🌻 TWiB August 8, 2022
Here's another collection of the links shared by people following us on Twitter. That last proviso, following us on Twitter, means I can miss things. and Jim Shugg kindly pointed to an interesting tweet thread about last week's story on a gene that can improve rice yield. Merritt Khaipho-Burch points out there are a few problems with the paper.
I'm finishing the week in a good mood as next week you'll be able to read about an interesting paper that could have implications for your garden, if you have one. That will be out on Botany One some time on Monday and mentioned here when I send the email at the usual time next week. With the usual assumption that COVID or heatstroke doesn't strike.
Until then, take care.
Alun (webmaster@botany.one)
In Botany One
An orchid gives assistance, forests reduced persistence, and weeds’ electrical resistance — botany.one Botanists uncover the reason for an orchid's delicate shape, deforestation is probably worse than you thought, and a test of killing weeds without herbicide.
Unexpected responses to wildfire by seedlings in the Yukon — botany.one Fire-adapted trees should be able to take advantage of wildfires, but on the boundary between the boreal forest and the tundra, something odd is happening.
For fans of fungi – The magic of mushrooms — botany.one
Nigel Chaffey reviews The Magic of Mushrooms: Fungi in folklore, superstition and traditional medicine by Sandra Lawrence,
News & Views
Poisoned oaks, slain sycamores: who’s behind Britain’s tree murders? In affluent areas across the UK, unknown assassins are striking. Their weapons? Herbicides and hatchets. Their victims? Once mighty trees. We join the plant detectives on their trail
This Pushy Plant Is the First Proved to Shove Its Neighbor — www.nytimes.com The behavior could help study a longstanding mystery of how so many plants share small amounts of space.
The rebellious gardeners defying their local climate — www.bbc.com From India to England, gardeners are casting aside the rulebook and growing what they really want to eat – with some unexpected results.
The Idea That Trees Talk to Cooperate Is Misleading — www.scientificamerican.com It’s a romantic notion, but pretending they’re like humans could actually harm the cause of conservation
Nature-friendly farming does not reduce productivity, study finds Results of 10-year project reveal that rewilding areas can boost biodiversity and crop yields
Africa in bloom: the key to fighting plant disease — www.nature.com A conversation with Brenda Wingfield, Professor of Fungal Genomics at FABI
‘Myconauts’ aim to reveal the often hidden soil fungi that shape ecosystems A new nonprofit has launched an ambitious effort to raise the profile of often invisible soil fungi
Six tips for better spreadsheets — www.nature.com Microsoft Excel and Google Sheets are powerful and widely used. But there’s a right way and a wrong way to use them, data scientists say.
Exclusive: PLOS ONE to retract more than 100 papers for manipulated peer review In March, an editor at PLOS ONE noticed something odd among a stack of agriculture manuscripts he was handling. One author had submitted at least 40 manuscripts over a 10-month period, much more than expected from any one person.
Magnolia species lost to science for 97 years rediscovered in Haiti Conservationists find native magnolia for first time since 1925 after original habitat destroyed by deforestation
How to plant micro forests in Los Angeles — www.latimes.com If we’re trying to really fight climate change and mass extinctions, the whole natural world needs to be part of the conversation, especially in urban areas, says native plant horticulturist Katherine Pakradouni.
Understanding cooperation and conflict in plant symbionts — phys.org The traditional idea of symbiosis—long-term interactions between two organisms—is that the participants mutually benefit each other. However, researchers have debated whether the interests of the symbionts always line up with the hosts they inhabit, or whether genes that benefit symbionts might come at the expense of their hosts.
Scientific Papers
PHYTOMap: Multiplexed single-cell 3D spatial gene expression analysis in plant tissue
Nobori et al. present PHYTOMap (Plant HYbridization-based Targeted Observation of gene expression Map), a multiplexed fluorescence in situ hybridization method that enables single-cell and spatial analysis of gene expression in whole-mount plant tissue in a transgene-free manner and at low cost. They applied PHYTOMap to simultaneously analyze 28 cell type marker genes in Arabidopsis roots and successfully identified major cell types, demonstrating that our method can substantially accelerate the spatial mapping of marker genes defined in single-cell RNA-seq datasets in complex plant tissue.
