đ± TWiB February 28, 2022
Usually, I describe this as a collection of the top links shared by people following @BotanyOne on Twitter. This week most botanists are talking about something else. If you want to read about the main topic of conversation, there are many people better informed than me. When the news is bad, I'm lucky because I can immerse myself in work and take a break from the worst of what is happening. If you also need a break, there was still plenty of interesting Botany shared this week.
If you're struggling with the news on social media or the television at the moment, then it's perfectly ok to step away for a few days. It's important to look after yourself, and I doubt you've had an easy 2020 or 2021.
Unless something goes wrong in the office, there should be another email with you around the same time next week. Until then, take care.
Alun (webmaster@botany.one)
In Botany One
Botanists find the effects of ancient climates in the modern genomes of two closely related oak species â www.botany.one Botanists examined the genomes of two species, Quercus acutissima and Q. chenii, to see if changes in the climate three million years ago affected how they hybridised.
Phylogenomic analyses of the East Asian endemic Abelia â www.botany.one Sun et al. used genomic data to reconstruct the phylogeny of Abelia and found a clear pattern of reticulate evolution in the group.
Reverse archaeology reveals new insights into global warming â www.botany.one Often archaeologists will examine differences in vegetation to gain information on buried sites. Now, some botanists have reversed this and are using archaeological sites to learn about the effect of nutrient differences on plants.
Below-ground hydraulics control stomatal closure â www.botany.one Botanists find that during soil drying, stomatal regulation is controlled by below-ground hydraulics in a predictable way.
From fossils to landscapes: the art of reconstructing plants in the past â www.botany.one How can you reconstruct the vegetation of deep time? One professor has turned to canvas and paint.
News & Views
easystats: Quickly investigate model performance
Easystats performance is an R package that makes it easy to investigate the relevant assumptions for regression models. This was popular among the people who understand R this week.
A year in the life of Durham University Botanic Gardens: January â heatherkelly.blog January is not the most obvious time to be out in a garden but there is always something to see. The first time I visited, in the middle of the month, it was all about frost-rimed leaves.
A Staggering Amount of Amazon Rainforest Disappeared in January 2022 â gizmodo.com Deforestation has increased rapidly under Brazilian President Jair Bolsonaro, as new satellite data reveals.
Why Weâre Not Doomed After All (If We Act Quickly On Climate) Scientists say âbaked-inâ climate warming is a myth but we must reduce emissions now.
The Food Programme - Fresh Grounds: The Search for the World's Rarest Coffee â www.bbc.co.uk Dan Saladino meets the plant hunters looking for the world's forgotten coffee varieties.
A taste for wild cereal sowed farmingâs spread in ancient Europe â www.sciencenews.org Balkan hunter-gatherers ate starchy grains several millennia before they cultivated crops
Gene-edited wheat resists dreaded fungus without pesticides New strain survives powdery mildew, a costly disease, without side effects
Climate Change Could Increase Risk of Wildfires 50% by Century's End â www.nytimes.com Worsening heat and dryness could lead to a 50 percent rise in off-the-charts fires, according to a United Nations report.
New study reveals algae can help further reduce CO2 emissions â techxplore.com Argonne study shows that carbon emissions that come from making ethanol can cultivate algae which in turn can be used to make biofuel.
Scientific Papers
PyUUL provides an interface between biological structures and deep learning algorithms â www.nature.com
Orlando et al. present PyUUL (https://pyuul.readthedocs.io/), a library to translate biological structures into 3D tensors, allowing an out-of-the-box application of state-of-the-art deep learning algorithms. The library converts biological macromolecules to data structures typical of computer vision, such as voxels and point clouds, for which extensive machine learning research has been performed. Moreover, PyUUL allows an out-of-the box GPU and sparse calculation.
Rusman et al. compared the preference and performance of two florivores on flowering Brassica nigra plants damaged by one of three herbivores feeding from roots or leaves. To investigate the underlying mechanisms, they quantified expression patterns of marker genes for defence-related phytohormonal pathways, and concentrations of phytohormones and glucosinolates in buds and flowers.
