December 5, 2022

🌻 The Week in Botany December 5, 2022

It’s taken longer than usual to compile this week’s newsletter. This is partly due to bronchitis, which has kept me from sleeping. Additionally, every time I opened Substack to work on the newsletter, the office manager would want to play with a feather, eat some kitten biscuits or else want scratching under his chin. But the biggest time sink is a change in how I’m handling the Careers section.

I’m now adding the jobs and funded projects to a Jobs section on the Botany One website. From next week, I plan just to list the new jobs below, rather than anything I see shared. It means that if you’re following Botany One on Twitter, Mastodon, or Tumblr then you should be able to see these jobs appear earlier.

An event to watch out for this week is the final New Phytologist Now webinar of 2022. Tansley Medal winner Jana Sperschneider will be talking about Machine learning in plant–pathogen interactions: empowering biological predictions from field scale to genome scale on Wednesday December 7, at 09:00 UTC. You can also see their previous seminars on their Cassyni channel. Cassyni seems much better equipped for displaying presentations than a vanilla platform like YouTube or Vimeo. The ability to flip back to a specific slide is very helpful, and the captions (that I’ve seen so far) seem accurate. The archive is well worth a look.

I’ll be back at the same next week, with more of the stories you’re sharing on Twitter and Mastodon. Until then, take care.

Alun (webmaster@botany.one)

News and Views

Climate change: Could centuries-old wheat help feed the planet?
Could the key to feeding the world with a changing climate be hiding in a 300-year-old museum collection? That's one of the hopes of scientists combing through 12,000 specimens of wheat and its relatives held in the Natural History Museum's archives.

Vihreät kannattaa GMO-sääntelyn purkamista (The Greens support the dismantling of GMO regulation)
The Green party council supports the dismantling of the regulation on genetically modified organisms (GMO). The party council approved an updated agricultural political program, which states that breeding methods using genetic technology should be regulated in the same way as traditional breeding methods.
Auto-translated to English from Finnish.

Increasing crop yields by breeding plants to cooperate
A simple breeding experiment, combined with genetic analysis, can rapidly uncover genes that promote cooperation and higher yields of plant populations, according to a new study published November 29 in the open access journal PLOS Biology, by Samuel Wuest of the University of Zurich and Agroscope, Switzerland, and colleagues. The results have the potential to quickly increase crop productivity through conventional breeding methods.

The mystery of the mimic plant
There’s drama in the plant world — and a shape-shifting vine is at the center of it.

Cocaine synthesized in a tobacco plant
A team of researchers at the Chinese Academy of Sciences, working with a colleague from Syngenta Jealott's Hill International Research Centre in the U.K., has developed a way to synthesize cocaine using a tobacco plant. The group describes how they synthesized the notorious drug and possible uses for their process in their paper published in Journal of the American Chemical Society.

Native plants are bringing new life to L.A.'s ravaged areas. Here’s how to help
‘Tis the season for restoration, right? Restoring ties with family and friends, restoring faith in our fellow humans, restoring hope that somehow love can prevail ....
.... and restoring habitat in the fire-and-human-ravaged areas of Southern California (which actually sounds a lot more doable than world peace).

In praise of research in fundamental biology
Science funders must remember the value of addressing the intrinsic biological questions that help to explain the natural world.

« Il n'y pas de raison que les scientifiques fassent une cession exclusive gratuite de leurs œuvres aux éditeurs »
The CNRS now asks its researchers to apply the strategy of non-assignment of copyright when submitting their articles to publishers.
Auto-translated to English from French.

Rain garden roll-out expands in Dublin's inner city
A project which offers a nature-based solution to urban water problems is expanding in Dublin. Social enterprise Bí Urban is aiming to install 100 rain garden planters in the north inner city following the success of a pilot project in Stoneybatter last year.

In Canada, scientists are struggling with stagnant funding
Lackluster growth in federal spending squeezes research community

‘Citizen rewilders’ invited to buy shares in Scottish Highlands projects
Firm restoring nature on two estates hopes to give ordinary investors 5% annual return over 10 years.

A UK tree provides hundreds of pounds of benefits a year, report finds
Trees standing alone and in small groups worth billions to UK, which researchers say justifies spending to protect them.

Gardening: What a walk around the block revealed about these plants
Walking in my neighborhood the other day, I saw two sights worthy of mention here. One carries with it a cautionary note and the other an opportunity for adding a distinctive ornamental touch to your garden.

New garden, greenspace attraction opens at Winnipeg’s Assiniboine Park
Canada’s newest horticultural attraction opened to the public at Assiniboine Park in Winnipeg on Saturday. It’s called ‘The Leaf’ and features 30 acres of new gardens and greenspace, complete with trees, shrubs, flowers, and other plant life that is flourishing in four indoor biomes.

Scientific Papers

RNAlysis: analyze your RNA sequencing data without writing a single line of code
Teichmann et al. have developed RNAlysis, a modular Python-based analysis software for RNA sequencing data. RNAlysis allows users to build customized analysis pipelines suiting their specific research questions, going all the way from raw FASTQ files, through exploratory data analysis and data visualization, clustering analysis, and gene-set enrichment analysis. RNAlysis provides a friendly graphical user interface, allowing researchers to analyze data without writing code.

