đ± TWiB November 22, 2021
Here comes another collection of stories shared by people following @BotanyOne on Twitter. I'm pleased we got Philip White's bibliometrics article out this week. It's interesting to see how bibliometrics can do more than just keep score.
The photo of the week is also the story of the week. Click on the photo to see the whole thing on Twitter.
There should be another collection of stories with you the same time next week.
Alun (webmaster@botany.one)
Photo of the Week
In Botany One
Estimating genetic variation in seed collections using seed morphology â www.botany.one Can variation in seed morphological traits allow us to estimate genetic variation in seed banks of vulnerable plant species?
How using bibliometrics can help guide people to your research, the case of the Ionome, Nutriome and Metallome â www.botany.one You might think of bibliometrics as something that happens to scientific articles after theyâre published. However, in new and innovative fields like ionomics, bibliometrics can also help shape them.
Target capture sequencing for investigating repetitive DNA â www.botany.one Botanists find a way to recycle genomic data and contribute to a better characterization of plant biodiversity.
Plant computational model explains how leaf veins develop â www.botany.one Polar auxin transport dynamics control vein patterning.
Brassinosteroids regulate petal spur length in Aquilegia â www.botany.one Botanists used virus-induced gene silencing and gene expression experiments to understand the function of brassinosteroid-related transcription factors in Aquilegia coerulea petal spurs.
News & Views
Forests: Tree deaths are increasing across Europe due to climate change â www.newscientist.com Annual mortality rates are rising for all major tree species in Europe, which means forests will soak up less carbon and wildfire risks will increase
MSU research team working with 142-year-old seeds still seeing growth In April, a team of Michigan State University plant biologists dug up a bottle of seeds buried by botanist W.J. Beal in 1879. The seeds have been subjected to various tests to see if they would grow nearly a century and a half later.
Rewilding: 60 years ago, scientists let a farm go wild â the results are in The Monks Wood Wilderness experiment was a rewilding study before the term existed. This is what we can learn from it
This Colorado 'solar garden' is literally a farm under solar panels "Our farm has mainly been hay producing for fifty years," Kominek said, on a recent chilly morning, the sun illuminating a dusting of snow on the foothills to his West. "This is a big change on one of our three pastures." That big change is certainly an eye opener: 3,200 solar panels mounted on posts eight feet high above what used to be an alfalfa field on this patch of rolling farmland at the doorstep of the Rocky Mountains.
Farro Grain: The oldest grain in the world that is eaten even today â timesofindia.indiatimes.com There are a lot of grains out there that have existed since time immemorial. But do you know which among them is the oldest? Farro Monococcum, also called Einkorn, Small Farro and Little Spelt is the oldest grain that exists today.
Keeping plant hormone levels in check A team of researchers led by Bert De Rybel (VIB-UGent Center for Plant Systems Biology) discovers that a single transcriptional complex, called TMO5/LHW, coordinates vascular development in the plant root meristem by controlling cytokinin levels in space and time. Based on these insights, targeted modulation of specific tissue types in plant roots could lead to more efficient water usage and promote drought resistance.
Hedges Do Way More Than Block Your View They also link ecosystems together, supporting thousands of species.
Woodland and hedgerow creation will be crucial to support pollinators in Wales The largest survey of pollinator abundance in Wales has found that woodland and hedgerow creation can play a crucial role in action to reverse declines in insects that are essential for crop yield and other wildlife.
From asylum seeker to superstar gardener â www.rhs.org.uk Meet Kuda Chimbudzi, Head Kitchen Gardener for Tottenham Hotspur Football Club
Scientists solve 50-year-old mystery behind plant growth â phys.org A team of researchers led by UC Riverside has demonstrated for the first time one way that a small molecule turns a single cell into something as large as a tree. For half a century, scientists have known that all plants depend on this molecule, auxin, to grow. Until now, they didn't understand exactly how auxin sets growth in motion.Â
Scientific Papers
Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales
Wu et al. aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales, by comparing the genomes of 21 symbiotrophic species to their saprotrophic brown-rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae.