Progressive maturation of the root apical meristem in Arabidopsis thaliana lateral roots
Berthet er al. characterize the de novo establishment of the root apical meristem in lateral roots. While the position of the new stem cell niche is set early during morphogenesis, its cellular layout, unique gene expression profile and mitotic quiescence are only acquired after emergence concomitant to the establishment of two diverging growth axis. Their results show that the intertwined attributes of the mature root stem cell niche are progressively acquired during lateral root formation, and support a model in which the position of the stem cell niche emerges from the establishment of diverging growth axis.
Thirty years of resistance: Zig-zag through the plant immune system
Ngou et al. provide a list of characterized pattern recognition receptors (PRRs) and nucleotide-binding leucine-rich repeat receptors (NLRs). In addition to immune receptors, many components of immune signaling networks were discovered over the last 30 years. They review the signaling pathways, physiological responses, and molecular regulation of both PRR- and NLR-mediated immunity. Recent studies have reinforced the importance of interactions between the two immune systems. They provide an overview of interactions between PRR- and NLR-mediated immunity, highlighting challenges and perspectives for future research.
Moore et al. highlight new research directions to elucidate how introduced plant growth-promoting rhizobacteria impact resident microbiomes and ecosystem functions and their capacity for legacy effects.
Does green space influence assaults? Evidence from Toronto, Canada
Criminal behavior has been traditionally linked to green space. However, studies on the relationship between green space and crime vary in their conclusions and even contradict each other. This variability is primarily attributed to the mixing-up of specific crimes and the less-explored influencing mechanisms. This study considers Toronto and focuses on a specific kind of crime, assault, for exploring whether green space influences the neighborhood assault rate. If so, then how does it affect the assault rate? Spoiler: High percentages of green space, grass, and trees reduce assault risk.
Climate and crown damage drive tree mortality in southern Amazonian edge forests
Using 10Â years of data from a widespread network of long-term forest plots, Reis et al. assessed how trees die (standing, broken or uprooted) and used generalised mixed-effect models to explore the contribution of plot-, species- and tree-level factors to the likelihood of tree death.
Structural organization of the spongy mesophyll
Using micro-computed tomography imaging, topological analysis, and a comparative physiological framework, Borsuk et al. examined the structure of the spongy mesophyll in 40 species from 30 genera with laminar leaves and reticulate venation.
Careers
Summer Internship Programme 2022 We are delighted to announce details of our 2022 Summer Internship Programme at Trinity College Botanic Garden.
Post-doc position direct validation of greenhouse gas emission reduction measures in circular agriculture The recently approved ERA-NET Relive project, a collaboration of 11 universities and institutes ranging from Ireland to New Zealand and Finland to Chile, including the Netherlands, will take a holistic approach to the sustainable reintegration of livestock and cropping systems
Scientist/Postdoc/Group Leader Molecular Phytopathology The candidate should focus and develop research on molecular plant pathology. Research should preferably focus on barley or other Triticeae crops. Possible research areas are to develop, improve and apply genome editing techniques in crops to study plant pathology or cell biology of crop plant pathogen interactions.
Postdoctoral Research Associate We are recruiting a postdoctoral researcher to join a collaborative, NASA-funded project investigating the success of ferns following the K-Pg extinction. We seek a motivated candidate to lead the analysis of plant community and trait datasets related to questions about plant resilience and extinction across the K-Pg boundary. This project involves an exciting opportunity to analyze deep-time paleontological datasets using approaches in Quaternary paleoecology and community ecology. Experience working with fossil data is helpful, but not required. The successful candidate will have the opportunity to develop a project related to their interests in line with the themes of the grant (using modeling, lab analyses, or other approaches).
Now hiring: Plant Physiologist, Assistant Professor! The Department of Biological Sciences at East Stroudsburg University of Pennsylvania invites applications for a full-time, tenure-track position in Plant Physiology at the rank of Assistant Professor. Located in the beautiful Pocono Mountains of Pennsylvania, ESUâs proximity to New York City and Philadelphia provide convenient access to internships, careers and social activities. Just minutes from campus are the countryâs largest water parks, scenic Delaware Water Gap Recreation Area, Appalachian Trail, and other opportunities for recreational fun.
Research Assistant (Borrill Group) The Research Assistant (RA) will contribute to a BBSRC-funded project which explores how gene expression is controlled in polyploid wheat. The RA will carry out molecular biology experiments and generate plant germplasm to support this project.
