January 10, 2022

🌱 TWiB January 10, 2022

Welcome back. It's a shorter edition than usual, in places, partly because I took a little time off at the start of the week. I hope you managed to get some time off too. The distribution of paper shares was unusual this week. Initially, I only found a few papers to include - but after lowering the threshold slightly there were many. Instead of sharing coalescing around a few papers it seems people's reading was much more diverse than usual.

For complicated reasons, I've started walking with a cat at half-past four in the morning over the holiday. While the cat is happy finding somewhere in the undergrowth to sit and stare, it's a bit of a quiet time for me so a perfect time to catch up with podcasts. A new addition is No Time to Read by former Botany One guest blogger Arif Ashraf. Arif will be talking to a paper author about an article each episode. I'm looking forward to listening to it. If I can also persuade the cat that he doesn't need to go out till six in the morning, I'll enjoy it even more.

Until next week, take care,

Alun (webmaster@botany.one)

In Botany One

Simulating grass phenotypic plasticity as an emergent property — www.botany.one Integrating plant functioning at organ scale can simulate the phenotypic plasticity of plants.

An unexpected killer lurks deep in Italian lakes — www.botany.one

You would expect to see flowers of Utricularia australis on display just above the surface of a pond or lake. Now botanists have found open U. australis flowers on a lakebed over four metres below the surface.

Measuring the hidden phenotype using novel mathematical techniques — www.botany.one

A new study quantifies the shape of barley seeds using topological methods.

También en español.

Resilience of crops confirms that drought alone did not cause a 'collapse' in Mayan civilisation — www.botany.one In the 800s, Mayan cities in southeastern Mexico and Central America were abandoned - just as drought hit the region. But a botanical study shows that the connection between drought and depopulation was not simple.

News & Views

Ep. 350 - Exploding Flowers — www.indefenseofplants.com You may have heard about exploding fruit but what about exploding flowers? That is exactly what we are discussing in this episode. For Dr. Joan Edwards, there is no substitute for a walk in the woods, especially when we know so little about our botanical neighbors

Lychee genome tells a colorful story about a colorful tropical fruit — www.buffalo.edu Radiant and flavorful, lychees were so beloved that they were domesticated not just once in ancient times, but independently in two different regions of China, a study finds

Tracing the beginnings of Macroecology – Yoda et al. (1963) — brianjenquist.wordpress.com

"What I find so fascinating about this paper is that their approach is uniquely macroecological and was so ahead of its time, especially within botany and plant ecology."

A Weed is but an Unloved Flower “Whatever Otherness weeds may possess, it is an outcome of human artifice.”

Tips to Make a "Messy" Wildlife Garden Look Good — www.allaboutbirds.org One of the top worries we hear from people considering wildlife-friendly landscaping (or even just reducing the size of their manicured lawn) is a concern that it will look too messy. Like it or not, native and wildlife-friendly gardening has a reputation for not being tidy. We think, with a few little tricks, however, you can make even the wildest yard look tame enough to fit in on your block.

When Botany Was for Ladies In nineteenth century America, young women took to studying botany—a conjoining of interest, social acceptance, and readily available schooling.

How this Swiss city is using green roofs to combat climate change — www.euronews.com Basel, Switzerland has become the first city in the world to make green spaces a legal requirement on new buildings.

‘Ghost’ orchid that grows in the dark among new plant finds Hundreds of new species include pink voodoo lily and a ylang-ylang tree named after Leonardo DiCaprio

Ghost Forests Could Provide Respite for Marsh Birds as Coastal Habitat Disappears Scientists want to ensure that swaths of trees killed by saltwater flooding are more than dead forest, but become quality marsh habitat for birds.

Saving Seeds Can Be an Easy Way to Grow Pollinator Habitat — xerces.org Update on projects undertaken by Xerces' team of restoration ecologists, entomologists, plant ecologists, and researchers.

Trees Have the Potential to Live Indefinitely Trees die as a result of severe damage, but some have overcome storms, droughts, fires, and more to survive for thousands of years

Science visualization trends of 2021 — helenajambor.wordpress.com

"This year, while musing whether to keep or toss my Nature print issues (still undecided!), I browsed the science visualizations of 2021. Well, I checked those about biology and medicine as I really do not understand enough of physics to get the visualizations in Nature. Some visualizations and themes really stood out so I decided to summarize for you the top 10 science visualization trends of 2021 – enjoy!"

