlighting and responding to this story.

What is in the air that you breathe at home? It’s mostly nitrogen. There’s a significant amount of oxygen, along with some other chemicals. There are certainly some you’d want to track. For example, carbon monoxide is something you’d want to know about. That’s why you probably have a carbon monoxide detector. But what about other chemicals?

A new paper by Wilson and colleagues Phytoforensics: Trees as bioindicators of potential indoor exposure via vapor intrusion examines exposure to volatile organic compounds, known as VOCs, that are increasingly causing concern for environmental health.

The problem comes from organic compounds that leech into groundwater from industrial processes, like poor waste management. This pollution contaminates groundwater. The problem isn’t then about drinking water, but about the compounds evaporating from the water to become a health hazard as gas.

The usual method to see if a residence is at risk from VOCs is Sub-slab sampling, examining the soil beneath the foundations of a house to see if there is a build-up of VOCs that will then escape into the house and the air. The effectiveness of the sampling is going to vary by season and also by luck. The sub-slab environment can be very variable in VOCs, and the sample volume is relatively low. If the sample is taken from the wrong place, a danger could be missed.

What Wilson and colleagues have examined is how trees react to VOCs. If they’re in a residential area, then their groundwater is comparable to the groundwater in sub-slab environments. Their sample volume, however, is defined by their root system. The roots mean that trees are less likely to be troubled by the luck of the draw regarding VOC hotspots. But do trees process VOCs in a way that can be tracked meaningfully?

Wilson and co-authors find that the answer is yes — but trees bring their own problems. You can place probes where you like — and that’s likely to be around the area that you think has a problem. It might seem a bit silly to say so, but you can only sample trees where the trees are growing. If your local administration has removed trees to tidy things up, then your record of VOCs in the soil has gone. However, where you can use them, trees seem staggeringly useful. Wilson et al report:

The rapid and non-invasive nature of tree sampling are notable advantages: even with less than 60 trees in the vicinity of the source area, roughly 12 hours of tree-core sampling with minimal equipment at the PCE Southeast Contamination Site was sufficient to delineate vapor intrusion potential in the study area and offered comparable delineation to traditional sub-slab sampling performed at 140 properties over a period of approximately 2 years.

This, they argue, means that a tree survey could identify where to expect problem areas and, if needed, you can target your probes more effectively. If probes are turning up odd results, the tree data would also suggest which probes might need re-siting.

It seems that the water trees drink can help track the quality of the air you breathe.

Originally published at Botany One.

Can Trees Track the Air that You Breathe? was originally published in Alun Salt on Medium, where people are continuing the conversation by highlighting and responding to this story.

Originally published at Botany One.

Poképlants was originally published in Alun Salt on Medium, where people are continuing the conversation by highlighting and responding to this story.

Ben Goldacre’s book title I Think You’ll Find it’s a Bit More Complicated Than That, could easily be taken as a motto for botany. One example I’ve seen today is an opinion piece in Molecular Plant Pathology that looks at what plant pathogen effector proteins are doing.

Nick Snelders and colleagues ask if we should look at plant pathogen effector proteins as manipulators of host microbiomes, and along the way if we should be taking a different view on what effectors are.

If you’re wondering what an effector is Snelders et al. say: “According to the initial, narrowest, definitions, effectors are small, cysteine-rich proteins that function through the manipulation of plant immune responses.” What happens is a microbe wants to invade a plant, but there’s not much point doing that if it’s guaranteed to get killed in the process. So what it does is secrete molecules to interfere with plant immunity.

If you know more about plant pathology than me (nearly everyone), then you’ll not be happy with this definition. Snelders and his co-authors note that these molecules are doing a lot more than just effecting the immunity, and that there are other kinds of molecules pathogens use to fight the plant. So they note instead that: “effectors should be defined as microbially secreted molecules that contribute to niche colonization.”

They don’t mention plants in this new definition, and that’s no accident.