Botany360 Botany360 is a community event calendar that highlights events happening during the 360 days outside of the Botany Conferences. The goal of this program is to connect the plant science community throughout the year with professional development, discussion sessions, and networking and social opportunities.
Assistant Professor â Plant Molecular Geneticist: Molecular Genetics for Plant Adaptation The successful candidate will conduct innovative, extramurally funded research to understand molecular networks underlying plant traits and develop novel trait biotechnology, leveraging natural variation, induced variation, and/or genome editing. Individuals working on molecular genetics in model plants with an interest in translating discoveries to crop species are encouraged to apply. This is part of a series of faculty hires focused on improving plant adaptation in agroecosystems. The knowledge and technology generated by the program will contribute to improved plant adaptation, broadly defined: this may include adaptation of crop plants to environmental stressors, related to climate, soils, or pests; and/or adaptation of plants to societal needs, such as productivity, value, wellness, or sustainability.Â
Research Assistant (Bioimaging Platform) The post-holder will be based within the Bioimaging platform, helping to establish the Volume EM techniques of serial block face scanning electron microscopy (SFB-SEM) and array tomography, utilising recent capital investments in new equipment and supporting the local research community working on plants and microbes.
Assistant Professor - Botany The successful candidate will be expected to direct and advance the mission of the Ronald L. Jones Herbarium, the largest in the Commonwealth of Kentucky, which is housed in the recently completed (August 2017) Science Building. Knowledge of the flora of the eastern United States is essential for both teaching and direction of the herbarium. In addition, the incumbent will establish an active research program, mentor undergraduate and graduate (MS) students, and engage with conservation-oriented organizations such as the Kentucky Native Plant Society, the Office of Kentucky Nature Preserves, and US Fish and Wildlife Service. Areas of research may include, but are not limited to, computational biology, population biology, plant phylogenetics/systematics, and organismal diversity.Â
Postdoctoral Research Scholar The Department of Plant and Microbial Biology at North Carolina State University invites applications for a Postdoctoral Research Scholar position in the lab of Dr. Terri Long. The Postdoctoral Research Scholar will collaborate with mathematical modelers to conduct hypothesis-driven molecular, genetic, and biochemical experimentation that will delineate the molecular rules underlying systemic Fe homeostasis in Arabidopsis. The candidate will be expected to contribute to a variety of studies to characterize protein function and dynamics in Arabidopsis that will require the use of in vitro protein analysis (ie. Immunoprecipitation, immunoblotting), as well as confocal, enzymatic, and physiological analysis. The candidate will be expected to design and conduct quality, substantive, and methodological research, and share and report research findings by publishing papers in peer-reviewed scientific journals and participating in research conferences, seminar series, and other appropriate professional activities. The postdoc will meet frequently with Dr. Long to discuss best practices in grant writing, manuscript preparation, and mentoring.Â
Research Leader â Temperate Pastures The successful applicant will work with leading scientists and technical team to achieve key economic and environmental outcomes to support the future growth of agriculture across and have oversight of a diverse research portfolio including perennial grains, clovers for honey and anti-methanogenic pastures to reduce GHG emissions.
Junior Professorship for âMolecular Plant Physiologyâ The successful candidate's responsibilities will include developing a cutting-edge research program to lead and recruit an associated team in the field of molecular plant physiology and/or plant systems biology.
Field Ecologist We are looking for an accomplished field ecologist who will be a key team member in the delivery of large,  complex, multi-organisation field surveys.  Based in Bangor on the coast of North Wales at the foothills of the Snowdonia National Park, this role will contribute to the delivery of  annual field surveys throughout Wales. Â
Data Production Officer (Completing the Plant Tree of Life) It is an exciting time to join Kew Science and, the âCompleting the Plant Tree of Lifeâ project, part of the Tree of Life Initiative, one of Kew Scienceâs key strategic goals for 2021- 2025. This ambitious project aims to complete the tree of life for all flowering plant genera using high throughput sequencing data and provide a unifying framework for comparative plant and fungal research.
Curator-Botanist This is an excellent opportunity to join the dynamic Herbarium Curation team in the Science Collections department. The successful candidate will curate the Herbarium Collections to a high standard, which includes processing new acquisitions, preparing loans and working with Kew databases. In addition to this, the role includes facilitating access for our many visitors to the collections from around the world, identifying specimens from the Asian and Pacific region and providing research support within Kew Science.
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