Ran Duan
@drduanran.bsky.social
PhD candidate at Marine and Environmental Biology @USC cyanobacteria/omics/evolution/climate change/trace metal
We know how photosynthesis works in incredible molecular detail, but how this vital process evolved is far less clear. It seems the road to photosynthesis was far longer and stranger than anyone expected. www.quantamagazine.org/an-early-ste...
An Early Step on the Long, Strange Road to Photosynthesis | Quanta Magazine
An ancient lineage of cyanobacteria is helping biologists uncover an early evolutionary stage of the mind-boggling process that turns light into life.
quantamagazine.org
Coordination of N2-fixing cell specialization and patterning in filamentous cyanobacteria by a uniquely structured σ factor www.pnas.org/doi/abs/10.1... #jcampubs
Iron-catalyzed active lipid peroxides drive ultrafast collective cell death in blooming algae | Science www.science.org/doi/10.1126/...
Iron-catalyzed active lipid peroxides drive ultrafast collective cell death in blooming algae
Harmful algal blooms, the most severe ecological hazards worldwide, terminate abruptly within a few days. In this work, we identified that iron-catalyzed active lipid peroxides predominantly trigger i...
science.org
The dynamic mesoscale sink and source niches for eukaryotic phytoplankton in a subtropical gyre www.pnas.org/doi/abs/10.1... #jcampubs 🌊
The dynamic mesoscale sink and source niches for eukaryotic phytoplankton in a subtropical gyre | PNAS
By tracking the water mass histories of genetic samples, we investigated the biophysical dynamics shaping eukaryotic phytoplankton populations in a...
pnas.org
Spent the last two years developing a new Intro to Physics course for undergrad biology majors. It features tons of examples from biology (especially Ecology & Evolution!) and requires only middle school-level math. Lecture note here shorturl.at/0PiVp Any comments or feedback are highly welcome!
physics_for_biologists.pdf
drive.google.com
Abiotic sources of fixed nitrogen sustained early ecosystems for several hundred million years after the origin of life | Science Advances https://www.science.org/doi/full/10.1126/sciadv.aec4450?af=R
Tracing the evolution of microbial alkaline phosphatases and their role in phosphorus recycling through time | bioRxiv https://www.biorxiv.org/content/10.64898/2026.06.08.730957v1?rss=1
Tracing the evolution of microbial alkaline phosphatases and their role in phosphorus recycling through time
Phosphorus (P) recycling in seawater is critical for maintaining nutrient availability and marine primary productivity. This process is catalyzed by alkaline phosphatases enzymes, which hydrolyze dissolved organic phosphorus (DOP) compounds, releasing inorganic P for cellular assimilation. Here, we reconstructed the evolutionary history of three major alkaline phosphatase families through deep time using phylogenetic reconciliation across the tree of life. We further quantified their distribution and cellular localization across major metabolic groups using extant genomes to assess how the oceans capacity for P regeneration has changed through time. Our results demonstrate that alkaline phosphatases emerged early in the Archaean, indicating that DOP has sustained marine ecosystems for most of Earths history. A pronounced expansion and diversification of alkaline phosphatases occurred during the Neoproterozoic, coinciding with the rise and ecological diversification of algae. Across metabolic groups, extracellular alkaline phosphatases are particularly concentrated in ferric iron reducers, fermenters, and aerobic heterotrophs, but are comparatively rare in other metabolisms. This distribution suggests that the efficiency of marine P recycling has been strongly influenced by prevailing metabolic strategies and environmental redox conditions. Overall, our results provide new insights into the enzymatic drivers of marine P cycling and the mechanisms that maintained marine productivity as Earths surface became progressively oxygenated and biologically complex. ### Competing Interest Statement The authors have declared no competing interest. Heising-Simons Foundation, https://ror.org/01mp52y34
biorxiv.org
Polyphosphate synthesis is essential for phosphate and ATP homeostasis during nutrient upshift www.pnas.org/doi/10.1073/... #jcampubs
Polyphosphate synthesis is essential for phosphate and ATP homeostasis during nutrient upshift | PNAS
Inorganic polyphosphate (polyP) is a ubiquitous molecule found across all domains of life. Although implicated in diverse cellular processes, inclu...
pnas.org
Non-diazotrophic Trichodesmium species are active in N2 fixing colonies #USC_MEB #jcampubs 🌊 academic.oup.com/ismecommun/a...