It’s easy to focus on the plant-pathogen interaction, that’s probably why we’re interested in the microbe in the first place, but that’s not the only interaction the pathogen has. There’s likely to be quite a microbial community around the roots of a plant, and that’s a competition for resources. Instead of looking for plant immunity effectors, Snelders et al. argue we should be looking for three types of effector. The first is obviously the effectors targeted at plants. There’s a second, aimed at plants and microbes. The example they give is the Zt6 effector from the wheat pathogen Zymoseptoria tritici.

The final category they have are effectors that a pathogen aims at other microbes. They point out that weakening a plant by removing some of its microbial support could indirectly aid colonisation of the new plant.

I can see that this is a perfectly reasonable idea, but it also looks much more difficult to investigate. It means that looking at the plant is no longer enough and there’s a lot of diversity to tackle to examine microbe-microbe interactions. What makes the paper more than merely interesting is that the authors acknowledge this does look like a problem, but they also show how you might go about tackling it.

“Subsequently, functional screens aimed to determine their direct effect on other microbes should reveal whether or not the effector candidates have potential microbiota-manipulating abilities. An initial (and potentially overlooked) medium- to high-throughput screen might be to first test whether candidate proteins can be expressed in either prokaryotic or eukaryotic recombinant expression systems. Our recent discovery of the multifunctional Zt6 effector from Z. tritici initially came from our inability to express full-length recombinant protein in either Escherichia coli or Pichia pastoris expression systems, potentially due to toxicity (Kettles et al., 2017).”

Studying this means we getting a better idea of how pathogens are attacking plants, but Snelders and colleagues conclude with one more idea. These effectors are toxic to microbes, so how to the pathogens — which are microbes themselves — survive them? If you can understand the biochemistry around that, then you can start making novel advances in pathogen control.

Both papers below are Open Access, so worth visiting if pathogens are your thing. The MPP paper is a bit too new for the DOI to work, so once that’s live I’ll update the post and remove this sentence. In the meantime there’s a direct link to the paper.

Originally published at Botany One.

What is it that plant pathogens are attacking? was originally published in Alun Salt on Medium, where people are continuing the conversation by highlighting and responding to this story.

Over the weekend we’ve been busy changing the name and the address of this site from AoBBlog to Botany One. It’s part of a process of tidying up all our social media handles. We remain a weblog owned by the Annals of Botany Company, a charity set up to promote Botany internationally. However, with this new name we might be able to do that a bit better.

The reason we took the name AoBBlog originally was that we wanted to be open that we were owned by the Annals of Botany Company. There was a reason why so many of our posts were related to papers from either Annals of Botany or AoB PLANTS. However, it’s not just those two journals that contribute posts to the blog. Thanks to Danielle Marias and Joseph Stinziano, we’ve had input from Tree Physiology for years.

We’d like to expand our coverage of research in other journals, as well increase our own independent production. But we know that some potential contributors have wondered if they have to be connected to an AoB journal. We hope the name change will reflect that we want to cover anything of interest to a plant biology audience.
Following the change of name for the blog, we’re making these other changes:

• Twitter: The blog is moving to @botanyone from @annbot. There will be a new @annbot account covering just the Annals of Botany.
• Facebook: The name has changed to Botany One instead of the Annals of Botany name we have had till now.
• LinkedIn: AoBBlog has changed to Botany One.

We also have a plan to promote older posts. Often we’ll say on Facebook that a paper will be free access after a year. It’s a policy that plenty of other journals share. If we blog a paper that will be becoming free access, then we’ll try to repromote the post when the paper is free. We’ll be putting the posts on Instagram @botany_too and on our Tumblr Botany Too.

You’re welcome to comment and complain about the new name below. For context, names that we rejected included: Axis of Botany, Botany & Beyond, and Alright Orchid?

Originally published at Botany One.

