Nonia Pariente

A photo of the MOP foundation library

Stunning library at MOP foundation in A Coruña

Formalizing our commitment to code sharing In support of open science, PLOS Biology routinely asks authors to openly share their research code before publication. We are now formalizing this practice with a mandatory code sharing policy and…

In support of #OpenScience, we routinely ask authors to openly share their #research #code before publication.

We are now formalizing this practice with a mandatory #CodeSharing policy and clarifying what we mean by code sharing.

Lauren Cadwallader and I explain @plosbiology.org 's new mandatory code sharing policy and offer guidance on best practice

We are not changing, but rather formalizing, current practice and providing clarity around what we mean by code generation

plos.io/47dPeOW
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New @plosbiology.org code sharing policy. In this Editorial, @npariente.bsky.social and Lauren Cadwallader explain the policy and offer guidance on compliance, noting that code sharing remains less well understood than equivalent requirements for data and ethics.

journals.plos.org/plosbiology/...

I should have said, this takes us to about 2.8 million genomes in total. We don't have annotations, etc for the latest data yet, this will be an ongoing process

The imperiled peer review system
@carlbergstrom.com @plosbiology.org
journals.plos.org/plosbiology/... open-access

Screening, sorting, and the feedback cycles that imperil peer review The process of peer review is vital to contemporary science, but is also under enormous strain. This study uses mathematical models to dissect the threats to the long-term viability of peer review, su...

1. Kevin Gross and I have a new paper out today PLOS Biology.

We used economic models based around screening games and the market for unpaid labor to highlight a meltdown cycle threatening peer review.

Could sleep engineering be used to combat PTSD and depression? Could sleep engineering be developed to provide a drug-free, non-invasive avenue to treat depression and post-traumatic stress disorder? This Perspective proposes using machine learning with EEG…

Could #SleepEngineering be developed to treat #depression and post-traumatic stress disorder? This Perspective proposes using machine learning with EEG signals to develop and optimize this type of intervention.
🧪 #NeuroSky

Window art depicting a happy meal box as if it were a rocket (but also looking like a phage)

Would you look at that? Even fast food chains pay homage to #phage 😝🚀🧪

Wednesday

Inside Russia’s Secret Campaign of Sabotage in Europe How Russian military intelligence is recruiting young people online to carry out espionage, arson, and other attacks across the Continent.

Eye-opening article on Russia’s low-level war on Europe by recruiting ‘single-use agents’. Inside Russia’s Secret Campaign of Sabotage in Europe www.newyorker.com/magazine/202...

Synapse type density in the mouse brain. PSD95 and SAP102, two postsynaptic scaffolding proteins expressed at excitatory synapses, were fluorescently imaged at single-punctum resolution across the whole mouse brain. Top row: Axial, coronal, and sagittal view of the 137-region parcellation used for analyses involving tract-tracing data (left) and the 88-region parcellation used for analyses involving fMRI data (right). Regions are coloured and labeled according to ontological structure. Other roaws show axial, coronal, and sagittal views of mean long-lifetime PSD95 synapse density, mean short-lifetime PSD95 synapse density, and mean SAP102 synapse density, mapped to both 137- and 88-region parcellations.

How do diverse synapses relate spatially to whole-brain dynamics? @misicbata.bsky.social &co map ~1 billion synaptic puncta from a single mouse brain onto #hemodynamic features, revealing links between #synapse features, #brain networks & synaptic engagement @plosbiology.org 🧪 plos.io/4rmeef6

Regardless, I am very looking forward to a few days in the one place I still think of as home, despite not having lived there since the fall of 1996 (God I am old!)

Regardless, I am very looking forward to a few days in the one place I still think of as home, despite not having lived there since the fall of 1996 (God I am old!)

Cartoon of A Coruña, Galicia, Spain, water logged due to heavy rain

How your email will find me tomorrow and next week

😎 paper alert!

Nice work from the Laub lab showing that binding to ring structures made by different phage defense proteins activates RNAse to inhibits translation and phage infection. It needs to be in a 24-meric ring structure to cut.

🧪#microsky

😎 paper alert!

Nice work from the Laub lab showing that binding to ring structures made by different phage defense proteins activates RNAse to inhibits translation and phage infection. It needs to be in a 24-meric ring structure to cut.

🧪#microsky

The James Chen lab does it again!

PI(3,5)P2 identified as the molecular glue that mediates STING oligomerization upon cGAMP binding, necessary for downstream signaling

😎 work!

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The James Chen lab does it again!

PI(3,5)P2 identified as the molecular glue that mediates STING oligomerization upon cGAMP binding, necessary for downstream signaling

😎 work!

🧪

The hometown newspaper that I read as a teenager through Watergate and Vietnam and made me crave the life of a reporter is now being butchered by a billionaire who had $75 million to bribe and flatter a president and his wife but nothing to save journalism, an bulwark of the republic itself. Got it.

