š» The Week in Botany January 9, 2023
This weekās newsletter has been put together at the last minute as Iāve been away most of the week. I should be back at my desk mid-morning tomorrow. Thereās a delay, as I have to make a follow-up trip to the optician. Iāve found out that cutting caffeine out of drinks has improved my eyes. On the one hand, thatās good news - but itās going to mean staying on the decaf tea and coffee.
On my jobs list for this week, thereās writing up guidelines for new writers and also working on lesson plans for a science blogging course. I think I can probably cut ānā paste that sentence into next few emails, as they look like big tasks, but they need doing. Iām along hoping top pick up more jobs for the careers section next week, as this week is a little sparse.
Until then, take care.
Alun (webmaster@botany.one)
From Botany One
Streetlamps create an artificial summer for urban trees
The long days of summer are stretching into winter, with LED street lights replacing the retreating sun.
How to account for clonal pup mass
Modeling differences in reproductive effort between iteroparous and semelparous reproductive strategies in Bromeliaceae.
Yew Only Live Twice
Biologists have talked about bringing back extinct species like the dodo, but now botanists have drawn up a list of extinct plants that might be able to return to the wild.
Pollinators like moths are increasingly missing from a warming subarctic
The complex relationships between plants and their pollinators in subarctic Finland have changed dramatically across the last century.
News & Views
How to turn your garden into a carbon sink
From patches of wilderness to decomposing plants, turning your garden into a carbon sink isnāt just about adding lots of trees.
New Year Plant Hunt 2023: Day One
We opted to start our twelfth New Year Plant Hunt on New Year's Eve 2022, as it was a Saturday so many people were off work and free to go out plant-hunting. Weather forecasts were not great and rain stopped play in many places but neither bad weather nor even pitch darkness can stop some botanists: once again the inimitable Ger Scollard was out with a flashlight and, within minutes of the Hunt starting, had recorded Red Dead-nettle in bloom near Tralee. What a legend!
12 inquiry-based labs to explore the 12 principles of plant biology
The 12 Principles of Plant Biology are a framework to support understanding of the critical roles of plants to create, improve and sustain life. These 12 inquiry-based activities were by Jane Ellis, Mary Williams, and Jeffrey Coker with support from the ASPB Education Foundation. They were developed to support the teaching of plant biology, and are developed for use by students in middle school (approximately 11 ā 13 years old).
Download and illustrate current and projected climate data in R
Current climate data, and projections how climate may change in the (near) future, are important for various reasons. For example, such data can be used to predict how habitat suitability for different animal and plant species or agricultural productivity changes over time. Thus, in this post, I am showing how to get data on recent and projected climate directly into R, crop the obtained object to the area of interest (here: South America), and then calculate and illustrate the projected change. These data can then be used for further analyses in R.
How to do 'good' ecological research: 10 points to consider
Ten general points to consider when you are about to start a new experiment or study.
The hidden underwater forests that could help tackle the climate crisis
Kelp absorbs carbon dioxide and has high nutritional value, but it is under threat from rising temperatures, pollution and invasive species.
The Fossil Flowers That Rewrote the History of Life
Some of the worldās first flowers burned in wildfires more than a hundred million years ago. Else Marie Friis rediscovered them.
A community garden in Watts provides solace, fresh produce for immigrants
Where Esquivel grew up, in MichoacĆ”n, Mexico, he didnāt eat loroco, but here he learned to cultivate it for the Salvadorans who stuff it in pupusas and other dishes. That is the nature of this community garden, its more than 200 plots tilled by immigrants from all over Mexico and Central America. They have planted foods from their hometowns ā the leafy greens papalo and chipilin, the herb hierba mora ā sharing them with each other until one personās traditions become everyoneās.
2022: The year we built the biggest genome in Britain and Ireland
Darwin Tree of Life genomicists at the Wellcome Sanger Institute and University of Edinburgh have certainly earned an end-of-year break, having spent much of 2022 tackling a fittingly festive species. The European mistletoe (Viscum album) has the largest genome of any species from Britain and Ireland. It has now had its DNA sequenced, its genome assembled to top chromosomal-level quality, and ā following a thorough final check of our work ā will be submitted by the DToL project to public databases in the new year.
Farming Destroyed Brazilās Rain Forests. It Could Also Save Them
In a field of bare red dirt in SĆ£o Paulo state, Paula Costa is trying to turn back the clock. Five hundred years ago, this land was part of the Mata Atlantica, a dense, diverse rain forest that covered 15% of Brazil. Its trees stretched more than 2,000 miles along the eastern Atlantic coast, and far inland. But today 93% of the forest has been stripped of trees, with much of it turned over to monoculture farming. Costa, a 36-year-old biologist, bangs the ground with her fist: itās hard, the dry soil degraded by the tropical sun.
