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Biology subjects

Mendoza, C.

Publications and source records attributed to Mendoza, C..

4 recordsLinked to original sources

Modeling the effects of Huntington disease on age-related genes reveals CXXC4 as an epigenetic target to restore health and excitability of Drd1-expressing striatal neurons

Neurons adapt gene expression to counter aging, yet the mechanisms by which they harness age- related genes to resist neurodegenerative disease remain elusive. We found that transcriptionalaging inversion (TAGI) in the Drd1-expressing striatal neurons (Drd1 SNs) of Huntingtons disease (HD) knock-in (Hdh) mice exhibits discrete patterns against a TAG-like (TAGL) signature. Strikingly, TAGI dynamics may explain disease progression more accurately than TAGL. Moreover, in Drd1 SNs, genes affected by 3UTR accumulation during aging are predisposed to downregulation in aging and deregulation in Hdh mice. By integrating age-related 3UTR data and Hdh-mice data, we identified a CAG-repeat-dependent network of upregulated genes with compensatory potential. This network features (i) Atad-5, a P CNA unloader that modifies CAG expansion in human HD plasma samples, and (ii) CXXC4 (IDAX), an epigenetic regulator whose early-stage upregulation is lost as behavioral symptoms worsen in Hdh mice. Functionally, CXXC4 reduces the senescence marker p16INK4a and restores glutamate excitability in human HD iPS cell-derived SNs. Collectively, these findings suggest that Drd1 SN resilience capacity against HD relies on discrete age-related patterns and responses transiently activated in early disease stages. The reactivation of specific age-related genes such as CXXC4 may notably restore cortico-striatal function in HD.

neuroscience↗

Frequency-Dependent Neurostimulation in Whole Brain Network models

BackgroundBrain stimulation at specific frequencies has been shown to have therapeutic effects for certain neurological disorders. However, it remains unclear how these oscillatory inputs interact with neuronal dynamics and what drives this frequency selectivity. Here, we propose that this is achieved by targeting specific brain circuits through frequency-selective network entrainment. MethodsTo demonstrate that this type of entrainment can occur in the brain connectome structure, we use a minimal physics-based model of coupled oscillators that preserves only the essential structural connectivity of real brain networks. Using this model, we test how periodic stimulation influences network oscillatory dynamics, identifying sub-networks that synchronize with specific stimulation frequencies. Furthermore, we validate the suitability of the model to reproduce well-known frequency-selective entrainment using visual and auditory periodic stimulation. ResultsOur model reproduces selective network entrainment, whereby distinct stimulation frequencies favor the synchrony of different sub-networks. Crucially, entrainment exhibits a physics-predicted inverse relationship with frequency: lower-frequency stimulation favors broader synchrony across the network, while higher-frequency inputs produce spatially confined effects. These patterns emerge purely from network structure and oscillatory physics, independent of biological details. ConclusionThis physics-based approach elucidates the fundamental mechanistic principles governing frequency-selective brain network stimulation. Our minimal model demonstrates that selective entrainment of specific subnetworks can be achieved through frequency selection alone, largely determined by network structure and oscillatory dynamics. These findings provide a theoretical foundation for understanding how network architecture determines stimulation selectivity, supporting the development of principled approaches to targeted neuromodulation. Author summaryIn this work, we explore how external rhythmic stimulation interacts with the brains own rhythms. We use a physics-based model that represents the brain as a network of interconnected oscillators, linked according to the human connectome. Through this model, we show that stimulation effects are not limited to the targeted region but spread across the network, depending on the stimulation frequency, its spatial location and the underlying network dynamics. Our results reveal that low-frequency rhythms promote large-scale synchrony, while high-frequency rhythms engage more localized areas, all emerging from the brains structural connections and communication delays. The simulated cortical activation exhibits a frequency-selective profile that aligns strongly with that estimated from sensory-evoked electroencephalographic activity. This agreement suggests that differences between individuals in how their brain networks operate may explain why stimulation affects each person differently. Our findings offer a mechanistic framework for designing personalized stimulation protocols, illustrating how computational modeling can guide the optimization of noninvasive brain stimulation in both research and clinical contexts.

bioengineering↗

Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain-dependent

Akkermansia muciniphila are mucin degrading bacteria found in the human gut and are often associated with positive human health. However, despite being detected as early as one month of age, little is known about the role of Akkermansia in the infant gut. Human milk oligosaccharides (HMOs) are abundant components of human milk and are structurally similar to the oligosaccharides that comprise mucin, the preferred growth substrate of human-associated Akkermansia. A limited subset of intestinal bacteria has been shown to grow well on HMOs and mucin. We therefore examined the ability of genomically diverse strains of Akkermansia to grow on HMOs. First, we screened 85 genomes representing the four known Akkermansia phylogroups to examine their metabolic potential to degrade HMOs. Furthermore, we examined the ability of representative isolates to grow on individual HMOs in a mucin background and analyzed the resulting metabolites. All Akkermansia genomes were equipped with an array of glycoside hydrolases associated with HMO-deconstruction. Representative strains were all able to grow on HMOs with varying efficiency and growth yield. Strain CSUN-19 belonging to the AmIV phylogroup, grew to the highest level in the presence of fucosylated and sialylated HMOs. This activity may be partially related to the increased copy numbers and/or the enzyme activities of the -fucosidases, -sialidases, and {beta}-galactosidases. Utilization of HMOs by strains of Akkermansia suggests that ingestion of HMOs by an infant may enrich for these potentially beneficial bacteria. Further studies are required to realize this opportunity and deliver long-lasting metabolic benefits to the human host. ImportanceHuman milk oligosaccharides (HMOs) are utilized by a limited subset of bacteria in the infant gut. Akkermansia are detected in infants as young as one month of age and are thought to contribute to the HMO deconstruction capacity of the infant. Here, using phylogenomics, we examined the genomic capacity of different Akkermansia phylogroups to potentially deconstruct HMOs. Furthermore, we experimentally showed that strains from all the currently known phylogroups of Akkermansia can deconstruct all the major types of HMOs, albeit with different utilization efficiencies. This study thus examines Akkermansia-HMO interactions that can potentially influence the gut microbial ecology during the first 1,000 days of life - a critical phase for the development of the gut microbiome and infant health. This study will be of interest to a wide range of scientists from microbiologists, glycochemists/glycobiologists, to functional food developers investigating Akkermansia as probiotics or functional foods containing milk oligosaccharides as prebiotics.

microbiology↗

Genomic and physiological analyses reveal that extremely thermophilic Caldicellulosiruptor changbaiensis deploys unique cellulose attachment mechanisms

The genus Caldicellulosiruptor are extremely thermophilic, heterotrophic anaerobes that degrade plant biomass using modular, multifunctional enzymes. Prior pangenome analyses determined that this genus is genetically diverse, with the current pangenome remaining open, meaning that new genes are expected with each additional genome sequence added. Given the high biodiversity observed among the genus Caldicellulosiruptor, we have sequenced and added a 14th species, Caldicellulosiruptor changbaiensis, to the pangenome. The pangenome now includes 3,791 ortholog clusters, 120 of which are unique to C. changbaiensis and may be involved in plant biomass degradation. Comparisons between C. changbaiensis and Caldicellulosiruptor bescii on the basis of growth kinetics, cellulose solubilization and cell attachment to polysaccharides highlighted physiological differences between the two species which are supported by their respective gene inventories. Most significantly, these comparisons indicated that C. changbaiensis possesses unique cellulose attachment mechanisms not observed among the other strongly cellulolytic members of the genus Caldicellulosiruptor.

microbiology↗