š± TWiB November 15, 2021
Welcome to another collection of the stories shared by people following @BotanyOne on Twitter. If you're wondering why there's been a lot of papers about scanning trees on Botany One recently, the answer is we've had the articles in from Annals of Botany, who have a special issue on 3D Forest Models and Laser Scanning Data out. Most of the papers are open access, but the few that are not are available through free access for the next couple of months.
Next week we should have an interesting item on bibliometrics. Philip White has explained how they can help shape an emerging scientific field. I learned a lot chatting with him on Zoom.
Beyond that, at the moment I have no idea what else next week will bring. I'm hoping for a haircut, as I haven't had one for months. Whatever it brings, I plan to be back at the same time next week with the stories you're sharing. Until next week, take care,
Alun (webmaster@botany.one)
In Botany One
Forest above-ground volume assessments with terrestrial laser scanning: a ground-truth validation experiment in temperate, managed forests ā www.botany.one
Demol et al. aimed to evaluate terrestrial laser scanning for estimating tree volumes by comparison with reference volumes and volumes from allometric scaling models.
Sampling forests with terrestrial laser scanning ā www.botany.one
Boucher et al. evaluate the prevalence and sources of occlusion that limit line of sight to forest stems for terrestrial laser scans, assess the impacts of terrestrial laser scanning sample incompleteness, and evaluate sampling strategies and data analysis techniques aimed at improving sample quality and representativeness.
Genetic control of height and branch number of Brassica napus at low Phosphorus ā www.botany.one Liu et al. aimed to mine candidate genes for plant height and branch number by genome-wide association study (GWAS) and determine low-P-tolerance haplotypes.
Conservation strategies for the endangered Dianthus superbus in Latvia ā www.botany.one
Can a combination of in situ, ex situ and inter situ conservation strategies help the recovery of Dianthus superbus populations in Latvia?
Spatial arrangement of stomata in Michelia ā www.botany.one The spatial pattern of stomata is mainly caused by small-scale epidermal competition.
News & Views
Botany in Action ā www.phipps.conservatory.org
The Botany in Action Fellowship at Phipps Conservatory and Botanical Gardens supports emerging plant-focused scientists through research grants and science communication training.Ā Now through Fri., Jan. 7, the Botany in Action Fellowship program is open to applicants. Review the guidelines and submit your proposal to be considered for a $5,000 research grant, training and more.
A Calendar of Gardening Talks & Events Held Via Zoom or Online
A calendar compiled by Pumpkin Beth.
BGCI Announces the Global Biodiversity Standard at COP 26 Botanic Gardens Conservation International (BGCI) announced theĀ Global Biodiversity Standard, the worldās first and only standard to specifically recognise and promote the protection, restoration, and enhancement of biodiversity.
Scammers impersonate guest editors to get sham papers published ā www.nature.com Hundreds of junk-science papers have been retracted from reputable journals after fraudsters used āspecial issuesā to manipulate the publication process. And the problem is growing.
Philippines becomes first country to approve nutrient-enriched āGolden Riceā for planting Filipino farmers will become the first in the world to be able to cultivate a variety of rice enriched with nutrients to help reduce childhood malnutrition, after receiving the green light fromĀ regulators.
Open Chemistry: What if we just give everything away? A group leader decided that his lab would share the fluorescent dyes they create, for free and without authorship requirements. Nearly 12,000 aliquots later, he reveals what has happened since.
Avocados and vanilla among dozens of wild crop relatives facing extinction Study finds agriculture and pesticide use threaten relatives of worldās most important crops, considered crucial to food security
Exploring social justice in ecosystem restoration ā campusbuzz.blog Elaine Marshall has just started her PhD research with Jane Stout (Botany) and Susan Murphy (Geography), School of Natural Sciences. Here she describes what her research will focus onā¦
5 Ways to Make Your Writing Less Wordy (or, how to write concisely) Falling short of a required word count? Trying to sound more formal? Iām sure weāve all committed the crime of wordiness at some stage. But what does it actually do for our writing?