The multistable dynamics of the Atlantic Ocean circulation pose a central problem in climate physics, because instabilities of the flows can have large climate impacts. A Review in Nature Reviews Physics unifies much of the model behaviour that has been found. go.nature.com/49HW9kQ ⚛️🌊🧪
This month we launch a Focus issue on the impacts of extreme events on biodiversity, highlighting research and opinion pieces on their variable impacts, short- and long-term consequences, and conservation measures to mitigate their effects: www.nature.com/collections/... Read more 👇
Impacts of extreme events on biodiversity
Climate warming is increasing the frequency and intensity of extreme events globally, including heatwaves, cold snaps, droughts, floods and wildfires.
nature.com
Why do climate models disagree so much in forecasting ocean net primary production under different emissions scenarios? Check out this new paper by @natlegrix.bsky.social and I 🌊 agupubs.onlinelibrary.wiley.com/doi/10.1029/...
Sources of Uncertainty in Ocean Net Primary Productivity Projections Under Climate Change
Disagreement on the preindustrial state of net primary productivity (NPP) dominates the uncertainty in absolute rates of NPP Earth system models project divergent long-term shifts in the decadal ...
agupubs.onlinelibrary.wiley.com
New #ecoevo paper @pnas.org: Evolution of species’ range and niche in changing environments. I show that feedback between evolutionary and population dynamics can create a tipping point where genetic variance erodes, and species’ ranges contract or fragment www.pnas.org/doi/10.1073/... #popgen 🧬🧪 🌎
Jitka Polechová@polejit.bsky.social · 2y agoPreprint finally out! I show that eco-evo feedback can drive a tipping point where genetic drift overwhelms adaptation. This can result in a contraction of a species' range border or range fragmentation. Fragmentation is abrupt and arises readily under rapid temporal change. doi.org/10.1101/2025...
A redox-sensitive phosphatase regulates glycolysis as a metabolic switch in the bacterial inner membrane www.science.org/doi/full/10.... #jcampubs
A redox-sensitive phosphatase regulates glycolysis as a metabolic switch in the bacterial inner membrane
Redox-sensitive phosphatase PgpA couples glycolysis and redox balance to control metabolic adaptation in E. coli.
science.org
The heterogeneous selection landscape of genome evolution in prokaryotes www.pnas.org/doi/10.1073/... #jcampubs
The heterogeneous selection landscape of genome evolution in prokaryotes | PNAS
Evolution of prokaryote genomes appears to be defined by the interplay of selection for genome streamlining, deletion bias, and selection for funct...
pnas.org
📢Out now: Na Jiao and colleagues present DeepSeMS, a framework for predicting secondary metabolite structures from biosynthetic gene cluster sequences. www.nature.com/articles/s43... #microbiome 🧫 🔓 rdcu.be/fgic0
DeepSeMS: revealing the hidden biosynthetic potential of the global ocean microbiome with a large language model - Nature Computational Science
This work presents DeepSeMS, a transformer-based framework that translates biosynthetic gene clusters into candidate secondary metabolite structures, enabling scalable exploration of chemical diversit...
nature.com
Our first collaboration with the Levine lab! Defining metabolic niches for marine microbial heterotrophs www.science.org/doi/full/10.... #jcampubs 🌊
Defining metabolic niches for marine microbial heterotrophs
Understanding carbon cycling requires simplifying bacterial diversity into functional groups defined by genetic signatures.
science.org
Polyphosphate acts as an architectural regulator of carbon fixation and nucleoid structure in cyanobacteria www.biorxiv.org/content/10.6... #jcampubs
The maturation of the unique FeMo-cofactor of molybdenum nitrogenase is a multistep process requiring the sequential action of a series of maturase complexes. Cryo-EM structures capture trafficking of a key intermediate of cofactor assembly www.nature.com/articles/s41...
