đ» TWiB May 2, 2022
It's not been a slow week due to workload, but rather with me limiting the work I do. Looking at the list this week I clearly need to improve how we find more general news stories on Twitter - though there has been a lot of talk about one non-Botany story on Twitter this week.
The Musk takeover of Twitter means collating the top links shared by people following @BotanyOne on Twitter, might become more difficult in the future. It might improve massively, but his approach to improving products for users is patchy. I'll be surprised if the site fails like MySpace - but we're watching to see how things develop and decide where our efforts are best spent to support botanists.
I also have a final call for anyone who wants to apply for an editor post at Botany One. The deadline is tomorrow 0900 UTC. I've written a post of some tips saying why we're asking what we're asking.
Alun (webmaster@botany.one)
In Botany One
Infectious bacteria force host plants to feed them â botany.one Not only do bacteria have tools to try to shut down plant defences, pathogens can also try to get the plant to direct water and food to help feed the attack.
Integrative and Multiscale Modelling Special Issue: Call for Papers â botany.one in silico Plants is calling for papers for a special issue on integrative and multiscale modelling. This special issue will aim to publish research describing improved and newly developed multiscale models and tools.
You canât beat a good book â botany.one
Nigel Chaffey reviews A Cultural History of Plants edited by Annette Giesecke and David Mabberley
Botanists uncover the cost of cloning â botany.one If a plant wants to produce a clone of itself, then it's usually best to keep the new shoots close.
What is it that makes some plants rare? â botany.one What's behind the patterns of plant distribution, and are there any common features of rare plants? A team of botanists has been reviewing articles to find out.
You can protect blueberries from cold with some help from the Antarctic â botany.one Botanists have found a bodyguard that can protect blueberry plants from cold or drought shocks - but instead of protecting the outside of the plant, it lives inside it.
News & Views
Plants hold key to developing future cancer treatments Scientists say the natural world has an important role to play in creating new drugs to fight the disease
15 Gardening Books Perfect for Newbies and Seasoned Green Thumbs Alike â www.purewow.com From potentially improving your mood to burning some calories, taking on gardening has plenty of upsides, but getting started is no easy feat.
âThe tuber man of Keralaâ on a quest to champion Indiaâs rare and indigenous crops Shaji NM has devoted his life to collecting and farming tubers such as yam, cassava and taro, and promoting them across the country
How to attract bumblebees to your garden â www.wildlifetrusts.org The best plants for bumblebees! Bees are important pollinating insects, but they are under threat. You can help them by planting bumblebee-friendly flowers.
Some jack-in-the-pulpit plants may use sex to lure pollinators to their death â www.sciencenews.org Two species of jack-in-the-pulpits may use sex scents to lure male fungus gnats
Scientific Papers
Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium â www.mdpi.com
Pucker et al. present Knowledge-based Identification of Pathway Enzymes (KIPEs) as an automatic approach for the identification of players in the flavonoid biosynthesis. KIPEs combines comprehensive sequence similarity analyses with the inspection of functionally relevant amino acid residues and domains in subjected peptide sequences. Comprehensive sequence sets of flavonoid biosynthesis enzymes and knowledge about functionally relevant amino acids were collected. As a proof of concept, KIPEs was applied to investigate the flavonoid biosynthesis of the medicinal plant Croton tiglium on the basis of a transcriptome assembly. Enzyme candidates for all steps in the biosynthesis network were identified and matched to previous reports of corresponding metabolites in Croton species.
Managing for the unexpected: Building resilient forest landscapes to cope with global change
Mina et al. investigated how expected and unexpected variations in climate and biotic disturbances affect ecological resilience and carbon storage in a forested region in southeastern Canada. Using a process-based forest landscape model (LANDIS-II), they simulated ecosystem responses to climate change and insect outbreaks under different forest policy scenariosâincluding a novel approach based on functional diversification and network analysisâand tested how the potentially most damaging insect pests interact with changes in forest composition and structure due to changing climate and management. They found that climate warming, lengthening the vegetation season, will increase forest productivity and carbon storage, but unexpected impacts of drought and insect outbreaks will drastically reduce such variables.