AoBBlog and Botany One was originally published in Alun Salt on Medium, where people are continuing the conversation by highlighting and responding to this story.

We’re still at Bioenergy Genomics 2017, streaming talks when we can.

We’ll be processing these to go on to YouTube. In the meantime you can see the rushes, as it were, through the tweets and Periscope links.

Linking improved genetic and physiological understanding to deliver greater water productivity to commercial breeding programs.
The Annals of Botany Lecture — Greg Rebetzke, CSIRO Canberra, Australia

Botany One on Twitter

Linking improved genetic and physiological understanding to deliver greater water productivity to commercial breedi... https://t.co/f6TNS3s3C1

Botany One @BotanyOne

Transcriptomic analysis of interspecific diploid and triploid willow hybrids.
Larry Smart, Cornell University, USA

Botany One on Twitter

Transcriptomic analysis of interspecific diploid and triploid willow hybrids. Larry Smart https://t.co/rfi0X5h2kw

Botany One @BotanyOne

Water stress from phenomics to field: towards identifying a suitable ideotype for resilient yield in the bioenergy crop miscanthus.
Paul Robson, IBERS Aberystwyth University, UK

Botany One on Twitter

Water stress from phenomics to field: towards identifying a suitable ideotype for resilient yield in miscanthus https://t.co/d3Y1iHVRvv

Botany One @BotanyOne

The nature of the progression of drought stress drives differential metabolomic responses in Populus deltoides.
Timothy Tschaplinski, Oak Ridge National Laboratory, USA

Botany One on Twitter

The nature of the progression of drought stress drives differential metabolomic responses in Populus deltoides. https://t.co/Y0P8WprnTf

Botany One @BotanyOne

Plastic or adaptive? Linking genotype to phenotype to define an ideotype for drought tolerance in Populus nigra L.
Gail Taylor, University of California, Davis, USA and University of Southampton, UK

Botany One on Twitter

Plastic or adaptive? Linking genotype to phenotype to define an ideotype for drought tolerance in Populus nigra L. https://t.co/Qed5x9MPc7

Botany One @BotanyOne

Drought adaptation characteristics of a giant reed mutant.
Walter Zegada-Lizarazu, University of Bologna, Italy

Botany One on Twitter

Drought adaptation characteristics of a giant reed mutant. https://t.co/diMRVqZV38

https://www.pscp.tv/w/1dRKZnlwvOgKB

Morphological and physiological comparison of Arundo donax ecotypes to drought stress in the field.
Matthew Haworth, National Research Council CNR-IVALSA, Italy

Botany One on Twitter

Morphological and physiological comparison of Arundo donax ecotypes to drought stress in the field. https://t.co/0eSxzgUXMl

Botany One @BotanyOne

Originally published at Botany One.

Ideotypes for yield in a changing climate — drought stress and beyond was originally published in Alun Salt on Medium, where people are continuing the conversation by highlighting and responding to this story.

We’ll be processing these to go on to YouTube. In the meantime you can see the rushes, as it were, through the tweets and Periscope links.

Inter-Kingdom signalling — a Populus case study.
Jerry Tuskan, Department of Energy, Oak Ridge National Laboratory, USA

Botany One on Twitter

Inter-Kingdom signalling - a Populus case study. Jerry Tuskan. https://t.co/IzzGJcysqd

Botany One @BotanyOne

Brachypodium functional genomics: pan-genomics, polyploidy and a cast of mutants.
John Vogel, DoE Joint Genome Institute, USA

Botany One on Twitter

Brachypodium functional genomics: pan-genomics, polyploidy and a cast of mutants. John Vogel https://t.co/cKEPVyj4zc

Botany One @BotanyOne

Mutagenesis and genomic analysis in Arundo donax.
Silvio Salvi, University of Bologna, Italy

Botany One on Twitter

Mutagenesis and genomic analysis in Arundo donax. Silvio Salvi https://t.co/ESjYzm74iZ