Breakthrough in plant breeding: Grafting and mobile CRISPR for genome editing in plants
A ground-breaking twist to the CRISPR toolāaka "genetic scissors"āis being put to use to edit plant genomes by scientists from the Max Planck Institute of Molecular Plant Physiology, signaling a methodology change. The discovery, recently published in the journal Nature Biotechnology, could simplify and speed up the development of novel, genetically stable commercial crop varieties by combining grafting with a "mobile" CRISPR tool.
Eelgrass: the endangered marine plant vital to keeping climate stable
Efforts under way to restore seagrass meadows capable of capturing more carbon than rainforests.
Can you eat history? This Maui hotel gardener uses plants to educate guests on Maui's culture.
Jim Heid says he has the best job in the world. He begins each workday at the Grand Wailea Maui, a Waldorf Astoria Resort, located in sunny south Maui. As the Landscaping Manager, Heid spends the day taking care of the over 600 species of plants on the sprawling 40-acre property (or as he puts it, "talking" to them), redesigning the gardens when needed and, his favorite activity, taking guests on weekly intimate, interactive tours of the property. On these tours, people can smell, touch and even taste plants likely not found outside of Hawaii.
Why 'plant blindness' matters ā and what you can do about it
A phenomenon called āplant blindnessā means we tend to underappreciate the flora around us. That can have disastrous consequences not only for the environment, but human health.
Scientific Papers
The nuclear effector ArPEC25 from the necrotrophic fungus Ascochyta rabiei targets the chickpea transcription factor CaĪ²LIM1a and negatively modulates lignin biosynthesis, increasing host susceptibility
Kumar Singh et al. describe the effector protein Ascochyta rabiei PEXEL-like Effector Candidate 25 (ArPEC25), which is secreted by the necrotroph A. rabiei, the causal agent of Ascochyta blight disease in chickpea (Cicer arietinum), and is indispensable for virulence. After entering host cells, ArPEC25 localizes to the nucleus and targets the host LIM transcription factor CaĪ²LIM1a. CaĪ²LIM1a is a transcriptional regulator of CaPAL1, which encodes phenylalanine ammonia lyase, the regulatory, gatekeeping enzyme of the phenylpropanoid pathway. ArPEC25 inhibits the transactivation of CaĪ²LIM1a by interfering with its DNA binding ability, resulting in negative regulation of the phenylpropanoid pathway and decreased levels of intermediates of lignin biosynthesis, thereby suppressing lignin production.
A multi-omics integrative network map of maize
Networks are powerful tools to uncover functional roles of genes in phenotypic variation at a system-wide scale. Han et al. constructed a maize network map that contains the genomic, transcriptomic, translatomic and proteomic networks across maize development. This map comprises over 2.8 million edges in more than 1,400 functional subnetworks, demonstrating an extensive network divergence of duplicated genes. They applied this map to identify factors regulating flowering time and identified 2,651 genes enriched in eight subnetworks.
Multiple mechanisms behind plant bending
Jonsson et al. attempt to summarize and link different viewpoints on bending mechanisms: genes and signalling, mathematical modelling and biomechanics. They argue that quantifying cell growth and physical forces could open a new level in our understanding of bending and resolve some of its paradoxes.
Bringing Plant Immunity to Light: A Genetically Encoded, Bioluminescent Reporter of Pattern Triggered Immunity in Nicotiana benthamiana
Garcia and Steinbrenner describe a genetically encoded bioluminescent reporter of immune activation by heterologously-expressed PRRs in the model organism Nicotiana benthamiana. They characterized N. benthamiana transcriptome changes in response to Agrobacterium tumefaciens (Agrobacterium) and subsequent PAMP treatment to identify PTI-associated marker genes, which were then used to generate promoter-luciferase fusion fungal bioluminescence pathway (FBP) constructs. A reporter construct termed pFBP_2xNbLYS1::LUZ allows for robust detection of PTI activation by heterologously expressed PRRs.
New semi-dwarfing alleles with increased coleoptile length by gene editing of gibberellin 3-oxidase 1 using CRISPR-Cas9 in barley (Hordeum vulgare L.)
The green revolution was based on genetic modification of the gibberellin (GA) hormone system with "dwarfing" gene mutations that reduces GA signals, conferring shorter stature, thus enabling plant adaptation to modern farming conditions. Strong GA-related mutants with shorter stature often have reduced coleoptile length, discounting yield gain due to their unsatisfactory seedling emergence under drought conditions. Cheng et al. present gibberellin (GA) 3-oxidase1 (GA3ox1) as an alternative semi-dwarfing gene in barley that combines an optimal reduction in plant height without restricting coleoptile and seedling growth.