Multi-omics and perturbation screens as discovery tools in immunometabolism Metabolic regulation of immune function is a complex and dynamic process. This Perspective highlights how systems biology approaches, including multi-omics profiling and perturbomics screening, are be...

In their Perspective, Nicole Chapman and Hongbo Chi advocate for the use of systems biology approaches in #immunometabolism research as discovery tools for new therapeutic targets.
plos.io/4aR959z

Immunometabolism in obesity: Understanding the beneficial and detrimental roles of inflammation Chronic low-grade metabolic inflammation (known as metaflammation) drives insulin resistance and metabolic dysfunction in obesity. This Essay discusses the immunometabolic mechanisms underlying metafl...

In his Essay, Yun Sok Lee investigates the process of metaflammation, the chronic low-grade inflammatory response that occurs in metabolic diseases such as obesity and type 2 diabetes, exploring how systemic changes in #metabolism can affect tissue-resident immune cells plos.io/4sOCOqh

How do immunometabolites shape bacterial infections? Metabolites generated by both host and pathogen have a major impact on the severity and outcomes of infection. This Essay investigates how the study of immunometabolism has yielded insight into the mo...

In their Essay, Griffin Gowdy and Alice Prince look at the role of immunometabolites in both driving and combating bacterial infections, with a focus on #pathogens that infect the lungs plos.io/4jpVnNb

Targeting immunometabolism in cancer through pharmacological and lifestyle interventions Immunometabolism is often disrupted in diseases such as cancer, suggesting it could be useful target for therapy. This Essay explores the potential for incorporating both lifestyle changes and drug th...

Finally, on a more holistic level, Guang Sheng Ling and colleagues suggest a two-pronged approach to targeting #immunometabolism therapeutically through pharmaceutical and lifestyle interventions, with a focus on #cancer plos.io/4jNASKk

An image of the author on the right, with the text: "The field of immunometabolism not only promises to provide fresh insights into the mechanisms of immune dysfunction, but also offers tools that could be used to restore homeostasis, or at least dial immune responses up or down. I am most excited to see how basic research that elucidates the mechanisms by which metabolism affects immunity will lead to deeper insights into how the immune system shapes physiology."

Senior Editor Lucas Smith discusses his hopes for the field of #immunometabolism in his blog post plos.io/4qd5EOo

An image of the author on the right, with the text: "The field is clearly moving towards trying to address real medical problems using the knowledge we have gained over the past few decades of how immune metabolic pathways govern and guide the immune response. Understanding the interplay between systemic metabolism and the immune response will be crucial if we want to find ways to intervene in conditions with altered metabolism"

First, our Collection Editor Claudio Mauro introduces the theme for the Collection and his vision for the future of #immunometabolism research in his Editorial
plos.io/4qTmEu1

Our latest collection of commentary and Essays is devoted to #immunometabolism, highlighting how molecular & cellular mechanisms impact tissue and organismal functions, as well as the therapeutic potential of manipulating immunometabolism

#cancer #aging #metabolism #inflammation
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@plosbiology.org

Knowledge gaps and research priorities to understand sex differences in immunity Immunity differs profoundly according to biological sex, leading to sex differences in autoimmunity, infections, cancer and responses to immunotherapy and vaccines. This Essay explores the major…

Why are there such big differences between the sexes when it comes to immune responses? This Essay looks at what further research is required to fully determine sex-differential mechanisms in #immunity.🧪 #immunosky

Fungi can become drug-resistant without changing their DNA. They just... turn off the gene. And turn it back on when the drug's gone. This is wild and concerning for treating infections like mucormycosis (50-90% mortality). From Joe Heitman's group at @duke-university.bsky.social.

Top: FK506-resistant strains isolated from the Mucor circinelloides complex. Phenotypic analysis of FK506-resistant isolates in Mucor janssenii CBS185.68 (PS1), Mucor bainieri CBS293.63 (PS3), and Mucor atramentarius CBS202.28 (PS6). WT, wild-type; M, mendelian mutant; E, epimutant. Bottom: Schematic overview of epigenetic silencing contributing to antifungal resistance in Mucor species. fkbA expression enables FKBP12 production and FK506 sensitivity (yeast-like morphology). Epigenetic silencing of fkbA via RNAi and/or heterochromatin leads to FK506 resistance and hyphal growth. Generated with BioRender.com.

#Antifungal resistance is a global threat, but epigenetic mechanisms drive rapid, reversible adaptation in fungi. This study shows that #RNAi or #heterochromatin driven #epimutations transiently silence the gene fkbA to confer FK506 #tacrolimus resistance in #Mucor @plosbiology.org 🧪 plos.io/4qdttWc