Trafficking of a nitrogenase FeMo-cofactor assembly intermediate - Nature Chemical Biology
The maturation of the unique FeMo-cofactor of molybdenum nitrogenase is a multistep process requiring the sequential action of a series of maturase complexes. Here, the authors report on how cryo-elec...
nature.com
Want to convert old relative abundance ocean amplicon data into absolute abundances? Williams et al. show a flow cytometry "anchor" can provide reasonable absolute abundances, validated by internal-standard corrected metagenomics with single copy genes, and amplicons academic.oup.com/ismecommun/a...
Converting Relative Amplicon Abundances to Absolute Abundances via Flow Cytometry: Metagenomic Validation and Application to Long Ocean Transects
Abstract. With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. Whil
academic.oup.com
One of the most-viewed PNAS articles in the last week is “Characterization of phytoplankton-excreted metabolites mediating carbon flux through the surface ocean.” Explore the article here: https://ow.ly/zPNG50YBfRR For more trending articles, visit https://ow.ly/iZnr50YBfRS.
Biochemical remodelling of phytoplankton cell composition under climate change www.nature.com/articles/s41... #jcampubs 🌊
Biochemical remodelling of phytoplankton cell composition under climate change - Nature Climate Change
The authors simulate phytoplankton macromolecular composition—proteins, carbohydrates and lipids—under present and future scenarios. They show increased protein allocation in subtropical phytoplankton...
nature.com
Alkaline phosphatase activity supports heterotrophic carbon acquisition in a coastal time series site and a representative marine bacterium www.biorxiv.org/content/10.6... #jcampubs 🌊
In a new Nature study, we show that extreme global climate outcomes may occur even under moderate 2°C warming for several sectors. The findings reinforce the urgency of limiting warming well below 2°C. Together with @erichfischer.bsky.social @janasillmann.bsky.social @zscheischlerjak.bsky.social
Moderate global warming does not rule out extreme global climate outcomes - Nature
Extreme global climate outcomes may occur even under moderate 2 °C warming and may turn out to be more extreme than model-averaged projections at 3 °C or 4 °C warming.
nature.com
Statistical Rethinking 2026 is done: 20 new lectures emphasizing logical and critical statistical workflow, from basics of probability theory to causal inference to reliable computation to sensitivity. It's all free, made just for you. Lecture list and links: github.com/rmcelreath/s...
New Perspective form Rory Maizels & me: "Gene regulatory networks: from correlative models to causal explanations" Gene regulatory networks are supposed to give us mechanistic explanations of development, so why are we drowning in 'hairballs' of statistical correlations? rdcu.be/e7zx7
Gene regulatory networks: from correlative models to causal explanations
Nature Reviews Genetics - In this Perspective, Maizels and Briscoe discuss the limitations of current models of gene regulatory networks and outline solutions to harness data abundance without...
rdcu.be
Trace elements incorporated into grains of pyrite preserve information about the chemistry of ancient oceans, allowing researchers to reconstruct the interplay of biology and tectonics driving long-term oxygen fluctuations. In PNAS: https://ow.ly/RJSO50YwsLC
Experimental evolution of fission yeast in the same environment as a previous experiment with budding yeast reveals parallel evolution but distinct molecular mechanisms and targets of adaptation in the two species 🧪 www.nature.com/articles/s41...
Parallel but distinct adaptive routes in the budding and fission yeasts after 10,000 generations of experimental evolution - Nature Ecology & Evolution
Experimental evolution of fission yeast (Schizosaccharomyces pombe) in the same environment as a previous experiment with budding yeast (Saccharomyces cerevisiae) reveals parallel evolution but distin...
nature.com
AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄 research.nvidia.com/labs/dbr/ass... 🌐 alphafold.ebi.ac.uk
🚨 Next Friday 20/03 15:30 EU, Julia Schwartzman (University of Southern California) will present the talk Ecological Dynamics of Bacterial Groups at the Population Dynamics Seminars. Subscription sites.google.com/view/popdyn/