Outram et al. review the recent advances in understanding hostâpathogen co-evolution provided by the structural determination of effectors alone, and in complex with immunity receptors. We highlight the use of recent advances in structural prediction within this field and its role for future development of designer resistance proteins.
Plant phosphorus-use and -acquisition strategies in Amazonia
Reichert et al. synthesize current knowledge of leaf P resorption, fine-root P foraging, arbuscular mycorrhizal symbioses, and root acid phosphatase and organic acid exudation and discuss how these strategies vary with soil P concentrations and in response to elevated atmospheric CO2. They identify knowledge gaps and suggest ways forward to fill those gaps. Additionally, we propose a conceptual framework for the variations in plant P-use and -acquisition strategies along soil P gradients of Amazonia.
A highly photostable and bright green fluorescent protein â www.nature.com
Hirano et al. present StayGold, a green fluorescent protein (GFP) derived from the jellyfish Cytaeis uchidae. StayGold is over one order of magnitude more photostable than any currently available fluorescent protein and has a cellular brightness similar to mNeonGreen. They used StayGold to image the dynamics of the endoplasmic reticulum (ER) with high spatiotemporal resolution over several minutes using structured illumination microscopy (SIM) and observed substantially less photobleaching than with a GFP variant optimized for stability in the ER.
plotsr: visualizing structural similarities and rearrangements between multiple genomes â academic.oup.com
Goel and Schneeberger present plotsr, an efficient tool to visualize structural similarities and rearrangements between genomes. It can be used to compare genomes on chromosome level or to zoom in on any selected region. In addition, plotsr can augment the visualization with regional identifiers (e.g. genes or genomic markers) or histogram tracks for continuous features (e.g. GC content or polymorphism density).
Semchanko et al review the evidence for host-specificity in plant-associated microbes and propose that specific plantâsoil feedbacks can also be driven by generalists. They outline the potential mechanisms by which generalist microbial pathogens, mutualists and decomposers can generate differential effects on plant hosts and synthesize existing evidence to predict these effects as a function of plant investments into defence, microbial mutualists and dispersal. Importantly, the capacity of generalist microbiota to drive plantâsoil feedbacks depends not only on the traits of individual plants but also on the phylogenetic and functional diversity of plant communities
Selection on the gametophyte: Modeling alternation of generations in plants
The degree of gametophyte dependence on the sporophyte life stage is a major feature that differentiates the life cycles of land plants, yet the evolutionary consequences of this difference remain poorly understood. Most evolutionary models assume organisms are either haploid or diploid for their entire lifespan, which is not appropriate for simulating plant life cycles. Sorojsrisom et al. introduce shadie (Simulating HaploidâDiploid Evolution), a new, simple Python program for implementing simulations with biphasic life cycles and analyzing their results, using SLiM 3 as a simulation back end.
The Cycas genome and the early evolution of seed plants â www.nature.com
Liu et al. report the 10.5-Gb reference genome of Cycas panzhihuaensis, complemented by the transcriptomes of 339 cycad species. Nuclear and plastid phylogenomic analyses strongly suggest that cycads and Ginkgo form a clade sister to all other living gymnosperms, in contrast to mitochondrial data, which place cycads alone in this position. They found evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms.