Scientific Papers

Vegetation‐type conversion of evergreen chaparral shrublands to savannahs dominated by exotic annual herbs: causes and consequences for ecosystem function

Woody, evergreen shrublands are the archetypal community in mediterranean-type ecosystems, and these communities are profoundly changed when they undergo vegetation-type conversion (VTC) to become annual, herb-dominated communities. Recently, VTC has occurred throughout southern California chaparral shrublands, likely with changes in important ecosystem functions. The mechanisms that lead to VTC and subsequent changes to ecosystem processes are important to understand as they have regional and global implications for ecosystem services, climate change, land management, and policy. The patterns described for California are mostly relevant to the other mediterranean-type shrublands of the globe, which are biodiversity hotspots and threatened by VTC. This review examines the extent and causes of VTC, ecosystem effects, and future research priorities.

Integration of nutrient and water availabilities via auxin into the root developmental program

In this review, Liu and von Wirén highlight current knowledge on nutrient- and water-related developmental processes that impact root foraging and involve auxin as a central player. A deeper understanding and exploitation of these auxin-related processes and mechanisms promises advances in crop breeding for higher resource efficiency.

Belowground plant–microbe communications via volatile compounds

In this review, Sharifi et al. attempt to clarify the volatile-mediated intra- and inter-kingdom communications in the rhizosphere, and propose improvements in experimental design for future research.

Are Palmer's Elm-Leaf Goldenrod and the Smooth Elm-Leaf Goldenrod Real? The Angiosperms353 Kit Provides Within-Species Signal in Solidago ulmifolia s. l.

Beck et al. use a dataset obtained exclusively from herbarium specimens to evaluate the status of Solidago ulmifolia var. palmeri, a morphologically subtle taxon potentially confined to Alabama, Arkansas, Mississippi, and Missouri. A multivariate analysis of both discrete and continuous morphological data revealed no clear distinction between S. ulmifolia var. palmeri and Solidago ulmifolia var. ulmifolia. Solidago ulmifolia var. palmeri's status was also assessed with a phylogenomic and SNP clustering analysis of data generated with the “Angiosperms353” probe kit. Neither analysis supported Solidago ulmifolia var. palmeri as a distinct taxon, and we suggest that this name should be discarded.

The Andes through time: evolution and distribution of Andean floras

Pérez-Escobar et al. present an evolutionary and floristic synthesis of Andean plant diversity and evolution across time and space.

Nectaries in ferns: their taxonomic distribution, structure, function, and sugar composition

Extrafloral nectaries have mainly been studied in angiosperms, but have also been reported in 39 fern species. Mehltreter et al. provide a global review of nectaries in ferns and examined their structure, function, and nectar sugar composition in two genera.

Plant TOR signaling network: Complexes, conservations and specificities

Target of Rapamycin (TOR) is an evolutionarily conserved protein kinase that functions as a central signaling hub to integrate diverse internal and external cues to precisely orchestrate cellular and organismal physiology. Liu and Xiong review recent discoveries on the plant TOR signaling network. They present an overview of plant TOR complexes, analyze the signaling landscape of the plant TOR signaling network from the upstream signals that regulate plant TOR activation to the downstream effectors involved in various biological processes, and compare their conservation and specificities within different biological contexts. Finally, they summarize the impact of dysregulation of TOR signaling on every stage of plant growth and development, from embryogenesis and seedling growth, to flowering and senescence.

Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae

The genomic diversity underpinning high ecological and species diversity in the green algae (Chlorophyta) remains little known. Repetti et al. aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the core Chlorophyta.

Are Cenozoic relict species also climatic relicts? Insights from the macroecological evolution of the giant sedges of Carex sect. Rhynchocystis (Cyperaceae) Most of the Paleotropical flora widely distributed in the Western Palearctic became extinct during the Mio-Pliocene as a result of global geoclimatic changes. A few elements from this Cenozoic flora are believed to remain as relicts in Macaronesia, forming part of the laurel forests. Although the origins of the present species assembly are known to be heterogeneous, it is unclear whether some species should be considered climatic relicts with conserved niches. An ideal group for studying such relict characteristics is a Miocene lineage of Carex sect. Rhynchocystis (Cyperaceae), which comprises four species distributed in mainland Palearctic and Macaronesia.