Forest fires and climate-induced tree range shifts in the western US â www.nature.com
Hill and Field test the sensitivity of tree range shifts (measured as the difference between seedling and mature tree ranges in climate space) to wildfire occurrence, using 74,069 Forest Inventory Analysis plots across nine states in the western United States. Wildfire significantly increased the seedling-only range displacement for 2 of the 8 tree species in which seedling-only plots were displaced from tree-plus-seedling plots in the same direction with and without recent fire. The direction of climatic displacement was consistent with that expected for warmer and drier conditions.
Fly pollination drives convergence of flower coloration
Garcia et al. show by comparing flower signals that occur in different environments including total absence of bees, a mixture of bee and fly pollination within one plant family (Orchidaceae) from a single community, and typical flowers from a broad taxonomic sampling of the same geographic region, that perceptually different colours, empirically measured, do evolve in response to different types of insect pollinators.
Diverse forests are cool: Promoting diverse forests to mitigate carbon emissions and climate change â onlinelibrary.wiley.com
Beugnon et al. argue that focusing on planting diverse forests in reforestation efforts can help to reduce climate change effects on ecosystems: first, by increasing resistance and resilience to extreme climatic events, and second, by buffering microclimatic conditions in natural and urban areas. Diversifying forests plantations and reforestation projects may not always be feasible and cannot solve the climate crisis by itself. However, they highlight that a focus on diverse forests could maximize the benefits of reforestation programs by promoting sustainable land management.
A donor-DNA-free CRISPR/Cas-based approach to gene knock-up in rice â www.nature.com
Lu et al. show that new genes and traits can be created in rice by designed large-scale genomic inversion or duplication using CRISPR/Cas9. A 911âkb inversion on chromosome 1 resulted in a designed promoter swap between CP12 and PPO1, and a 338âkb duplication between HPPD and Ubiquitin2 on chromosome 2 created a novel gene cassette at the joint, promoterUbiquitin2::HPPD.
A beginner's guide to lowâcoverage whole genome sequencing for population genomics
In this introductory guide to lcWGS, Lou et al. first illustrate how the per-sample cost for lcWGS is now comparable to RAD-seq and Pool-seq in many systems. They then provide an overview of software packages that explicitly account for genotype uncertainty in different types of population genomic inference. Next, they use both simulated and empirical data to assess the accuracy of allele frequency, genetic diversity, and linkage disequilibrium estimation, detection of population structure, and selection scans under different sequencing strategies.
HernĂĄndez-Herrera et al. developed a plugin âLive Plant Cell Trackingâ (LiPlaCeT) coupled to the publicly available ImageJ image analysis program and generated a pipeline that allows, with the aid of LiPlaCeT, 4D cell tracking and lineage analysis of populations of dividing and growing cells. The LiPlaCeT plugin contains ad hoc ergonomic curating tools, making it very simple to use for manual cell tracking, especially when the signal-to-noise ratio of images is low or variable in time or 3D space and when automated methods may fail.
Zhang et al. review the current body of knowledge of the transport pathways and regulatory mechanisms of macromolecules in plants and assess systemic, long-distance signal trafficking that mediates stress responses, and plantâenvironment or plantâinsect community interactions. Additionally, they propose several methods for identifying mobile mRNAs and proteins. Finally, they discuss the challenges facing systemic signaling research and put forth the most urgent questions that need to be answered to advance our understanding of plant systemic signaling.
Bauman et al. utilise an exceptional dataset of 49 years of growth data for 509 tree species across 23 tropical rainforest plots along a climatic gradient to examine how multiannual tree growth responds to both climate means and anomalies, and how speciesâ functional traits mediate these growth responses to climate. They show that anomalous increases in atmospheric evaporative demand and solar radiation consistently reduced tree growth. Drier forests and fast-growing species were more sensitive to water stress anomalies. In addition, species traits related to water use and photosynthesis partly explained differences in growth sensitivity to both climate means and anomalies.
Functional disruption of cell wall invertase inhibitor by genome editing increases sugar content of tomato fruit without decrease fruit weight â www.nature.com
Sugar content is one of the most important quality traits of tomato. Cell wall invertase promotes sucrose unloading in the fruit by maintaining a gradient of sucrose concentration between source leaves and fruits, while invertase inhibitor (INVINH) regulates this process. In this study, knock-out of cell wall INVINH in tomato (SlINVINH1) was performed by genome editing using, CRISPR/Cas9 and Target-AID technologies. Most of the genome-edited lines set higher soluble solid content (SSC) fruit than the original cultivar âSuzukomaâ, while fruit weight was different among the genome-edited lines. The mature fruits of genome edited line 193â3 showed the highest sugar content, and the fructose and glucose contents were 29% and 36% higher than that of the original cultivar, respectively.
