🌻 TWiB November 7, 2022
For my week off we had more stories out than usual. I've been using my time off to experiment with sharing to Mastodon and Tumblr. Every time I needed to test something I'd use a press release with some fairly minimal editing to see how servers were talking to each other. Tumblr is going badly, but you can see Mastodon at work at @botanyone@botany.social. We'll still be sticking with Twitter for now, but I can understand why many scientists are leaving. There's a noticeable reduction in the science people are sharing, but maybe it will pick up in the New Year.
The other holiday project, the coding for the redesign, has gone well but I need to prettify it. The goal will be to get that done for Wednesday, and then see how everyone reacts to it as a draft. I don't know if or when it will go live.
The only thing I can say for certain is that I'll be aiming to get another email with you at the same time next week. Until then, take care.
Alun (webmaster@botany.one)
In Botany One
Study examines how well-timed cover crops can suppress weeds in California orchards — botany.one Experiments show a variety of cover crop management programs can produce weed-suppressing cover crops.
Want to save the bees? Pay attention to pathogens and flowers — botany.one Researchers at UMass Amherst deploy fluorescent paint, pipettes, tents, tweezers and scissors to trace three-way connection between plants, pathogens and bees
Vegetation regulates energy exchange in the arctic — botany.one Despite the importance of high-latitude surface energy budgets for land-climate interactions in the rapidly changing Arctic, uncertainties in their prediction persist.
Bats protect young trees from insect damage, with three times fewer bugs — botany.one Not only did the bats reduce the number of caterpillars, they also reduced defoliation by a factor of five.
Plant hormones to help prevent Striga invasion — botany.one Blocking the biosynthesis of canonical strigolactones by TIS108, a specific enzyme inhibitor, significantly lowered Striga infestation without affecting rice growth.
The importance of light for grassland plant diversity — botany.one Field experiment shows that competition for light is the key mechanism driving loss of plant diversity under eutrophication and lack of grazing.
News & Views
Cover stories: Inferring plant–plant interactions using remote sensing — jecologyblog.com While one can use sophisticated experiments to study plant-plant interactions under well-controlled conditions, it is difficult to say how often and how strong these interactions are in natural ecosystems, especially at large spatial scales. For instance, would it be possible to tell if co-existing plants are mostly friendly or hostile to one another, just from a glimpse of the landscape, like in the cover image?
To Fight Misinformation, We Need to Teach That Science Is Dynamic Science is a social process, and teaching students how researchers work in tandem to develop facts will make them less likely to be duped by falsehoods
Leave, Adapt, Resist – Time to rethink Academic Twitter? — blogs.lse.ac.uk As Twitter moves to become a private company owned by the billionaire Elon Musk, Mark Carrigan, reflects on the increasing importance academic social media and academic twitter has secured in universities for building academic communities and for public engagement and impact.
Genome editing in plants: why it is urgent for Europe to change its legislation — sciencemediacentre.es The Spanish Confederation of Scientific Societies (COSCE) has just published a report, submitted to the EU, which proposes and compares different possibilities for reform of the regulatory framework for genome editing techniques.
Nearly a third of southern Sierra forests killed by drought and wildfire in last decade — www.latimes.com As climate change continues to transform California’s landscape in staggering and often irreversible ways, researchers have zeroed in on yet another casualty of the shift: the forests of the southern Sierra Nevada.
Japan-led team finds plants may be using hormones to communicate, control growth — mainichi.jp A research group led by an Ehime University associate professor has shown that plants may use hormones to communicate beneath the soil and control their growth above it when they sense the presence of neighboring plants.
Orchidelirium. Colonialism through the lens of botany — we-make-money-not-art.com Even though Emilie Rosalie Saal is a rather obscure figure in Estonian history, artists Kristina Norman and Bita Razavi, in close collaboration with curator Corina L. Apostol, have made her the focus of the Estonian pavilion at the Venice Biennial.
Native voices were finally heard at California's biggest native plant conference — www.latimes.com Something’s happened in the four years since the California Native Plant Society — CNPS — had its last statewide conference. The state’s premier environmental group “dedicated to the preservation and celebration of California’s native flora” finally got the memo about diversity and inclusion.