Hseih et al. used gene expression analysis, peptide treatment and virus-induced gene alteration assays to demonstrate that C-terminally encoded peptide (CEP2) expression in tomato was downregulated during AM symbiosis to mitigate its negative effect on plant lateral root formation through an auxin-related pathway
Global assessment of relationships between climate and tree growth
Tree-ring records provide global high-resolution information on tree-species responses to global change, forest carbon and water dynamics, and past climate variability and extremes. The underlying assumption is a stationary (time-stable), quasi-linear relationship between tree growth and environment, which however conflicts with basic ecological and evolutionary theory. Indeed, our global assessment of the relevant tree-ring literature demonstrates non-stationarity in the majority of tested cases, not limited to specific proxies, environmental parameters, regions or species. Non-stationarity likely represents the general nature of the relationship between tree-growth proxies and environment. Studies assuming stationarity however score two times more citations influencing other fields of science and the scienceâpolicy interface. To reconcile ecological reality with the application of tree-ring proxies for climate or environmental estimates, Wilmking et al. provide a clarification of the stationarity concept, propose a simple confidence framework for the re-evaluation of existing studies and recommend the use of a new statistical tool to detect non-stationarity in tree-ring proxies.
Careers
Assistant Professor - Crop Sciences
We invite outstanding scientists to apply for the Soybean Improvement faculty position. The position will augment traditional cultivar development with innovative genomics, computational, and/or sensor-based approaches to advance and accelerate plant breeding efforts and conduct breeding and genetics research. The successful candidate will have a strong record of original research in plant breeding or other relevant disciplines such as genomics, quantitative genetics, plant biotechnology, or phenomics.
Post Doc Position : Role of genetic load in woody plant adaptation (Perfit) A 14 months (+9) position supported by Bordeaux Plant Science (BPS) research program is available at the UMR BIOGECO in Bordeaux, France. This post-doc position is one of 19 offered positions as part of Bordeaux University excellence BPS program, which will provide access to many scientific events and resources. The successful candidate will work on the project Perfit.
Postdoctoral Researcher This project will explore the genetic and epigenetic factors that influence the inheritance of homoeolog expression patterns in wheat. This will provide a first step towards being able to manipulate homoeolog expression patterns for crop improvement. The post holder will design, execute and analyse genomic experiments, although there is scope for molecular biology work.
Research Associate in Computational Biology (Plant Circadian Clock) Applications are invited for a BBSRC funded Post-doctoral Research Associate position to work in the group of Dr James Locke at the Sainsbury Laboratory, in close collaboration with Professor Alex Webb of the Department of Plant Sciences, focused on the modelling of the circadian (24-hour) clock in plants. The position involves developing the first model of the Wheat circadian clock. Wheat is a key crop and understanding the clock in wheat will have broad significance as the clock controls many key processes in plants. The candidate will analyse new RNA-seq clock data collected in Professor Webb's group and use machine learning techniques to develop an optimised computational model of the core wheat clock network.
Postdoct in plant biology and Biochemistry The recruited postdoctoral research will identify the protein complexes formed by signaling components upstream of transcription factors. This includes designing and building DNA constructs, genetic transformation of Marchantia, identification of interacting proteins by TurboID and biochemical validations. The recruited postdoc will present her/his work to diverse audience through seminars (team, department, national and international conferences) and publications.
Vineyard Soil Health Scientist The Scientific Assistant Senior performs the following non-inclusive list of tasks: sets up, maintains, and collect data from a long term vineyard soil health research site. Responsible for supervising/managing research operations and personnel. Also responsible for irrigating, spraying, mowing, fertilizing, harvesting, etc. The candidate will work closely with the Principal Investigator to manage all aspects of data generation and field activities.
Research Associate (for 3 years) in Bioinformatics The position is in the third-party funded DFG project: âEvolution of gene networks: The Ranunculales as a model order for evolutionary innovationsâ (RanOmics) at the Department of Biology and Chemistry (Prof. Dr. Alexander Goesmann).
Researcher cultivation and crop physiology in greenhouse horticulture We are looking for a colleague who conducts research about the reactions of the horticultural crops to, for example, the greenhouse climate, (LED) lighting, who integrates this knowledge in sustainable and innovative cultivation strategies together with a.o. plant nutrition and crop health aspects.
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