Goertz, J. | Search bioRxiv

bioRxiv2026

ABERRANT HIPPOCAMPAL NEUROGENESIS IS A CONSERVED RESPONSE TO STROKE IN MICE: A MULTI-CENTER MULTIMODEL STUDY

BackgroundAdult hippocampal neurogenesis is markedly altered after cerebral ischemia. Although stroke increases the production of newborn neurons, many of these cells display aberrant morphological and positional features that impair their functional integration and contribute to long-term cognitive decline. Given the clinical heterogeneity of ischemic stroke and the persistent translational failures of preclinical approaches relying on single-model studies it remains unknown whether post-stroke neurogenic alterations are conserved across different experimental paradigms. This study aimed to define common and model-specific features of hippocampal neurogenesis across complementary focal ischemia models. MethodsWe performed a multi-center, multimodel analysis within the STROKE-IMPaCT consortium using permanent and transient middle cerebral artery occlusion (MCAO) paradigms (MCAO via ligation or cauterization under normoxic (dMCAO) or hypoxic conditions (dMCAO+Hypoxia); and filament-based tMCAO across six international sites. Brains from adult C57BL/6J mice were collected 3 days, 7 days, or 2 months after ischemia, sham, or naive conditions. Hippocampal cell proliferation (Ki67) and neuroblast density (DCX) were quantified, and the morphological maturation of newborn neurons was evaluated using high-resolution analyses of dendritic architecture and somatodendritic polarity. All analyses were performed blind to experimental group. ResultsAcross all stroke models, ischemia induced a robust bilateral increase in hippocampal cell proliferation, most pronounced at 3 days and still elevated at 7 days, with levels returning to baseline by 2 months. Neuroblast density was similarly increased at 7 days, particularly in the ipsilateral hippocampus, but normalized by 2 months. Despite recovery in cell number, long-term morphological analysis revealed a consistent reduction in apical dendrite length and a higher proportion of neurons exhibiting aberrant features including ectopic localization, multipolar or inverted polarity, and abnormal lateral growth across all models. These abnormalities were observed both when pooling data across sites and when analyzing each model or center individually. ConclusionsIschemia induces an early, transient increase in hippocampal neurogenesis across diverse stroke paradigms, but the newborn neurons generated after stroke consistently display maladaptive morphological features. These cross-model, cross-site abnormalities indicate that aberrant hippocampal neurogenesis represents a robust hallmark of post-stroke pathology within the investigated species, independent of ischemia type or surgical approach, despite known differences in the spatial distribution of primary injury across experimental stroke models. Our findings support the concept that maladaptive neurogenesis may contribute to chronic post-stroke cognitive impairment and underscore the need to consider the quality not only the quantity of newborn neurons when developing therapeutic strategies.

animal behavior and cognition↗

bioRxiv2023

Overcoming the speed limit of four-way DNA branch migration with bulges in toeholds

Dynamic DNA nanotechnology involves the use of DNA strands to create programmable reaction networks and nanodevices. The key reaction in dynamic DNA nanotechnology is the exchange of DNA strands between different molecular species, which is achieved through three-way and four-way DNA exchange reactions. While both of these reactions have been widely used to build reaction circuits, the four-way exchange reaction has traditionally been slower and less efficient than the three-way reaction. In this paper, we describe a new mechanism to optimise the kinetics of the four-way DNA exchange reaction by adding bulges to the toeholds of the four-way DNA complexes involved in the reaction. These bulges facilitate an alternative branch migration mechanism and destabilise the four-way DNA junction, increasing the branch migration rate and unbinding rate of the four-way exchange reaction, bringing it closer to the kinetics of the three-way reaction. This new mechanism has the potential to expand the field of dynamic DNA nanotechnology by enabling efficient four-way DNA exchange reactions for in vivo applications.

biophysics↗

bioRxiv2021

Kinetics of RNA and RNA:DNA hybrid strand displacement

In dynamic nucleic acids nanotechnology, strand displacement is a widely used mechanism where one strand from a hybridized duplex is exchanged with an invading strand which binds to a toehold, a single-stranded region on the duplex. With proper design and kinetic control, strand displacement is used to perform logic operations on molecular level to trigger the conformational change in nanostructures, initiate cascaded reactions, or even for in vivo diagnostics and treatments. While systematic experimental studies have been carried out to probe the kinetics of strand displacement in DNA, there has not been a comparable systematic work done for RNA or RNA-DNA hybrid systems. Here, we experimentally study how toehold length, toehold location (5' or 3' end of the strand) and mismatches influence the strand displacement kinetics. Through comparing the reaction rates, combined with previous theoretical studies, we observed reaction acceleration with increasing toehold length and placement of toehold at 5'end of the substrate. We find that mismatches closer to the interface of toehold and duplex slow down the reaction more than remote mismatches. Comparison of RNA displacement and DNA displacement with hybrid displacement (RNA invading DNA or DNA invading RNA) is in part explainable by the thermodynamic stabilities of the respective toehold regions, but also suggest that the rearrangement from B-form to A-form helix in case of RNA invading DNA might play a role in the kinetics. The measured kinetics of toehold-mediated strand displacement will be important in understanding and construction of more complex dynamic nucleic acid systems.

bioengineering↗