Machine learning approaches to identify core and dispensable genes in pangenomes

Yocca and Edger aim to leverage the previously characterized core and dispensable gene content for two grass species [Brachypodium distachyon (L.) P. Beauv. and Oryza sativa L.] to construct a machine learning model capable of accurately classifying genes as core or dispensable using only a single annotated reference genome. Such a model may mitigate the need for pangenome construction, an expensive hurdle especially in orphan crops, which often lack the adequate genomic resources.

A permineralized Early Cretaceous lycopsid from China and the evolution of crown clubmosses New, exceptionally well-preserved permineralized lycopsid fossils from the Early Cretaceous (125.6 ± 1.0 Ma) of Inner Mongolia, China, were examined in detail using acetate peel and micro-computed tomography techniques. The anatomy of extant Lycopodiaceae was analyzed for comparison using fluorescence microscopy. Phylogenetic relationships of the new fossil to extant Lycopodiaceae were evaluated using parsimony and maximum likelihood analyses.

Careers

PhD position @ the group of Specialized Metabolism - Goossens lab In this project, the PhD candidate will employ cutting-edge protein-protein and protein-DNA interactomics technologies to further advance our understanding of jasmonate signalling, using tomato as a model. The candidate will specifically investigate transcription factor complex condensates that dynamically assemble following jasmonate perception and that steer the possible distinct outputs of the jasmonate signalling cascade in a spatiotemporal correct manner.

Postdoctoral researcher @ the group of Specialized Metabolism - Goossens lab Phosphoregulation has emerged as an important step in the regulation of jasmonate-mediated plant defence programs, but our molecular understanding of this mechanism is still limited. To fill this knowledge gap, the candidate will be involved in a project that aims to generate a high-resolution phosphoproteomics network that will pinpoint kinases involved in the modulation of mechanical stress and jasmonate signalling in the model plant Arabidopsis. The candidate will first use phosphoproteomics analysis and targeted kinase screens to pinpoint the lead kinases. Subsequently, the candidate will use cutting-edge proximity labelling technology to map the protein-protein interaction landscape in which these kinases are operating. Finally, phenotypic and functional characterization of the most relevant kinases will be carried out through an innovative strategy that combines genome editing and protein engineering to reveal the molecular activity and physiological role of the Arabidopsis kinases in the regulation of jasmonate signalling and plant defence responses.

Junior Postdoctoral researcher @ the group of Specialized Metabolism - Goossens lab The candidate will take up a central role in the usage of our different cutting-edge interactomics platforms to study jasmonate signalling and plant metabolism. Our in-house developed interactomics platforms allow visualising both protein-protein (Y2H-seq and TurboID) and protein-metabolite (LiP-MS) interactions and are intensively being employed to unravel the molecular mechanisms behind plant metabolite biosynthesis, perception, signalling and activity.

Research Assistant The primary role of the postholder is to generate constructs, prepare genomic DNA and perform routine PCR and Southern blotting. Other activities will involve, but is not limited to, sterile propagation of plants, somatic hybridisation and phenotypic screening of plants.

Research Assistant (two posts available) Are you looking for a hands-on technical role in a position that involves research in biological sciences, practical horticulture and finding solutions for environmental challenges? The RHS, the world’s leading gardening charity, is looking to recruit two Research Assistants to join our Plant Health and Environmental Horticulture teams, helping to support the work of more than 70 scientists. Both roles will be based at RHS Wisley Gardens, in Surrey, assisting with laboratory-based science in our new Hilltop “Home of Gardening Science” building, and in addition helping with the field trials and the advisory services of the RHS.

United Kingdom and Ireland - 2022 Call for Application | For Women in Science The L’Oréal-UNESCO UK and Ireland For Women in Science Rising Talent Programme offers awards to promote, enhance and encourage the contribution of women pursuing their research careers in the UK or Ireland.