Scientists discover ‘world’s largest’ seagrass forest – by strapping cameras to sharks New study, carried out using tiger sharks in the Bahamas, extends total known global seagrass coverage by more than 40%
Scientific Papers
Reverse Chromatin Immunoprecipitation Technique Based on the CRISPR-dCas9 System
DNA-protein interaction is one of the most crucial interactions in biological processes. However, the technologies available to study DNA-protein interactions are all based on DNA hybridization; however, DNA hybridization is not highly specific and is relatively low in efficiency. RNA-guided DNA recognition is highly specific and efficient. To overcome the limitations of technologies based on DNA hybridization, Wang et al. built a DNA-binding protein capture technology based on the clustered regularly interspaced palindromic repeats (CRISPR)-dead Cas9 (dCas9) system and transient genetic transformation, termed reverse chromatin immunoprecipitation based on CRISPR-dCas9 system (R-ChIP-dCas9).
Insight into the control of nodule immunity and senescence during Medicago truncatula symbiosis
Medicago (Medicago truncatula) establishes a symbiosis with the rhizobia Sinorhizobium sp, resulting in the formation of nodules where the bacteria fix atmospheric nitrogen. Loss of immunity repression or early senescence activation compromises symbiont survival and leads to the formation of non-functional nodules (fix-). Despite many studies exploring an overlap between immunity and senescence responses outside the nodule context, the relationship between these processes in the nodule remains poorly understood. To investigate this phenomenon Berrabah selected and characterized three Medicago mutants developing fix- nodules and showing senescence responses.
The trajectory in catalytic evolution of Rubisco in Posidonia seagrass species differs from terrestrial plants — academic.oup.com
The CO2-fixing enzyme Ribulose bisphosphate carboxylase-oxygenase (Rubisco) links the inorganic and organic phases of the global carbon cycle. In aquatic systems, the catalytic adaptation of algae Rubiscos has been more expansive and followed an evolutionary pathway that appears distinct to terrestrial plant Rubisco. Capó-Bauçà et al. extend this survey to differing seagrass species of the genus Posidonia to reveal how their disjunctive geographical distribution and diverged phylogeny, along with their CO2 concentrating mechanisms (CCMs) effectiveness, have impacted their Rubisco kinetic properties
Genome editing in plants using the compact editor CasΦ
Li et al. demonstrate that the hypercompact CasΦ nuclease is able to generate stably inherited gene edits in Arabidopsis, and that CasΦ guide RNAs can be expressed with either the Pol-III U6 promoter or a Pol-II promoter together with ribozyme mediated RNA processing.
Cooltools: enabling high-resolution Hi-C analysis in Python
OPen2C et al. introduce cooltools (https://github.com/open2c/cooltools), a suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Cooltools leverages the widely-adopted cooler format which handles storage and access for high-resolution datasets. Cooltools provides a paired command line interface (CLI) and Python application programming interface (API), which respectively facilitate workflows on high-performance computing clusters and in interactive analysis environments.
Light competition drives herbivore and nutrient effects on plant diversity — www.nature.com
Eskelinen et al. show that experimentally restoring light to understory plants in a natural grassland mitigates the loss of plant diversity that is caused by either nutrient enrichment or the absence of mammalian herbivores. The initial effect of light addition on restoring diversity under fertilization was transitory and outweighed by the greater effect of herbivory on light levels, indicating that herbivory is a major factor that controls diversity, partly through light. Their results provide direct experimental evidence, in a natural system, that competition for light is a key mechanism that contributes to the loss of biodiversity after cessation of mammalian herbivory.
Improving quantitative synthesis to achieve generality in ecology — www.nature.com
Spake et al. review current practice in ecological synthesis and demonstrate that, when researchers fail to define the assumptions underpinning generalizations and transfers of effect sizes, generality often misses its target. They provide guidance for communicating nuanced inferences and maximizing the impact of syntheses both within and beyond academia.
Small rainfall changes drive substantial changes in plant coexistence — www.nature.com
Van Dyke et al. explored how changes in precipitation alter competitive dynamics via direct effects on individual species, as well as by the changing strength of competitive interactions between species, using an annual grassland community in California.
