Ran Duan

Ran Duan

@drduanran.bsky.social

PhD candidate at Marine and Environmental Biology @USC cyanobacteria/omics/evolution/climate change/trace metal

102 Followers 272 Following 3 Posts Joined Nov 2024
5 days ago
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The Pokémon Company Is Actively Recruiting PhD Holders With Backgrounds in Ecology to Work in Tokyo - IGN The Pokémon Company is actively recruiting PhD holders with backgrounds in ecology to work in Tokyo. This is perhaps the closest chance Pokémon fans have to channel their inner Professor Oak in real l...

This could be your dream job!
PhD in ecology, and English and Japanese language skills required... working for POKEMON!!!

www.ign.com/articles/the...

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1 week ago
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International Women's Day 2026 Nature highlights developments in women’s health research and career guidance for women in science.

International Women’s Day celebrates the Earth’s 4 billion female inhabitants. Nature brings you a collection of the latest on advancements in women’s health and career guidance, advice and inspiration for women in science. 🧪 #IWD2026

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The image shows two figures, a and b. Figure a shows a map of Europe with thermal positions indicated by color-coded hexagons, ranging from -1.0 to 1.0. Arrows point to "Reduced negative impacts" and "Increased negative impacts." Figure b shows a scatter plot of effect size vs thermal position with a fish illustration on top. "Biomass change estimates" indicated by circle size.

A study published in Nature Ecology & Evolution reports that long-term ocean warming reduces global fish biomass by up to 19.8% annually. Warmer years and marine heatwaves were linked to sharp biomass losses of up to 43.4%. go.nature.com/40b6AIB 🧪 🌍

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1 month ago

Check out our new review in Nature Reviews Genetics on de novo emerged genes and proteins. How they emerge, are lost and persist - and how de novo emerged proteins relate to randomized proteins! @bornberglab.bsky.social www.nature.com/articles/s41...

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Ocean warming enhances iron use efficiencies of marine ammonia-oxidizing archaea #USC_MEB www.pnas.org/doi/abs/10.1... #jcampubs

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DECODE: deep learning-based common deconvolution framework for various omics data - Nature Methods DECODE is a universal deconvolution framework for both cell types and cell states that can be applied to transcriptomic, proteomic and metabolomic data.

DECODE: deep learning-based common deconvolution framework for various omics data www.nature.com/articles/s41... #jcampubs

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2 weeks ago
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Pokémon turns 30 — how the fictional pocket monsters shaped science The Japanese media sensation has inspired generations of researchers in fields as diverse as evolution, biodiversity and research integrity.

Happy 30th birthday, Pokémon! Since 1996, the Japanese media sensation has inspired generations of researchers in fields as diverse as evolution, biodiversity and research integrity. go.nature.com/4bcjZ9w

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3 weeks ago
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Evolving synchronization of the Gulf Stream and Kuroshio-Oyashio Extension in a changing climate Summer SST covariability across the North Pacific and North Atlantic may be linked to Arctic sea-ice loss and climate change.

We have a new study out! In this work, we examine how the Gulf Stream and Kuroshio-Oyashio Extension co-vary, and this is tied to atmospheric variability and potentially sea-ice anomalies. However, this linkage may be changing in a warming world...

➡️ #OpenAccess: www.science.org/doi/10.1126/...

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2 weeks ago
Genomics of adaptation to extreme thermal environments As climate change continues to influence ecosystems around the globe, understanding the genomics of adaptation to hot and cold environments is becoming ...

Calling all researchers working on *Genomics of Adaptation to Extreme Thermal Environments*
I'm serving as a guest editor of an upcoming collection in BMC Genomics and am eager to read your submission! More on scope and how to contribute here: bit.ly/4kH3PIx 🧪 @springer.springernature.com

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3 weeks ago
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Decoupled timescales of organic carbon and phosphorus recycling in the global ocean | PNAS The ocean’s biological carbon pump exports atmospheric CO2 to the deep ocean, where it can remain sequestered for decades to centuries, and attempt...