Timber Poachers Set a Forest on Fire. Tree DNA Sent One to Prison. ā www.nytimes.com Loggers seeking a prized hardwood started the fire in the Olympic National Forest, prosecutors said. The use of timber DNA evidence was a first in a federal criminal trial.
Scientific Papers
Unraveling the role of MADS transcription factor complexes in apple tree dormancy
da Silveira Falavigna et al. describe a gene regulatory network (GRN) formed by MdSVPa-containing complexes, which regulate the dormancy cycle in response to environmental cues and hormonal signaling pathways. Additionally, novel molecular evidence regarding the evolutionary functional segregation between DAM and SVP proteins in the Rosaceae is presented.
An siRNA-guided ARGONAUTE protein directs RNA polymerase V to initiate DNA methylation ā www.nature.com
Sigman et al. find that Pol V follows and is dependent on the recruitment of an AGO4-clade ARGONAUTE protein, and any siRNA can guide the ARGONAUTE protein to the new target locus independent of pre-existing DNA methylation. These findings reject long-standing models of RdDM initiation and instead demonstrate that siRNA-guided ARGONAUTE targeting is necessary, sufficient and first to target Pol V recruitment and trigger the cycle of RdDM at a transcribed target locus, thereby establishing epigenetic silencing.
ReadCube: https://rdcu.be/cA3R1
Effective methods for isolation and purification of extracellular vesicles from plants
Huang et al. compare published plant EV isolation methods, and provide our recommended method for the isolation and purification of plant EVs. This method includes a detailed protocol for clean AWF collection from Arabidopsis thaliana leaves, followed by EV isolation via differential centrifugation. To further separate and purify specific subclasses of EVs from heterogeneous vesicle populations, density gradient ultracentrifugation and immunoaffinity capture are then utilized.
Epigenetics: a catalyst of plant immunity against pathogens
Hannan Parker et al. review the cis- and trans-acting mechanisms by which stress-inducible epigenetic changes at transposable elements (TEs) regulate genome-wide defence gene expression and draw particular attention to one regulatory model that is supported by recent evidence about the function of AGO1 and H2A.Z in transcriptional control of defence genes. Additionally, they explore how stress-induced mobilisation of epigenetically controlled TEs acts as a catalyst of Darwinian evolution by generating (epi)genetic diversity at environmentally responsive genes.
Strong and tunable antiāCRISPR/Cas activities in plants
This study describes the characterization of two anti-CRISPR proteins, AcrIIA4 and AcrVA1, in Nicotiana benthamiana. Results demonstrate that AcrIIA4 prevents site-directed mutagenesis in leaves when transiently co-expressed with CRISPR/Cas9. In a similar way, AcrVA1 is able to prevent CRISPR/Cas12a-mediated gene editing. Moreover, using a N. benthamiana line constitutively expressing Cas9, Calvache et al. show that the viral delivery of AcrIIA4 using Tobacco etch virus is able to completely abolish the high editing levels obtained when the guide RNA is delivered with a virus, in this case Potato virus X.
A chickpea genetic variation map based on the sequencing of 3,366 genomes ā www.nature.com
Varshney et al. present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. They constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21āmillion years.
Griffiths et al. phenotyped root system traits and deep 15N nitrate capture across 1.5 m vertical profiles of solid media using tall mesocosms in switchgrass (Panicum virgatum L.), a promising cellulosic bioenergy feedstock. Root and shoot biomass traits, photosynthesis and respiration measures, and nutrient uptake and accumulation traits were quantified in response to a water and nitrate stress factorial experiment for switchgrass upland (VS16) and lowland (AP13) ecotypes. The two switchgrass ecotypes shared common plastic abiotic responses to nitrogen (N) and water availability, and yet had substantial genotypic variation for root and shoot traits.