Botany One @BotanyOne

Targeting the gene space using genotyping-by-sequencing with single primer enrichment technology to identify the genetic basis of drought tolerance in bioenergy Populus nigra.
Michele Morgante, IGA Technology Services, Italy

Botany One on Twitter

Targeting the gene space using genotyping-by-sequencing with single primer enrichment technology to identify geneti... https://t.co/TI3Mbf2UX3

Botany One @BotanyOne

Towards expanding biomass availability for the European bio-economy: developments in breeding, agronomy and utilisation of the Asian C4 perennial grass Miscanthus.
John Clifton-Brown, IBERS Aberystwyth University, UK

Botany One on Twitter

Towards expanding biomass availability for the European bio-economy: developments in breeding, agronomy and utilisa... https://t.co/uZqZADN7ny

Botany One @BotanyOne

De novo transcriptome assembly and comprehensive expression profiling in the bioenergy crop Arundo donax to gain insights into moderate drought stress response.
Antoine Harfouche, University of Tuscia, Italy

Botany One on Twitter

De novo transcriptome assembly and comprehensive expression profiling in the bioenergy crop Arundo donax to gain in... https://t.co/ATMzyPo7dA

Botany One @BotanyOne

The phone shut down for no obvious reason, so I had to set up a new stream. This was the second most embarrassing thing to happen today. The next part is here.

Botany One on Twitter

https://t.co/wjkVS2wlsz

Botany One @BotanyOne

The most embarrassing thing was Antoine Harfouche telling me I’d done a good job. I’ll try to splice the two parts as painlessly as possible for the YouTube version.

Originally published at Botany One.

Generating, capturing and utilising genetic variation was originally published in Alun Salt on Medium, where people are continuing the conversation by highlighting and responding to this story.

We’re at Bioenergy Genomics 2017, streaming talks when we can. We got two yesterday.

How policy makers learned to start worrying and fell out of love with bioenergy

Why hasn’t bioenergy been as successful as hoped. Raphael Slade of Imperial College, London and Maglue covers some of the policy issues regarding the promotion of bioenergy and the challenges that are ahead.

Future biomass supply for low carbon European energy provision in a changing world

Astley Hastings (speaker), Pete Smith, G, Taylor, John Clifton-Brown

European nations have committed to reduce greenhouse gas (GHG) emissions to 20% of the 1990 emissions by 2050. Most have foresworn nuclear energy in favour of energy generated by renewable sources such as tidal, wave, wind, solar, hydro and bioenergy to achieve this goal. Most renewable energy sources are intermittent or cyclic and must be complemented by dispatchable power sources to balance the intermittency of supply to the base load and to supply peak demand. Historically this dispatchable power has been provided by fossil or nuclear power which can, by varying degrees, be increased and decreased to match demand. Pumped hydro storage is also used in this way.

Of the renewable technologies bioenergy and to a lesser extend natural flow hydro have the potential provide dispatchable energy as the energy source can be stored and used as required. Bioenergy in all its forms requires biomass feedstock, whose provision requires land and suitable soil and climatic conditions for it to grow. This biomass feedstock is also required to supply other bio-economy chains which will also assist in reducing GHG emissions.

The quantity of biomass feedstock is limited by land area and the net primary productivity of this land due to the environmental conditions, which will favour the growth of different types of feedstock species, each of which have their optimum bioclimatic envelope for maximum growth and hence biomass yield. As the climate changes the geographic range of each bioenergy feedstock species will move due to changes in temperature and rainfall.

Productive land is the factor limiting the amount of biomass that can be provided as land is also required to provide food for an increasing global population and their dietary aspirations as well as providing forestry for wood products, habitats for wildlife and terrestrial carbon storage.

Originally published at Botany One.

Climate change, land availability and biomass potential. was originally published in Alun Salt on Medium, where people are continuing the conversation by highlighting and responding to this story.