Phosphatidylinositol-4-phosphate controls autophagosome formation in Arabidopsis thaliana — www.nature.com
Gomez et al. uncover the importance of the lipid phosphatidylinositol-4-phosphate in autophagy using pharmacological and genetical approaches. Combining biochemical and live-microscopy analyses, they show that PI4K activity is required for early stages of autophagosome formation.
The receptor kinase SRF3 coordinates iron-level and flagellin dependent defense and growth responses in plants — www.nature.com
Platre et al. report a receptor kinase SRF3, with a role in coordinating root growth, iron homeostasis and immunity pathways via regulation of callose synthases. These processes are modulated by iron levels and rely on SRF3 extracellular and kinase domains which tune its accumulation and partitioning at the cell surface.
A monograph of the genus Polylepis (Rosaceae) — phytokeys.pensoft.net
Espinoza and Kessler present a monograph of the high Andean tree genus Polylepis (Rosaceae), based on a species concept considering morphological, climatic and biogeographic distinctness as indicators of evolutionary independence. They describe seven new species, one from Colombia (P. frontinensis), one from Ecuador (P. simpsoniae) and five from Peru (P. acomayensis, P. fjeldsaoi, P. occidentalis, P. pilosissima and P. sacra). Three species from Peru (P. albicans, P. pallidistigma and P. serrata) are re-instated as valid species. Two taxa from Bolivia (P. incanoides and P. nana) are elevated from subspecies to species rank. The morphology, habitat, distribution, ecology and conservation status of each species are documented.
Speed vernalization to accelerate generation advance in winter cereal crops — www.cell.com
Cha et al. tested a suite of environmental conditions and protocols to investigate whether the vernalization process can be accelerated. They identified a vernalization method consisting of exposing seeds at the soil surface to an extended photoperiod of 22 h day:2 h night at 10°C with transfer to speed breeding conditions that dramatically reduces generation time in both winter wheat (Triticum aestivum) and winter barley (Hordeum vulgare).
A lncRNA fine-tunes salicylic acid biosynthesis to balance plant immunity and growth — www.cell.com
Liu et al. uncover the role of a long non-coding RNA (lncRNA) in fine-tuning the balance of plant immunity and growth. They find that a lncRNA termed salicylic acid biogenesis controller 1 (SABC1) suppresses immunity and promotes growth in healthy plants.
Tang et al. developed an integrated isotopic labeling and freeze sampling apparatus (ILSA), which could finish freeze sampling automatically in 0.05 s. ILSA can not only be used for sampling of photosynthetic metabolism measurement, but also suit for leaf isotopic labeling experiments under controlled environments ([CO2] and light).
Sakamoto et al. demonstrate that transcriptional activation of auxin biosynthesis is crucial for reprogramming differentiated Arabidopsis (Arabidopsis thaliana) leaf cells. Their data show that interfering with the activity of histone acetyltransferases dramatically reduces callus formation from leaf mesophyll protoplasts.
Repeat-based holocentromeres influence genome architecture and karyotype evolution — www.cell.com
Hofstatter et al. compare genome organization and evolution as a function of centromere type by assembling chromosome-scale holocentric genomes with repeat-based holocentromeres from three beak-sedge (Rhynchospora pubera, R. breviuscula, and R. tenuis) and their closest monocentric relative, Juncus effusus. They demonstrate that transition to holocentricity affected 3D genome architecture by redefining genomic compartments, while distributing centromere function to thousands of repeat-based centromere units genome-wide.
A root phloem pole cell atlas reveals common transcriptional states in protophloem-adjacent cells — www.nature.com
Single-cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Otero et al. use a second-generation single-cell approach, where we zoom in on the root transcriptome sorting with specific markers to profile the phloem poles at an unprecedented resolution.
Careers
Laboratory Technician Applications are invited for the position of Laboratory Technician in the research group of Dr. Sebastian Schornack at the Sainsbury Laboratory, Cambridge University (www.schornacklab.net).
Assistant Professor of Biology The Frank R. Seaver College of Science and Engineering at Loyola Marymount University (LMU) invites applicants to apply for a tenure-track position as Assistant Professor in the Department of Biology. We seek to hire an innovative teacher-scholar to begin in Fall 2023. Applicants must hold a Ph.D. in Biology or closely related field, conferred no later than the position start date of August 16, 2023. Postdoctoral experience or significant equivalent training is required.
