Biology subjects

Greene, H.

Publications and source records attributed to Greene, H..

5 recordsLinked to original sources

bioRxiv2026

Bioplastic Production from simulated 100% in situ Mars resources

A sustained human presence on Mars requires local production of bulk materials, particularly polymers. Prior approaches to space biomanufacturing rely on human waste streams, Earth-sourced consumables, or complex chemical infrastructure, limiting their ability to scale. Here we demonstrate production of polyhydroxyalkanoate (PHA) bioplastic from simulated 100% martian resources: regolith-derived soluble nutrients, acetate electrochemically fixed from martian atmosphere, and water. We screened 16 candidate organisms for growth in a chemically defined Mars medium and identified Cupriavidus necator H16 and Pseudomonas putida KT2440 as promising chassis organisms. Adaptive laboratory evolution totaling more than 1012 cumulative cell divisions improved both species' tolerance to high concentrations of acetate and leached regolith. The top C. necator evolved isolate, referred to as sPL.001, produced more than three-fold higher PHA titer under simulated Mars conditions compared to its parent strain. These results establish a path to polymer production on Mars where consumable mass is derived entirely from local resources, decoupling bulk material production from Earth supply chains.

bioengineering↗

bioRxiv2026

Defined Mars Media (DMM), a chemically defined simulant of the soluble macro- and micro- nutrients in Mars regolith for use in biological research

Mars harsh yet workable surface conditions, such as manageable temperatures, availability of solar energy, and in situ resources like water ice, carbon dioxide, and mineral-rich regolith, make it a compelling target for supporting life beyond Earth. However, existing experiments testing chemical habitability in Mars conditions generally rely on leachates of physical regolith simulants, which vary in composition across simulant types, leaching conditions, and production batches. We introduce a defined Mars media (DMM) that accurately simulates the biologically relevant nutrients (nitrogen, phosphorus, and sulfur) and stressors (perchlorates, heavy metals) in Martian regolith when it is leached in water at neutral pH. We formulated DMM by combining direct rover and lander measurements from Mars with laboratory measurements of regolith simulant leachates. We validate DMM from a 1x to 20x concentrate, equivalent to 40 g/L to 800 g/L of leached regolith. Using DMM with acetate as a Mars atmosphere-derived carbon source, we grew eight bacteria, demonstrating that organisms can source all essential nutrients from Martian resources. We also demonstrate that microbial growth in DMM is robust to uncertainties in Martian regolith composition: sensitivity experiments can identify limiting trace element nutrients and toxins in DMM, and show that bacterial growth is maintained across at least an order of magnitude variation in their concentrations. This is the first defined Mars regolith media recipe containing both macro- and micro-nutrients, and designed specifically for biological experimentation. By shifting from variable leachate-based approaches to a defined aqueous analog, we enable controlled hypothesis testing of microbial survival, growth, and function in a Martian chemical environment. DMM will enable further research on astrobiology, biological in situ resource utilization, large-scale soil remediation, and terraforming. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/719001v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@37408forg.highwire.dtl.DTLVardef@16fabfforg.highwire.dtl.DTLVardef@84fa43org.highwire.dtl.DTLVardef@4a7c5e_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

BioBloom, a method for barcoded saturation mutagenesis of an entire bacterial genome

Saturation mutagenesis is a powerful tool for understanding and engineering the function of biological systems. and has been applied successfully to characterize the mutational landscape of individual proteins and genetic loci. However. it has not been applied at the whole-genome scale due to the challenges of both creating and quantifying a saturating set of mutations. Here we introduce BioBloom. a retron-based method for barcoded saturation mutagenesis at the scale of a whole bacterial genome. We constructed a barcoded BioBloom library with >99% projected sampling of saturating single - nucleotide polymorphism (SNP) mutations of the E. coli genome, and applied it to identify beneficial mutations under salt and antibiotic selection. Relative to other techniques like CRISPR-enabled mutagenesis or Adaptive Laboratory Evolution, BioBloom excels at identifying diverse causal SNPs quickly and at smaller working volumes. A barcoded, saturating mutation library is also a shared resource, and we are releasing the updated BioBloom-Ec.-2.0 library to the scientific community for broader adoption and application. Together. BioBloom makes barcoded saturation mutagenesis accessible at whole-genome scale, creating new opportunities for large-scale data collection and bacterial engineering.