The origin and evolution of salicylic acid signaling and biosynthesis in plants
Salicylic acid (SA) plays a pivotal role in plant response to biotic and abiotic stress. Several core SA signaling regulators and key proteins in SA biosynthesis have been well characterized. However, much remains unknown about the origin, evolution, and early diversification of core elements in plant SA signaling and biosynthesis. In this study, Jia et al. identified 10 core protein families in SA signaling and biosynthesis across green plant lineages. They found that the key SA signaling receptors, the nonexpresser of pathogenesis-related (NPR) proteins, originated in the most recent common ancestor (MRCA) of land plants and formed divergent groups in the ancestor of seed plants. However, key transcription factors for SA signaling, TGACG motif-binding proteins (TGAs), originated in the MRCA of streptophytes, arguing for the stepwise evolution of core SA signaling in plants.
Heritable transgene-free genome editing in plants by grafting of wild-type shoots to transgenic donor rootstocks
Generation of stable gene-edited plant lines using clustered regularly interspaced short palindromic repeats (CRISPR)āCRISPR-associated protein 9 (Cas9) requires a lengthy process of outcrossing to eliminate CRISPRāCas9-associated sequences and produce transgene-free lines. Yang et al. have addressed this issue by designing fusions of Cas9 and guide RNA transcripts to tRNA-like sequence motifs that move RNAs from transgenic rootstocks to grafted wild-type shoots (scions) and achieve heritable gene editing, as demonstrated in wild-type Arabidopsis thaliana and Brassica rapa.
The AFB1 auxin receptor controls the cytoplasmic auxin response pathway in Arabidopsis thaliana
The phytohormone auxin triggers root growth inhibition within seconds via a non-transcriptional pathway. Among members of the TIR1/AFBs auxin receptor family, AFB1 has a primary role in this rapid response. However, the unique features that confer this specific function have not been identified. Dubey et al. show that the N-terminal region of AFB1, including the F-box domain and residues that contribute to auxin binding, are essential and sufficient for its specific role in the rapid response.
Careers
4 Four PhD Fellowships Fully Funded in Plant Sciences at the Universidade Nova de Lisboa in Portugal
The Instituto de Tecnologia QuĆmica e BiolĆ³gica AntĆ³nio Xavier (ITQB NOVA) of the Universidade Nova de Lisboa opens a call to award of four research fellowships in the area of Plant Sciences, under the FCT Research Fellowship Regulation (RBI) and the Research Fellow Statute (EBI). The fellowships will be funded by the Foundation for Science and Technology (FCT) under the Collaboration Protocol for Financing the Multiannual Research Fellowship Plan for PhD Students, concluded between FCT and ITQB NOVA, through its research unit GREEN-IT Bioresources for Sustainability.
Assistant Professor of Molecular Breeding for Small Grains Crops
The Department of Plant Sciences is seeking applicants that focus on fundamental and applied plant breeding, genomics, and genetics to enable continued success of the small grains breeding program. The appointee is expected to lead the small grains breeding program through competitively funded research that will increase our understanding of crop genomics and genetics and ensure the program continues to release successful varieties. The appointee will be responsible for teaching all or part of undergraduate and graduate classes in plant breeding, genetics, statistics, crop agronomy or quantitative genetics as assigned by the department chair, depending on the interests of the candidate e.g., BIT 001 (Introduction to Biotechnology), PLS 1 (Agriculture, Nature and Society), PLS 111 (Principles of Agronomic Crop Production Systems), PLS 49 (Introduction to Organic Crop Production), PLS 206 (Applied Multi-variate Modeling in agricultural and Environmental sciences). The typical teaching load is equivalent to two undergraduate courses per year (on a quarter system).
Lecturer/Senior Lecturer/Associate Professor in Plant Sciences
We are seeking to appoint a new academic at the level of either Lecturer, Senior Lecturer or Associate Professor in Plant Sciences. The successful applicants will complement our School Research Strategy.
We are interested in applicants who we can support to build internationally outstanding plant science research programmes in areas linked to our strategic research priority, āTransforming sustainable food productionā. Research should address one of the highlighted challenges outlined in our School Research Strategy: Molecular mechanisms underpinning agriculture; Pollinators and crops; Combatting the losses in agriculture due to pests and diseases. We are particularly interested in applications from candidates using molecular approaches, who are engaged in or developing industrial partnerships, and can contribute broadly to teaching in molecular biology and plant science.
Project and Communications Coordinator in Higher Education
The Project and Communications Coordinator for Higher Education will organise and coordinate engagement activities with plant science for post-16 and undergraduate audiences. This varied and creative role would suit an experienced, detail orientated communications professional and event manager who takes pride in maintaining high standards. You will work closely with members of the GPSEP team and contractors to administer ambitious student engagement projects that aim to inspire the next generation of plant scientists.
Lecturer in Plant Sciences
Based on a successful track record to date and research plan, the successful applicant will have made a convincing case of adding value to, and being a strategic fit into, one of our groups. All our groups are highly active in their research with all staff submitted to REF2021, which placed us in the top 26 University departments for biological sciences research power, and the top 24 for research impact. The research in the School benefits from a collegial research environment, excellent lab and computational facilities and notable year-on-year increasing success in securing research funding.