Faculty Bibliography

Recent discoveries reveal that post-translational modifications (PTMs) do more than regulate protein activity - they encode conformational states that transform chaperones into epichaperomes: multimeric scaffolds that rewire protein-protein interaction networks. This emerging paradigm expands the framework of chaperone biology in disease and provides a structural basis for systems-level dysfunction in disorders such as cancer and Alzheimer's disease. This review explores how PTMs within intrinsically disordered regions drive epichaperome formation, how these scaffolds selectively regulate disease-enabling functions, and why their disruption normalizes pathological networks. By highlighting PTMs as molecular encoders of supramolecular assemblies, we propose a shift from targeting proteins to targeting network architectures that sustain and perpetuate disease - a concept with broad implications for cell biology, disease propagation, and therapeutic design.

We examine the neurobiology of intuition, a term often inconsistently defined in scientific literature. While researchers generally agree that intuition represents "an experienced-based process resulting in a spontaneous tendency toward a hunch or hypothesis," we establish a firmer neurobiological foundation by framing intuition evolutionarily as a pathfinding mechanism emerging from the brain's optimization of its relationship with the environment. Our review synthesizes empirical findings on intuition's neurobiological basis, including relevant brain networks and their relationship to cognitive states like insight. We propose that unsolved problems dynamically alter attractor landscapes, guiding future intuitions. We investigate "opportunistic assimilation" through nonlinear neurodynamics and identify hippocampal sharp wave ripples as potential neural correlates of intuition, citing their role in creativity, choice, action planning, and abstract thinking. Finally, we explore intuition through two complementary perspectives: the free energy principle, which models brains as minimizing uncertainty through predictive hierarchical coding, and metastable coordination dynamics, describing the brain's simultaneous tendencies toward regional cooperation and functional autonomy. Together, these principles provide a comprehensive neurodynamical account of intuition's neurophenomenology.

BACKGROUND:Urinary stone disease with a clear genetic cause, monogenic stone disease (MSD), is increasingly recognized as a significant proportion of the total population. When MSD is suspected, genetic testing provides a firm diagnosis that can alter management and treatment. Here we present testing results from a large cohort with suspected MSD. METHODS:Subjects with features suggestive of MSD (early onset, family history, frequent stones, nephrocalcinosis [NC], and/or CKD) were recruited by the Rare Kidney Stone Consortium and genotyped for up to 160 known or candidate MSD genes via a targeted massively parallel sequencing (tMPS) panel. We compared clinical and biochemical features between genetically resolved MSD and unresolved individuals. RESULTS:Of 426 families (657 patients) enrolled, 145 (34%) were resolved with identified disease associated variants in 22 known MSD genes. Ninety-nine families were biallelic, 37 monoallelic, and 2 digenic. An additional 21 of the 231 screened family members were resolved. Genes identified in 10 or more families were: AGXT, HOGA1, SLC34A3, CYP24A1, SLC3A1, and CLCN5. Compared to the unresolved group, MSD probands had a lower baseline and last visit estimated glomerular filtration rate (eGFR), earlier age of stone presentation, and more stone events and procedures/year of life. The resolve rate was higher in those less than 16 years, and NC was seen earlier in the MSD group. Overall, NC was a risk factor for lower eGFR. Among the specific disorders, primary hyperoxaluria patients had the earliest age of stone and NC diagnosis, and as expected, the highest urinary oxalate level. CONCLUSIONS:Our study emphasizes the value of selecting patients enriched for factors associated with MSD, and comprehensive genetic testing to achieve a high yield of genetic diagnoses. Significant clinical and biochemical characteristics of MSD patients were defined. A definitive MSD diagnosis facilitates individualized management and strategies to delay disease progression in probands and affected family members.

Fish actively control posture in the pitch axis (nose-up/nose-down) to counter instability and regulate their elevation in the water column. To test the hypothesis that environmental cues shape strategies fish use to control posture, we leveraged a serendipitous finding: larval zebrafish (Danio rerio) lose swim bladder volume and sink mildly after acute loss of lateral line hair cells. Using long-term (48 h) recordings of unrestrained swimming, we discovered that sinking larvae compensated differently depending on light conditions. In the dark, they swim more frequently with an increased nose-up posture. In contrast, larvae in the light do not swim more frequently, but do climb more often. Finally, after lateral line regeneration, larvae returned to normal buoyancy and swam comparably to control siblings. We conclude that larvae can switch postural control strategies depending on the availability of visual information. Our findings complement and extend morphological and kinematic analyses of locomotion. More broadly, by quantifying the variation in strategies our work speaks to the evolutionary substrate for different balance behaviors.