PICLN modulates alternative splicing and light/temperature responses in plants
Plants undergo transcriptome reprogramming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. Ion Chloride nucleotide-sensitive protein (PICLN) is part of the methylosome complex in both humans and Arabidopsis (Arabidopsis thaliana), and Mateos et al. show here that the human PICLN ortholog rescues phenotypes of Arabidopsis picln mutants.

The establishment of plants following long-distance dispersal
Wu et al. integrate quantitative long-distance dispersal frameworks with phylogeographic tools to provide a general framework for estimating the probability of colonizing a new site. This integration between biogeography and movement ecology is expected to yield important new tools and insights into the interplay between ecology, evolution, and biogeography in shaping patterns of biodiversity.

Increasing plant group productivity through latent genetic variation for cooperation
Wuest et al. developed a general and simple method for the discovery of alleles promoting cooperation in plant stands. Their method is based on the game-theoretical premise that alleles increasing cooperation benefit the monoculture group but are disadvantageous to the individual when facing noncooperative neighbors. Testing the approach using the model plant Arabidopsis thaliana, they found a major effect locus where the rarer allele was associated with increased cooperation and productivity in high-density stands.

The incongruity of validating quantitative proteomics using western blots
Similar to the age-old reviewer request for quantitative PCR validation of RNA-sequencing data, nearly every researcher who uses proteomics technologies has at one time or another been asked by a reviewer to provide ‘western blot validation’ of their mass-spectrometry-based protein abundance data. Mehta et al. believe that this request demonstrates a lack of awareness amongst the plant biology community about the extraordinary improvements in cost, sensitivity and reliability that the field of mass-spectrometry-based proteomics has made in recent years.

Smart reprograming of plants against salinity stress using modern biotechnological tools
Raza et al. highlight advances in modern biotechnological tools, such as omics (genomics, transcriptomics, proteomics, and metabolomics) approaches and different genome editing tools (ZFN, TALEN, and CRISPR/Cas system) for improving salinity tolerance in plants and accomplish the goal of “zero hunger,” a worldwide sustainable development goal proposed by the FAO.

Plant environmental sensing relies on specialized plastids
Mackenzie and Mullineaux review the plastid biology literature in light of recent reports supporting a class of ‘sensory plastids’ that are specialized for stress sensing and signaling. Abundant literature indicates that epidermal and vascular parenchyma plastids display shared features of dynamic morphology, proteome composition, and plastid–nuclear interaction that facilitate environmental sensing and signaling. These findings have the potential to reshape our understanding of plastid functional diversification.

Why do plants silicify?
Si plays a significant role in many aspects of plant ecology, but major gaps prevent us from understanding why this trait has been selected for and has contributed to the success of specific clades.

Structure, biochemical function and signaling mechanism of plant NLRs
To counter pathogen invasion, plants have evolved a large number of immune receptors including membrane-resident pattern recognition receptors (PRRs) and intracellular nucleotide-binding and leucine-rich repeat receptors (NLRs). In this review, Wang et al. first discuss structural and biochemical mechanisms of the non-canonical NLR Ca2+ channels, and then summarize our knowledge on immune-related Ca2+-permeable channels and their roles in PRR and NLR signaling. They also discuss a potential role of Ca2+ in the intricate interaction between PRR and NLR signaling.

How to improve scaling from traits to ecosystem processes
The foundation of trait-based ecology (TBE) is built on trait–environment relationships. Strong tests of TBE require approaches that effectively and explicitly elucidate the links between phenotypes, differential fitness, community assembly, and ecosystem functioning. Testing the assumptions and mechanisms underlying these links will resolve current debates about the merits of TBE and advance the promise of a more predictive science.

Endosperm cellularization failure induces a dehydration stress response leading to embryo arrest
Xu et al. show that triploid Arabidopsis thaliana embryos surrounded by uncellularized endosperm mount an osmotic stress response that is connected to increased levels of abscisic acid (ABA) and enhanced ABA responses. Impairing ABA biosynthesis and signalling aggravated triploid seed abortion, while increasing endogenous ABA levels as well as the exogenous application of ABA induced endosperm cellularization and suppressed embryo growth arrest.

Different combinations of laccase paralogs nonredundantly control the amount and composition of lignin in specific cell types and cell wall layers in Arabidopsis
Blaschek et al. show that combinations of multiple individual laccases (LACs) are nonredundantly and specifically required to set the lignin chemistry in different cell types and their distinct cell wall layers. We dissected the roles of Arabidopsis thaliana LAC4, 5, 10, 12 and 17 by generating quadruple and quintuple loss-of-function mutants. Loss of these LACs in different combinations led to specific changes in lignin chemistry affecting both residue ring structures and/or aliphatic tails in specific cell types and cell wall layers.