Removing the major allergen Bra j I from brown mustard (Brassica juncea) by CRISPR/Cas9 Food allergies are a major health issue worldwide. Modern breeding techniques such as genome editing via CRISPR/Cas9 have the potential to mitigate this by targeting allergens in plants. This study addressed the major allergen Bra j I, a seed storage protein of the 2S albumin class, in the allotetraploid brown mustard (Brassica juncea).
Careers
Tenure-Track Assistant Professor (Molecular Systems Biologist) The Department of Biology at Wilfrid Laurier University invites applications for a Tenure Track Assistant Professor position, subject to budgetary approval. We are seeking a Molecular Systems Biologist working with non-human experimental systems in the area of Food Safety, Security and Sustainability to begin July 1, 2022.
First bundled call for financed PhD-positions The announcement is made for 3 years, whereby the employment relationship is initially limited to 1.5 years and is automatically extended to a total of 3 years, unless the employer submits a declaration of non-renewal after a maximum of 12 months. In case of probation and appropriate work progress an extension to 4 years is possible.Â
Grassland Phenology: Ecological Modelling We are looking to appoint a post-doctoral fellow with expertise in soil and root microbial ecology to conduct research on the resistance and resilience of grasslands under combined extreme flood and drought events. The post is part of a 4 year Science Foundation of Ireland funded project entitled "Delivering food security from grasslands by understanding the link between root microbial networks and resilient agriculture".
Assistant Professor- Plant Biochemistry and Synthetic Biology This position is intended for early career scientists who have and will continue to leverage modern technological advances in biochemistry, synthetic biology or closely aligned disciplines. The Department seeks a highly collaborative and interdisciplinary scientist who will capitalize on a broad range of questions pursued at a variety of scales (from the molecular and cellular to the whole plant and ecosystem level).
Professor in Root-Soil Interaction The responsibilities include research and teaching as well as the promotion of early-career scientists. We seek to appoint an expert in the research area of process interactions at the root-soil interface with a focus on plant performance and adaptation in specific soil environments. Ideally, research should include molecular, genetic, developmental, cellular, physiological, microscopic and/or other advanced imaging approaches. Root-soil-microorganism interactions can be included as well.
Laboratory Technician The Miller laboratory at the Donald Danforth Plant Science Center has an immediate opportunity for a highly motivated individual to join our team as a full-time Laboratory Technician. Research in the Miller lab focuses on integrating diverse phenotyping approaches, genetics and statistical modeling to advance understanding of perennial plant diversity and evolution, and to optimize and expedite perennial crop development, with the goal of developing more sustainable agricultural systems.
Postdoc position The EPLM team, in the BIOGER Institute dedicated to fungal pathogens of crops (UR BIOGER INRAE - University Paris-Saclay), is looking for a postdoc with experience in plant-pathogen interactions and protein/ protein interactions to join us on a project funded by the French Research Agency (ANR) on the structural and functional characterization of fungal effectors in order to propose knowledge-driven plant resistance management.
PHD Student - Genetic analysis of Arabidopsis and Sorghum mutants, molecular clony and functional characterization of candidate genes â epsoweb.org The Center for Research in Agricultural Genomics (CRAG) is looking for a PhD Student to be part of the group Brassinosteroid signaling in plant development.
Postdoctoral Associate We are looking for a highly motivated postdoctoral researcher to participate in the NASA-funded project âEpigenetic Adaptation to the Spaceflight Environment â Accumulated Genomic Change Induced by Generations in Spaceâ, as well as other ongoing projects in the laboratory. The successful candidate will work in the University of Floridaâs Space Plants Lab lead by Dr. Robert Ferl and Dr. Anna-Lisa Paul.
KU Center for Genomics Postdoctoral Fellowship The KU Center for Genomics is pleased to support postdoctoral researchers in genomics research as the Center for Genomics Postdoctoral Fellow. The fellow will receive a competitive salary, benefits and a research and travel allowance. Fellow applicants should develop their own research program with guidance from Center for Genomics faculty.
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