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Updates from the group of Sophien Kamoun at The Sainsbury Lab
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Medium: Pikobodies: A new hope for made-to-order plant disease resistance (2023)

Medium: Pikobodies: A new hope for made-to-order plant disease resistance (2023) | Publications | Scoop.it

Plants lack an adaptive immune system, so Jiorgos Kourelis and Clémence Marchal in the Kamoun lab had the ambitious idea to piggyback mammalian adaptive immunity and produce made-to-order plant immune receptors called Pikobodies.

 

FIRST PUBLISHED: 03.03.23. Mia Cerfonteyn, The Sainsbury Laboratory.

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Medium: What is a scientist? Celebrating diversity at the Norwich Science Festival (2023)

Medium: What is a scientist? Celebrating diversity at the Norwich Science Festival (2023) | Publications | Scoop.it

The Norwich Science Festival is an annual celebration of science, technology, engineering, and mathematics (STEM) that takes place in Norwich, UK. The festival aims to inspire people of all ages and backgrounds to engage with science and to learn more about the latest research and discoveries. The festival features a wide range of events, including talks, workshops, exhibitions, and interactive activities, all designed to be informative, entertaining, and engaging.

 

This year, thanks to Dr. Emma Waters, a Postdoctoral Researcher at the Quadram Institute, the festival will cover the importance of diversity in science. Emma’s own story inspired her to develop an exhibition called “What is a scientist?” for Norwich Science Festival 2023. The exhibition showcases the diversity of scientists at our science campus and aims to inspire individuals from all backgrounds to pursue a career in science. You can read about Emma’s motivation for this project in her blog post: “Diversity in science; If you can see it, you can be it”.

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Medium: 3 unexpected things we owe to the plant pathogenic bacterium Xanthomonas (2023)

Medium: 3 unexpected things we owe to the plant pathogenic bacterium Xanthomonas (2023) | Publications | Scoop.it

I have a special relationship with the bacterium Xanthomonas. As a grad student at UC Davis, I did my thesis research on Xanthomonas campestris pathovar campestris, a species of this genus of bacterial pathogens that causes disease on the vegetable and seed crops known as brassicas, which include plants such as cabbage, broccoli, radish, and mustard.

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Medium: Three dialogs between a Professor and a student who performed an experiment without including controls (2023)

Medium: Three dialogs between a Professor and a student who performed an experiment without including controls (2023) | Publications | Scoop.it

These are fictional exchanges between a Professor and a student who didn’t include controls in their experiment. Which is your favorite?

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Medium: Deadlanuary — why do we have so many deadlines in January? (2023)

Medium: Deadlanuary — why do we have so many deadlines in January? (2023) | Publications | Scoop.it

The first month of the year is when people often make resolutions to improve their life. But for academics, January is Dedlanuary: the month of deadlines.

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Medium: How I used ChatGPT to co-write the story “Crispin is amazing” (2022)

Medium: How I used ChatGPT to co-write the story “Crispin is amazing” (2022) | Publications | Scoop.it

The limiting factor in writing a story should be the idea, not the specific writing skills. Here is a step-by-step guide to how I used ChatGPT to co-write the story “Crispin is amazing”.

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Medium: Hail to the Closer and more authorship considerations (2022)

Medium: Hail to the Closer and more authorship considerations (2022) | Publications | Scoop.it

The article “Authorship — Let’s talk about it!” sparked a lot of debate. Let’s go through the following issues once more: the significance of the closer, or the person who is given the opportunity to complete the work; who should be a corresponding author; and do we require a “legal” definition of authorship.

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Medium: Herding cats — how to get biologists to preprint (2022)

Medium: Herding cats — how to get biologists to preprint (2022) | Publications | Scoop.it

Managing academics is like herding cats. However, funding agencies — if they wish to — have the power to herd the academic cats and drive them to embrace open science and early sharing of research findings through preprints.