Deep learningābased quantification of arbuscular mycorrhizal fungi in plant roots
Evangelesti et al. developed Automatic Mycorrhiza Finder (AMFinder) which allows for automatic computer vision-based identification and quantification of AM fungal colonisation and intraradical hyphal structures on ink-stained root images using convolutional neural networks.
McInturf et al. explored Cd- and Fe-associated responses in wild-type Arabidopsis and in a mutant that overaccumulates Fe (opt3-2). Gene expression profiling revealed a large overlap between transcripts induced by Fe deficiency and Cd exposure. Interestingly, the use of opt3-2 allowed them to identify additional gene clusters originally induced by Cd in the wild type but repressed in the opt3-2 background.
Perceived Vulnerability and Propensity to Adopt Best Management Practices for Huanglongbing Disease of Citrus in California Huanglongbing (HLB) disease of citrus, which is associated with the bacterium āCandidatus Liberibacter asiaticusā, has been confined to residential properties in Southern California 8 years after it was first detected in the state. To prevent the spread of HLB to commercial citrus groves, growers have been asked to adopt a portfolio of voluntary best management practices. This study evaluates the citrus industryās propensity to adopt these practices using surveys and a novel multivariate ordinal regression model.
Floral traits and visitation were measured for five co-occurring Castilleja species (C. applegatei, C. linariifolia, C. miniata, C. nana, and C. peirsonii), representing three pollination syndromes (bee, fly, and hummingbird), at four sites in the Sierra Nevada Mountains. Hilpman and Busch used nonmetric multidimensional scaling (NMDS) and multiple linear regressions to address key questions in the differentiation of Castilleja and floral visitors.
Careers
Project Manager (HE) GPSEP [Temporary Cover] (Part Time) The Project Manager for Higher Education will jointly oversee initiatives for post-16 audiences. This exciting and creative role would suit an experienced engagement professional. You will work closely with members of the GPSEP team and external consultants to design and deliver ambitious student engagement projects.
Assistant Professor of Sustainable Horticulture The Department of Horticulture & Landscape Architecture announces an academic year, tenure track assistant professor position in sustainable horticulture. The successful candidate will develop an integrated teaching and research program.
The Department of Agronomy seeks a 9-month tenure track or tenured Forage Systems Agroecologist. The position carries a commitment to the three important functions of instruction, research, and outreach, as well as professional and university service as appropriate to the faculty rank. The incumbent will be expected to develop and grow an extramurally-funded research and Extension program recognized at the state, regional, national, and international levels.
Job Announcements for Four Open Faculty Positions
Forest Ecology, Forest Management, Wildlife Ecology and Management Forest Products Utilization.
Closing date is Dec. 17, 2021.
Research Assistant ā Inter-PWOs Applications are invited from suitably qualified candidates for a full-time, fixed term Research Assistant position in Plant Development & Chromatin within the Plant and Agricultural Biosciences Centre (PABC), Ryan Institute at the National University of Ireland, Galway.
We are looking for a new Postdoc!! ā Salazar Lab FIU A new Postdoctoral Associate position is now available at ourĀ Plant Chemical Ecology LabĀ at Florida International University.
PhD Why are there so few C2 grasses? This studentship will seek to identify why there are so few C2 grasses by investigating grass photosynthetic diversity within an ecological and phylogeographical context to understand how C4 photosynthesis emerged in the grasses. To do this, the student will train in plant phenotyping, fieldwork, phylogenetics, and use of public collections while undertaking fieldwork in Argentina and customized training at the University of Bangor and Kew Herbarium.
Greenhouse Coordinator This position will play a key role in the Plant Science Research Greenhouse Facility at Michigan State University.Ā The greenhouses have over 100,000 sq. ft. of research space and serve over 70 faculty in eight academic departments at MSU.Ā The Greenhouse Coordinator will oversee the maintenance and care of greenhouses facilities and equipment and provide advice to researchers regarding use of the greenhouse facility and plant care.
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.
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