microbiology↗

bioRxiv2026

Age-Related Upregulation and Strong Expression Correlation of the Proinflammatory Cytokines IL-1β and IL-6 Across Multiple Segments of the Mouse Eye

Emerging evidence suggests that ocular inflammation increases with age and is associated with various disease states. That said, the majority of studies suffer from a significant limitation--they only focus on a single segment of the eye. This represents a limitation because age-related increases in neuroinflammatory markers are not necessarily uniform within an organ, and other age-related changes in the eye are known to occur in a segment-specific manner. The present study aims to address this gap by comparting/contrasting age-related changes in the proinflammatory cytokines IL-6 and IL-1{beta} across multiple mouse ocular segments: the (i) anterior segment (i.e., cornea, ciliary body and muscle, and zonules), (ii) retina, and (iii) posterior segment (i.e., sclera, choroid, Bruchs membrane, retinal pigmented epithelium, and parts of the optic nerve). IL-6 and IL-1{beta} were selected as targets since they exhibit differential regional patterns of age-related increases within the brain. Eyes were collected on postnatal days (P) P28, P56, P98, P200 and P500 and processed by Western blot. Both IL-6 and IL-1{beta} protein levels increased across the lifespan in all three eye segments. Interestingly, correlational analyses revealed that IL-1{beta} and IL-6 expression correlated with each other not only within individual eye segments, but also across segments. In old mice, IL-1{beta} and IL-6 levels also correlated with expression of phosphodiesterase 11A (PDE11A), an enzyme known to regulate neuroinflammation. Together, these findings suggest that inflammaging in the eye is broadly controlled by a systemic governor, unlike the brain that shows region-specific changes in cytokines with age.

neuroscience↗

bioRxiv2025

Molecular mechanisms regulating PDE11A4 age-related liquid-liquid phase separation (LLPS) and its reversal by selective, potent and orally-available PDE11A4 small molecule inhibitors both in vitro and in vivo

PDE11A is a little-studied phosphodiesterase family that breaks down cAMP and cGMP, with the PDE11A4 isoform enriched in the memory-related hippocampus. Age-related increases in hippocampal PDE11A expression occur in human and rodents, causing age-related cognitive decline of social memories. Interestingly, this age-related increase triggers PDE11A4 liquid-liquid phase separation (LLPS), causing the enzyme to accumulate in the brain in filamentous structures termed "ghost axons". Here we sought to identify molecular mechanisms regulating PDE11A4 LLPS and therapeutic approaches capable of reversing it. PDE11A4 LLPS was reduced by phosphorylation of PDE11A4-S163 or-S239 and the D355A mutation that blocks the effect of cGMP binding the PDE11A4 GAF-A domain. PDE11A4 LLPS was increased by inhibiting kinases with staurosporine or stimulating packaging/repacking via the trans-Golgi network by overexpressing TGN38 or RhoB. 8 PDE11 inhibitors (MLG-122, MLG-185, MLG-199, SMQ-02-57, SMQ-03-30, SMQ-03-20, tadalafil, and BC11-38) across 3 scaffolds reverse overexpression-related PDE11A4 LLPS in HT22 mouse hippocampal neuronal cells. This effect of PDE11A4 inhibitors occurs within minutes, is reversed upon washout of lower but not higher concentrations, and occurs in part by reducing PDE11A4 homodimerization. PDE11A4 inhibitors also rescued exacerbated PDE11A4 LLPS triggered by aging-like S117D/S124D phosphomimic mutations, staurosporine, or TGN38/RhoB overexpression. In vivo, orally-administered 30mg/kg SMQ-03-20 reversed age-related increases in PDE11A4 ghost axons and neuroinflammation in old mice. Thus, PDE11A inhibitors that reverse age-related PDE11A4 LLPS in HT22 hippocampal cells also reduce PDE11A4 ghost axons and neuroinflammation in the aged mouse brain, indicating therapeutical potential.

neuroscience↗