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Medium: Je tweete, donc je suis — Why I’m sticking with Twitter (2022)

Medium: Je tweete, donc je suis — Why I’m sticking with Twitter (2022) | Publications | Scoop.it

Much chatter about Twitter after Elon Musk bought it for $44 billion. Who knows what’s next, but for now I’m sticking with the platform that serves as my diary and a grab bag for many of the things I care about.

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Medium: Introducing GetGenome — Genomics for all! (2022)

Medium: Introducing GetGenome — Genomics for all! (2022) | Publications | Scoop.it
GetGenome is our newly formed charitable organisation that provides equitable access to genomics technology for early career researchers all over the world. GetGenome also provides training in the…
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Medium: Could a new threat to cereal production be emerging in Europe? (2022)

Medium: Could a new threat to cereal production be emerging in Europe? (2022) | Publications | Scoop.it

For the first time, scientists have detected the blast fungus in Germany. The pathogen was found on diseased wild grasses and is also able to infect wheat and barley, suggesting that blast diseases pose an emerging threat to cereal production in central Europe.

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Medium: CRISPR gene editing in conservation biology (2022)

Medium: CRISPR gene editing in conservation biology (2022) | Publications | Scoop.it

Conservation biology requires a bigger toolbox to meet the biodiversity crisis. Is there a role for CRISPR and gene editing?

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Medium: Death by Statistics (2022)

Medium: Death by Statistics (2022) | Publications | Scoop.it

“Statistics cannot substitute for clear thinking. It can’t do the job of human inductive inference.”

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Medium: Humans are more closely related to fungi than the plant killer Phytophthora (2023)

Medium: Humans are more closely related to fungi than the plant killer Phytophthora (2023) | Publications | Scoop.it

After realizing that ChatGPT has finally learned that Phytophthora and other oomycetes are not fungi, making peace with it became easier.

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Medium: Are Google and Bing Featured Snippets more accurate than chatbots? (2023)

Medium: Are Google and Bing Featured Snippets more accurate than chatbots? (2023) | Publications | Scoop.it

A number of this blog’s posts were selected as Featured Snippets by Google and Bing, and they typically offered accurate answers to the queries. Will chatbot search engines be as good?

 

 

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bioRxiv: Bimodular architecture of bacterial effector SAP05 drives ubiquitin-independent targeted protein degradation (2023)

bioRxiv: Bimodular architecture of bacterial effector SAP05 drives ubiquitin-independent targeted protein degradation (2023) | Publications | Scoop.it

In eukaryotes, targeted protein degradation (TPD) typically depends on a series of interactions among ubiquitin ligases that transfer ubiquitin molecules to substrates leading to degradation by the 26S proteasome. We previously discovered that the bacterial effector protein SAP05 mediates ubiquitin-independent TPD. SAP05 forms a ternary complex via interactions with the von Willebrand Factor Type A (vWA) domain of the proteasomal ubiquitin receptor Rpn10 and the Zinc-finger (ZnF) domains of the SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) and GATA BINDING FACTOR (GATA) transcription factors (TFs). This leads to direct TPD of the TFs by the 26S proteasome. Here, we report the crystal structures of the SAP05-vWA complex at 2.17 Å resolution and of the SAP05-ZnF(SPL5) complex at 2.20 Å resolution. Structural analyses revealed that SAP05 displays a unique bimodular architecture with two distinct non-overlapping surfaces, a ‘loop surface’ with three protruding loops that form electrostatic interactions with ZnF, and a ‘sheet surface’ featuring two β-sheets, loops and ⍺-helices that establish polar interactions with vWA. SAP05 binding to ZnF TFs involves single amino acids responsible for multiple contacts, while SAP05 binding to vWA is more stable due to the necessity of multiple mutations to break the interaction. In addition, positioning of the SAP05 complex on the 26S proteasome points to a mechanism of protein degradation. Collectively, our findings demonstrate how a small bacterial bimodular protein can bypass the canonical UPS cellular proteolysis pathway, enabling ubiquitin-independent TPD in eukaryotic cells. This knowledge holds significant potential for the creation of novel TPD technologies.