Capture of mammal excreta by Nepenthes is an effective heterotrophic nutrition strategy
The collection of mammal faeces clearly represents a highly effective strategy for heterotrophic nitrogen gain in Nepenthes. Species with adaptations for capturing mammal excreta occur exclusively at high elevation (i.e., are typically summit-occurring) where previous studies suggest invertebrate prey are less abundant and less frequently captured. As such, Cross et al. propose this strategy may maximise nutritional return by specialising towards ensuring the collection and retention of few but higher-value N sources in environments where invertebrate prey may be scarce.

Careers

International Undergraduate Summer School, UK
Subject to the ongoing Covid-19 pandemic, the John Innes Centre are planning to run the 2023 International Undergraduate Summer School from 26 June to 18 August 2023. Applications for the 2023 summer school will close Monday 16 January 2023.

PhD Fully Funded in Ecosystem Service Modelling at Wageningen University, Netherlands
In this project you will investigate how satellite data from various sources in combination with spatial models can be used to develop ‘ecosystem accounts’. Ecosystem accounting is a new, ground-breaking methodology to help understand, monitor and asses the contributions of ecosystems to the economy. Much progress has been made in ecosystem accounting in recent years, and the methodology is now a UN standard that is being applied in at least 40 countries world-wide. At the same time, some methodological challenges remain. Several of these challenges are being addressed by PhD research projects in the ESA group.

Biological Science Technician (Botany), Oregon
The U.S. Geological Survey's Forest and Rangeland Ecosystem Science Center out of Corvallis, Oregon is seeking to hire 4 technicians that will work on a project to investigate the long-term ecological impacts of fuel reduction treatments in the intermountain sagebrush steppe and western juniper woodlands.  Find out more about the project at (www.sagestep.org).

Associate/Full Professor - Plant Biology, Berkeley
The Department of Plant and Microbial Biology in the Rausser College of Natural Resources at the University of California, Berkeley (UCB) seeks applications for a faculty position in plant biology (senior leadership, open discipline). This position may be filled at the tenured Associate or Full Professor level. Rank will be determined based on qualifications and experience.

Professorship of Plant Development, Cambridge
Candidates will have an outstanding research record of international stature in Plant Development with a strong interest in interdisciplinary work. The position is open to everyone who meets the requirements, including both established professors and earlier career group leaders looking for the next stage in their development. They are expected to have the vision, leadership, experience and enthusiasm to build on current strengths at the Institute and to help maintain and further develop its leading research profile. Duties include research, the training of students, the supervision and mentoring of postdoctoral fellows, as well as some teaching and administration. The Professor will be based in Cambridge.

Distinguished Professorship (Associate or Full Professor) – Vegetable Crop Pathology, University of Georgia
The successful candidate will develop a vigorous, innovative, internationally recognized, and extramurally funded research program in the area of vegetable crop pathology. The incoming faculty member is expected to develop and translate new knowledge in microbial and plant biology, genetics, genomics, and host resistance into novel disease management approaches with a focus on soilborne oomycete and fungal pathogens. Opportunities abound for collaborations with crop breeders/geneticists and with strong programs in pathogen biology, disease management, disease ecology and epidemiology, host resistance, and pathogen and population genetics in the Department of Plant Pathology.

Assistant/Associate Professor in Botany/Plant Ecology
Southeastern Oklahoma State University’s Department of Biological Sciences invites applications for a tenure track faculty position in the area of Botany at the Assistant / Associate Professor level.

Assessing the Environmental Benefits and Educational Value of Tree-Planting Projects in Schools, University of Essex.
This fully funded Masters by Dissertation project is ideal for someone who is enthusiastic about understanding and protecting the environment, and wants to contribute to society by interacting with school children, teachers and the wider community. You should have a good undergraduate degree in the area of environmental or biological sciences.

Postdoctoral Research Assistant, QMUL
Applications are invited for a Postdoctoral Research Assistant based at the School of Biological and Behavioural Sciences (SBBS), Queen Mary University of London. The Plant Cell and Molecular Biology group at SBBS, led by Dr Guy Hanke, is running a 3-year BBSRC funded project to better understand the function of photosynthesis in developing seeds of cereals, with a focus on barley. This involves genetic manipulation of barley, proteomics, electron and fluorescence microscopy and various techniques for measuring photosynthesis.

Postdoctoral Researcher, John Innes Centre
We are looking for a Postdoctoral Researcher to investigate interactions between circadian rhythms in bacteria and plants, in the laboratory of Professor Antony Dodd.

Assistant Professor (Quantitative Biologist), University of Hawaii at Manoa
The position is permanent, full-time (9-month), general funds and tenure-track to begin approximately August 2023 or as soon thereafter as possible. Review of applications will be on January 1, 2023 and will continue until the position is filled.   Our department and university have a strong commitment to recruit and retain diverse applicants. We encourage women and members of underrepresented groups to apply.   The School of Life Sciences (SoLS) at the University of Hawai‘i at Manoa welcomes applications for the position of Assistant Professor in Quantitative Biology. Candidates whose research incorporates plant diversity and systematics, marine biology, or conservation are particularly encouraged to apply, but candidates with research programs in any area of the life sciences will be considered.