Studying flowers in 3D using photogrammetry
Leménager et al. developed a floral photogrammetry protocol to reconstruct 3D models of flowers based on images taken with a digital single-lens reflex camera, a turntable and a portable lightbox.
Careers
Assistant Editor at Society for Experimental Biology You will be expected to be able to work independently and use your initiative. You should have relevant experience and be able to communicate effectively, accurately and empathetically. You should possess excellent IT skills and be well-organised.
PhD Project: Balancing human & biodiversity needs from agricultural landscapes The aim of this project is to gain an understanding of the relationship between agricultural land-use – in the context of the wider landscape – and functional diversity, covering a wide range of functions and taxonomic groups via the following questions: 1) which functional groups are most impacted by agricultural land-use?; 2) are communities in agriculturally intensive landscapes more functionally homogenised (and less resilient) compared to other land-uses?; and 3) how can we design agricultural landscapes to avoid loss of functional diversity and ecosystem services?
Spatial Scientist / Ecologist - Civil Service Jobs
Three, two-year spatial scientist posts are available within the Land Use and Ecosystem Services (LUES) Science Group with Forest Research. Forest Research (FR) is the research agency of the Forestry Commission, and a world leader in applied forest science and a trusted and recognised provider of expertise, data, products and services for governments and the tree, wood, forest and natural resource sectors.
Professorship of Plant Development - University of Cambridge The Board of Electors to the Professorship of Plant Development invite applications from individuals whose work falls within the general field of the Professorship to take up the appointment at the Sainsbury Laboratory at Cambridge University as soon as possible.
Laboratory Manager Assistant (Fixed Term) - University of Cambridge Applications are invited for a Laboratory Manager Assistant to ensure the smooth running of the laboratories at the Crop Science Centre. This is an exciting opportunity for somebody passionate about laboratory management to join a team of vibrant and friendly group of researchers and technicians and work in a state-of-the-art laboratory.
Postdoctoral Research Associate - Remote Sensing - UMaine The postdoctoral associate will conduct research to incorporate disturbance through time and remote sensing into a scaling framework of forest structure and functional diversity using in-situ and remotely sensed data, as well as assisting with other projects to provide research support for the PI. The typical hiring range for this soft-money, fixed-length position is $50,000 to $54,000 commensurate with qualifications and experience.
IMPRS Application - Max Planck Institute for Plant Breeding Research To be considered for selection, you must hold a Master’s degree or comparable and have completed 4 to 5 years of university studies in subjects relevant to the individual projects. While it is not necessary to hold the degree at the time of application, it must be awarded before PhD projects start.
University Associate Professor - University of Cambridge Applications are invited for an Associate Professor post in Plant Sciences, available from 1 October 2023. Key responsibilities include teaching undergraduates; conducting world-leading research; advising postgraduate students and post-doctoral workers; and other duties associated with academic life. There is the opportunity to become a Fellow of a College.
Postdoctoral Research Associate in Plant Immunity (Fixed Term) - University of Cambridge Applications are invited for a post-doctoral research associate in Plant immunity to work with Dr Lida Derevnina at the Crop Science Centre, starting between 1 January and 1 April 2023.
Postdoctoral Researcher (Sablowski Group) - John Innes Centre Two positions are available (please see a separate advert for position 1004341). The position with reference 1004340 will focus on the link between cell size and genome size and how it relates to the mechanism for cell size control. Within this broad aim, the post holder will design, execute, and interpret experiments to test hypotheses, then propose and test their own hypotheses, informed by results.
We seek a PhD student to measure whole ecosystem carbon fluxes and cycling along two contrasting forest age gradients in northern Sweden – one wildfire recovery gradient (spanning 3 and 370 years since wildfire) and one rotation forestry gradient (spanning the full spectrum of a typical 100-year rotation period).
Postdoctoral Researcher (Banfield Group) - John Innes Centre The role investigates the interaction between a polymorphic family of M. oryzae effector proteins and their putative host targets, with specific alleles associated with grass-specific pathogen lineages. The Postdoctoral Researcher will investigate how this can be used for immune engineering through the design of novel specificities in plant NLRs.
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