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Medium: Blue Monday and beyond: Coping strategies for scientists (2023)

Medium: Blue Monday and beyond: Coping strategies for scientists (2023) | Publications | Scoop.it

I didn’t start the year with the energy and drive I had hoped for. I found it hard getting out of bed in the early morning darkness. Sunrises at eight in the morning are nothing new for me — I’ve lived in the UK for more than 15 years — but this year feels different.

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Medium: J-Turing Test? ChatGPT struggles with Joekes like many of us (2023)

Medium: J-Turing Test? ChatGPT struggles with Joekes like many of us (2023) | Publications | Scoop.it

According to Proffunguy, a regular contributor to Urban Dictionary, a joekeis a joke told by Joe—a legendary character known for delivering ambiguous jokes with (hopefully) humorous puns.

Here is a joeke straight from the Dictionary: “Do you know where the fish keep their money? In the riverbank, of course.”

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Medium: Wisdom of the crowd — What’s the most important food crop (2022)

Medium: Wisdom of the crowd — What’s the most important food crop (2022) | Publications | Scoop.it

Is the collective opinion of a group of people more valuable than that of a single expert? I don’t know. What do you think?

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Medium: Authorship — Let’s talk about it! (2022)

Medium: Authorship — Let’s talk about it! (2022) | Publications | Scoop.it

In academia, authorship can be a touchy subject that is all too easy to sidestep. However, it’s always simpler to have a contentious conversation prior to submission.

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Medium: Celebrating alumni (2022)

Medium: Celebrating alumni (2022) | Publications | Scoop.it

Nothing — absolutely nothing — beats seeing an early career researcher blossom into a brilliant scientist and leader. This week brought to focus the successes of our lab alumni.

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Medium: Will the Academic Prisoner’s Dilemma impact eLife 2.0 (2022)

Medium: Will the Academic Prisoner’s Dilemma impact eLife 2.0 (2022) | Publications | Scoop.it

The life science publisher eLife is doing away with the accept/reject decision in a bold move to reinvent the journal as a publisher of peer-reviews. But why not publish editorial evaluations of the papers that are desk rejected to address concerns that conflicts of interest may influence editorial decisions.

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Current Opinion in Plant Biology: Emerging principles in the design of bioengineered made-to-order plant immune receptors (2022)

Current Opinion in Plant Biology: Emerging principles in the design of bioengineered made-to-order plant immune receptors (2022) | Publications | Scoop.it

Crop yield and global food security are under constant threat from plant pathogens with the potential to cause epidemics. Traditional breeding for disease resistance can be too slow to counteract these emerging threats, resulting in the need to retool the plant immune system using bioengineered made-to-order immune receptors. Efforts to engineer immune receptors have focused primarily on nucleotide-binding domain and leucine-rich repeat (NLR) immune receptors and proof-of-principles studies. Based upon a near-exhaustive literature search of previously engineered plant immune systems we distil five emerging principles in the design of bioengineered made-to-order plant NLRs and describe approaches based on other components. These emerging principles are anticipated to assist the functional understanding of plant immune receptors, as well as bioengineering novel disease resistance specificities.


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Medium: Unleash your inner Ninja — when the research tempo accelerates (2022)

Medium: Unleash your inner Ninja — when the research tempo accelerates (2022) | Publications | Scoop.it

Scientific research advances at different paces depending on the project. But sometimes, you may want to unleash your inner Ninja and fully press on the gas pedal.

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Medium: Do a predoc, young people (2022)

Medium: Do a predoc, young people (2022) | Publications | Scoop.it

What’s the rush in starting a PhD? Why don’t you instead do a predoc before committing to doctoral studies.

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