Postdoctoral Researcher A postdoctoral research position is available for studying molecular mechanisms in photosynthesis in the laboratory of James V. Moroney at Louisiana State University. Current areas of research emphasis include the CO2 concentrating mechanisms of algae, inorganic carbon transporters and carbonic anhydrase proteins.  We are also working to see if these components of the algal CO2 concentrating mechanism can be used to improve photosynthesis in crop plants. 

Tenure-track position in the field of ecology/evolutionary biology/conservation biology A tenure-track position in the field of ecology/evolutionary biology/conservation biology. The successful candidate is expected to establish a vigorous, externally funded research program, carry out and publish independent cutting-edge scientific research, advise graduate students, and contribute to the graduate and undergraduate curricula in ecology and conservation.

University Faculty - Plant Physiology The Department of Botany and Plant Ecology at Weber State University invites applications for a tenure-track position, with the appointment to begin in July 2022. We seek a person broadly trained in plant physiology who focuses on either plant molecular and cellular biology or plant structure and function. 

Curation and Digitisation Assistant (Fixed Term)

The Department of Plant Sciences is seeking to appoint a Curation and Digitisation Assistant in the University Herbarium. The post is available full-time but we also welcome applications from those wishing to work part-time. The main role will be to work on the auditing and digitisation (imaging and databasing) of historically and scientifically important herbarium specimens in the University Herbarium. The postholder will also assist with routine external enquiries and requests for specimens for collaborators, and supervise volunteers and students working in the collection when the Curator is unavailable.

Ecology Team Manager (Executive position) This position requires an experienced Ecologist to join and manage our Ecological consulting team. Our Ecology team works across a broad range of projects including ecosystem recovery, design, management and monitoring, development projects and tailored research programs to support project outcomes. The position will involve field work in locations throughout Australia (typically in SA) and office work based at Edwardstown.

Ecologist We are seeking an Ecologist to join our Ecological consulting team. This team works across a broad range of projects including ecosystem recovery, design, management and monitoring, development projects and tailored research programs to support project outcomes. The position will involve field work in locations throughout Australia (typically in SA) and office work based at Edwardstown.

Burpee Post-Doctoral Fellow in Botany A postdoctoral position is available in the laboratory of Dr. Chris Martine in the Department of Biology at Bucknell University. The position is a yearly appointment, renewable for up to three years, and has a preferred start date of summer 2022.

Part-Time Public Programmes Manager As a self-funded, independent Museum, the main purpose of this role is to generate income and develop our audience through the delivery of an exciting and effective annual Public Programme of events; talks, workshops, and courses. Organisation, collaboration and innovation are fundamental to the success of the role. The Public Programme is central to the life of the Museum, complementing the Garden Museum’s other programmes of festivals & fairs, Learning (including Food Learning), and community events which are led by other members of the team.

Freelance Assistant / Content Editor

The Botanical Society of America seeks a freelance assistant/content editor for its monthly peer-reviewed research journal, the American Journal of Botany (AJB). Candidates must have previous editing experience, a background in biology and/or botany, and the ability to work independently and collaboratively.

Postdoc/Ph.D. to study chloroplast degradation during leaf senescence

Postdoc position available in my lab at the Agricultural Research Organization (ARO) – Volcani Institute (in Israel) immediately. The Michaeli lab aims to identify molecular and cellular mechanisms that govern leaf senescence and fruit ripening. we further wish to harness our knowledge to increase plant produce lifespan (shelf life). I’m looking for a scientist interested in zooming into chloroplast degradation during leaf senescence (via autophagy and other pathways). Required skills include molecular biology, protein biochemistry & confocal live imaging. Knowledge in proteomics is an advantage.

PhD position; Inferring adaptation and genetic gain from crowdsourced crop performance data We are looking for a quantitative biologist, ecologist, agronomist, or statistician with a strong interest in tropical agriculture, plant breeding and genetic resources. In this exciting project, you will work on the development and implementation of statistical methods for the analysis of crop variety performance and environmental adaptation in large-scale, crowdsourced data from on-farm variety trials. You will play an important role in an international team of breeders, agronomists and statisticians looking for improved ways to measure, understand, and predict the suitability of crop varieties for contrasting environments.

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