Targeted in situ sequencing underlies many spatial transcriptomic, barcoded connectomic, and multiplexed perturbation techniques. Each experiment requires many cycles of chemical reactions and imaging...

Brain and Behavior, Volume 16, Issue 10, October 2026.

Beverage spoilage caused by microbes such as Alicyclobacillus poses a significant challenge for the food industry, leading to substantial economic losses and increased food waste. While it is known that some species, specifically those that produce the off-flavor compound guaiacol, are responsible for spoilage, current risk assessment practices often fail to accurately predict spoilage potential. These practices are often flawed because they rely on simple bacterial enumeration or use media-bas…

The actinorhizal symbiosis, formed between the nitrogen-fixing actinobacterium Frankia and its host plant, depends on a highly coordinated molecular dialogue that governs the transition from initial bacterial perception to the development of functional nitrogen-fixing nodules. Despite decades of progress in characterizing the legume- rhizobia association, the molecular underpinnings of actinorhizal symbiosis establishment remain poorly resolved, particularly the nature of the Frankia signaling molecule and the transcriptional programs that guide both partners toward nodule formation. This thesis narrows this gap through three complementary transcriptomic studies in the model actinorhizal plant Casuarina glauca and its symbiont Frankia casuarinae strain Ccl3. The first study examines global gene expression in C. glauca roots within the first 24 to 48 hours of exposure to Frankia cells and purified supernatant, revealing a defense and hormone-dominated transcriptional signature that transitions over time, with a small but coherent set of Common Symbiotic Pathway genes expressed for both treatments. The second study extends this analysis across the full 21-day nodulation window, characterizing stage-specific gene expression programs associated with infection, prenodule formation, and nodule maturation. The third study examines the Frankia side of the interaction, profiling bacterial transcriptional responses to host and non-host root exudates to identify candidate biosynthetic pathways underlying the novel Frankia signaling molecule. Together, these studies provide a comprehensive, multi-timepoint transcriptomic characterization of both partners across the actinorhizal symbiosis establishment process and lay the groundwork for future genetic dissection of this ecologically significant nitrogen-fixing association.