Decoupled timescales of organic carbon and phosphorus recycling in the global ocean www.pnas.org/doi/abs/10.1... #jcampubs 🌊

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3 weeks ago
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New paper from my team detailing a greatly expanded genomic database of Asgard archaea revealing of high energy metabolism those related to eukaryotes! Led by @katyappler.bsky.social lots of help from @jameslingford.bsky.social @valdeanda.bsky.social @kassipan.bsky.social doi.org/10.1038/s415...

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1 month ago
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A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?

Excited to share our latest work in @science.org on a new small polymerase.
1/n

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1 month ago
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Bacterial iron acquisition by Escherichia coli is facilitated by amino acid complexation in a rapid-renewal environment | PNAS In natural environments, bacteria often encounter low concentrations of nutrient mixtures that are continuously replenished by physical processes s...

🔥Hot off the press!

❓ How do bacteria get iron when nutrients are scarce and constantly washed away❓

A PriME collective effort reveals—using a new continuous culture device—how bacteria acquire iron under rapid nutrient renewal, beyond #siderophores.

www.pnas.org/doi/10.1073/...

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1 month ago
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Mechanism and reconstitution of circadian transcription in cyanobacteria Nature Structural & Molecular Biology, Published online: 10 February 2026; doi:10.1038/s41594-025-01740-0Fang et al. reveal how a bacterial circadian clock turns genes on and off at the right times of day and use the purified proteins to drive circadian gene transcription in a test tube for days.

ICYMI: New online: Mechanism and reconstitution of circadian transcription in cyanobacteria

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1 month ago
Repeatability of gene expression evolution in experimental environmental adaptation - Nature Communications Experimental evolution enables evaluation of the relative roles of chance and necessity in evolution. This study compiles transcriptomic data from experimental evolution of a prokaryotic and five euka...

Here, the authors compile transcriptomic data from experimental evolution of a prokaryotic and five eukaryotic species in 22 environments to reveal that gene expression evolution is often repeatable and deterministic.

www.nature.com/articles/s41...

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Nutrient availability modulates impacts of short‐term shifts in temperature and grazing on phytoplankton composition and size structure aslopubs.onlinelibrary.wiley.com/doi/10.1002/... #jcampubs 🌊

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1 month ago
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Proteomic and biogeochemical perspectives on cyanobacteria nutrient acquisition – Part 2: quantitative contributions of cyanobacterial alkaline phosphatases to bulk enzymatic rates in the subtropical ... Abstract. Microbial enzymes alter marine biogeochemical cycles by catalyzing chemical transformations that bring elements into and out of particulate organic pools. These processes are often studied t...

Proteomic and biogeochemical perspectives on cyanobacteria nutrient acquisition – Part 2: quantitative contributions of cyanobacterial alkaline phosphatases to bulk enzymatic rates in the subtropical North Atlantic bg.copernicus.org/articles/23/... #jcampubs 🌊

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1 month ago
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Proteomic and biogeochemical perspectives on cyanobacteria nutrient acquisition – Part 1: Zonal gradients in phosphorus and nitrogen acquisition and stress revealed by metaproteomes of Prochlorococcus... Abstract. Ocean productivity is maintained by key nutrients, including nitrogen, phosphorus and trace metals. The magnitude and stoichiometry of nutrient fluxes to the ocean is changing. Here, we inve...

Proteomic and biogeochemical perspectives on cyanobacteria nutrient acquisition – Part 1: Zonal gradients in phosphorus and nitrogen acquisition and stress revealed by metaproteomes of Prochlorococcus and Synechococcus bg.copernicus.org/articles/23/... #jcampubs 🌊

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1 month ago
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Photoholes within cyanobacterial mats can account for the origin of anammox bacteria and ancient nitrogen loss - Nature Ecology & Evolution The authors leverage experimental and phylogenetic data to propose that anammox bacteria during the Archaean period could have harvested photoholes from cyanobacterial mats for use as an electron acce...

Photoholes within cyanobacterial mats can account for the origin of anammox bacteria and ancient nitrogen loss www.nature.com/articles/s41... #jcampubs

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1 month ago
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Resurrected nitrogenases recapitulate canonical N-isotope biosignatures over two billion years - Nature Communications The study shows that nitrogenase enzymes have maintained stable isotope signatures over billions of years, revealing how ancient microbes shaped Earth’s nitrogen cycle and offering a new experimental ...