Assistant Professor in Plant Functional Phenomics (Tenure Track 1.0 FTE) We are looking for an enthusiastic, communicative, and highly motivated Tenure Track Assistant Professor with experience in big data approaches in plant science. You integrate high-throughput phenotyping with genomics, genetics or physiological approaches to discern how phenotypes mediate plant acclimation to environmental fluctuations. As a Tenure Track researcher, you will be the linking pin between, and member of, two research groups; Plant-Environment Signaling (headed by Ronald Pierik) and Plant Stress Resilience (headed by Rashmi Sasidharan).
Events Internship We are looking for a paid intern to join our events team at the British Ecological Society. This is an unrivalled opportunity for someone wanting to develop their skills and gain experience in event management and communications. If you are interested in gaining skills to work within the events industry, you know the importance of good customer service, and are interested in working in the science and environment sector, this is for you.
Assistant Director – Scientist (Forest Sciences)
We have a vacancy in our Forest and Land Sciences Program for somebody with a background in forest sciences. The program has a strong focus on integrated spatial analysis, holds key national datasets on forests and land use, and works collaboratively with other government and research agencies to deliver its information products.
Doctoral student position available immediately on transcriptional regulation of arbuscular mycorrhiza. The position is available immediately in the lab of Caroline Gutjahr at the Weihenstephan Campus of the Technical University in Freising, close to Munich. In 2023, the laboratory will move to the Max Planck Institute of Molecular Plant Physiology (MPI-MP) in Potsdam. The position (income level German 65% TVL E13) is initially for 1 year with planned extension for up to 4 years.
Assistant Professor (post-doc) RECTOR OF THE UNIVERSITY OF SILESIA IN KATOWICE announces an open call for the position of Assistant Professor (post-doc) in the group of research staff as a part of project “Quest for climate-smart barley - the multilayered genomic study of CBC function in ABA signalling”
Tenure Track Assistant Professor of Biology (Plant Biology) Kenyon College invites applications for a tenure-track position in the Department of Biology starting in July 2022. We seek a broadly trained biologist with expertise in plant biology at the organismal level.
Post-Doctoral Research Fellowship in Agriculture and Environmental at MORE in Portugal One Post-Doctorate Research Grant is opened at MORE – Mountains of Research Collaborative Laboratory – Association, in Mountain Environmental and Ecosystem Management, hereinafter referred to as the grant, under the terms of the Research Scholarship Regulation of the Portuguese Foundation for Science and Technology (FCT) and the Research Scholarship Holder Statute.
Post-Doctoral Researcher on Multi-Species Mixtures This post supports the Multi4More project in investigating the effect of plant diversity (grasses, legumes and herbs) on the agronomic and environmental performance of multi-species grassland mixtures. The research includes sampling, analysis and reporting of measurements from experimental plots (including nitrous oxide emissions and 15N), and quantifying legacy effects on soil fertility and plant growth. Includes day-to-day supervision of PhD student and temporary staff. The successful candidate will co-ordinate and contribute to multiple knowledge transfer activities in the project, and will support specific project management activities of the Multi4More project.
Assistant Professor, Organismal Biology & Ecology The Department of Organismal Biology and Ecology at Colorado College announces a tenure-track Assistant Professor position in organismal biology, ecology, and experimental design to begin in August 2023. A review of completed applicant files will begin on September 21 and continue until 1-2 positions are filled.
Faculty Positions in Computational Genomics and Evolutionary Genomics — cfopitt.taleo.net The Department of Biological Sciences at the University of Pittsburgh invites applications for two tenure-track faculty positions in the areas of Computational Genomics and Evolutionary Genomics. The positions are anticipated at the ASSISTANT PROFESSOR or ASSOCIATE PROFESSOR level.
Join the lab — caetanods.weebly.com The Caetano lab has open positions for Master's and undergraduate students. We are located at Towson University, about 30 min North of Baltimore, in Maryland. Our main research focus on comparative biology. We use phylogenetic trees, which describe the evolutionary relationship among lineages of organisms, to understand how the amazing diversity of colors, shape, sizes and functional traits have evolved over time. For that we apply modern statistical models and rely on morphology, behavior, and molecular data.
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