Our new paper, out today! We resurrected ancient nitrogenases first used by life on Earth 3 billion years ago. We combined synthetic biology and geology & validated their chemical #biosignature in rocks that helps reveal ancient life on Earth!(and beyond!)

Link: www.nature.com/articles/s41...

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1 month ago
Phylogenetic tree of 8,943 bacterial genomes. The shaded branches in the tree represent different types of oxygen requirements, and the outermost ring indicates taxonomic lineages.

Using machine learning to sort over 80,000 bacterial genomes into aerobes and anaerobes, researchers find that oxygen-breathing bacteria likely evolved in local oxygen-rich environments 200–400 million years before the Great Oxidation Event. In PNAS: https://ow.ly/jZWQ50Y3LhU

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1 year ago
RESEARCH ARTICLE Simulating 500 million years of evolution with a language model.

Figure 1E, shown here, displays unconditional generations from ESM3 98B (colored by sequence identity to the nearest sequence in the training set), embedded by ESM3, and projected by UMAP alongside randomly sampled sequences from UniProt (in gray). Generations are diverse, high quality, and cover the distribution of natural sequences.

An #AI model created to design proteins simulates 500 million years of protein evolution in developing a previously unknown bright fluorescent protein.

Learn more in a new Science study: https://scim.ag/40l2z3J

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1 month ago
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Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation - Nature Microbiology Without key cell cycle control genes, SAR11 cells experience aneuploidy and growth inhibition when exposed to changes in nutrients, carbon sources or temperature stress, a vulnerability that may repre...

Our latest. Led by the very talented @ahoiching.bsky.social

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊

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7 months ago
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Coupling of excitation energy to photochemistry in natural marine phytoplankton communities under iron stress | PNAS Oxygenic photosynthesis requires excitation energy transfer from light-harvesting complexes (LHCs) to reaction centers (RCs) to drive photochemical...

Coupling of excitation energy to photochemistry in natural marine phytoplankton communities under iron stress www.pnas.org/doi/abs/10.1... #jcampubs 🌊

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2 months ago

Phosphorus limitation heightens vulnerability of Crocosphaera watsonii to ocean warming compared with iron limitation www.frontiersin.org/journals/mic... #jcampubs 🌊

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2 months ago
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Biogenically driven marine organic aerosol production over the West Pacific Ocean Abstract. Marine organic aerosols play crucial roles in cloud formation and climate regulation within the marine boundary layer. However, the abundance of marine primary organic carbon (MPOC) generate...

Biogenically driven marine organic aerosol production over the West Pacific Ocean bg.copernicus.org/articles/23/... #jcampubs 🌊

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2 months ago
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The iron metalloproteome of Pseudomonas aeruginosa under oxic and anoxic conditions Abstract. Pseudomonas aeruginosa is a major contributor to human infections and is widely distributed in the environment. Its ability for growth under aero

iron metalloproteome of Pseudomonas aeruginosa under oxic and anoxic conditions url: academic.oup.com/metallomics/...

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2 months ago
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Systematic attribution of heatwaves to the emissions of carbon majors - Nature Climate change made 213 historical heatwaves reported over 2000–2023 more likely and more intense, to which each of the 180 carbon majors (fossil fuel and cement producers) substantially contributed.

A paper published in Nature in September suggests a quarter of heatwave events from 2000-23 would have been near impossible without anthropogenic climate change. The paper also indicates that major carbon emitters are responsible for around 50% of the increase in intensity of these events. ⚒️ 🧪

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2 months ago
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The changing roles of Escherichia coli - Nature Microbiology Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways.

The changing roles of Escherichia coli www.nature.com/articles/s41... #jcampubs

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3 months ago
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Diverse community of rhizobia-diatom symbioses fixes nitrogen in the South Pacific gyre Abstract. Nitrogen fixation is crucial for sustaining productivity in most of the open ocean. Cyanobacteria are the most prominent N2-fixers, but based on

Diverse community of rhizobia-diatom symbioses fixes nitrogen in the South Pacific gyre academic.oup.com/ismecommun/a... #jcampubs 🌊

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