Down syndrome (DS), stemming from the triplication of human chromosome 21, results in intellectual disability, with early mid-life onset of Alzheimer's disease (AD) pathology. Early interventions to reduce cognitive impairments and neuropathology are lacking. One modality, maternal choline supplementation (MCS), has shown beneficial effects on behavior and gene expression in neurodevelopmental and neurodegenerative disorders, including trisomic mice. Loss of basal forebrain cholinergic neurons (BFCNs) and other DS/AD relevant hallmarks were observed in a well-established trisomic model (Ts65Dn, Ts). MCS attenuates these endophenotypes with beneficial behavioral effects in trisomic offspring. We postulate MCS ameliorates dysregulated cellular mechanisms within vulnerable BFCNs, with attenuation driven by novel gene expression. Here, choline acetyltransferase immunohistochemical labeling identified BFCNs in the medial septal/ventral diagonal band nuclei of the basal forebrain in Ts and normal disomic (2N) offspring at ~11 months of age from dams exposed to MCS or normal choline during the perinatal period. BFCNs (~500 per mouse) were microisolated and processed for RNA-sequencing. Bioinformatic assessment elucidated differentially expressed genes (DEGs) and pathway alterations in the context of genotype (Ts, 2N) and maternal diet (MCS, normal choline). MCS attenuated select dysregulated DEGs and relevant pathways in aged BFCNs. Trisomic MCS-responsive improvements included pathways such as cognitive impairment and nicotinamide adenine dinucleotide signaling, among others, indicative of increased behavioral and bioenergetic fitness. Although MCS does not eliminate the DS/AD phenotype, early choline delivery provides long-lasting benefits to aged trisomic BFCNs, indicating that MCS prolongs neuronal health in the context of DS/AD.

Cochlear implants are neuroprosthetic devices that restore hearing and speech comprehension to profoundly deaf humans, and represent an exemplar application of biomedical engineering and research to clinical conditions. However, the utility of these devices in many subjects is limited, largely due to lack of information about how neural circuits respond to implant stimulation. Recently we showed that deafened rats can use cochlear implants to recognize sounds, and that this training refined the responses of single neurons in the primary auditory cortex. Here we asked how local populations of cortical neurons represent acute implant stimuli, using electrode arrays we developed for cortical surface recordings for micro-electrocorticography (μECoG), a form of intracranial electroencephalography (iEEG). We found that there was a limited tonotopic organization across recording sites, relative to a clearer tonotopic spatial representation in normal-hearing rats. Single-trial iEEG responses to acoustic inputs were more reliable than responses to cochlear implant stimulation, although stimulus identity could be successfully decoded in both cases. However, the spatio-temporal response profiles to acoustic vs cochlear implant stimulation were substantially different. Decoders trained on acoustic responses showed essentially zero information transfer when tested on electrical stimulation responses in the same animals after deafening and cochlear implant stimulation. Thus while acute cochlear implant stimulation might activate the auditory cortex in a cochleotopic manner, the dynamics of network activity are quite distinct, suggesting that pitch percepts from acoustic and electrical stimulation are fundamentally different.

Electroencephalography (EEG) connectomes offer powerful tools for studying brain connectivity and advancing our understanding of brain function and dysfunction in both healthy and pathological conditions. Celebrating the 100th anniversary of EEG discovery, this Perspective explores the frontiers of EEG-based brain connectivity in basic and translational neuroscience research. We review new concepts, emerging analysis frameworks and significant advances in harnessing EEG connectomes. We suggest that leveraging machine learning approaches may offer promising paths to maximize the strengths of EEG connectomes. We also discuss how combined EEG connectome and neuromodulation provide a personalized and adaptive closed-loop paradigm to promote neuroplasticity and treat dysfunctional brains. We further address the limitations and challenges of the current methodology and touch on important issues regarding research rigour and clinical viability for translational impact.

Immediate escape and gradual habituation are both crucial for animal survival in response to repeated threat exposures. In this issue of Neuron, Liu et al. identified key neural circuits supporting each of these two responsive patterns to repeated visual threats.¹.

Seventy % of mammals copulate using repeated pelvic thrusting, while the transfer of sperm requires just a single intromission. Why did thrusting evolve to be the dominant form of sexual intercourse? In this study, we investigate how the rate of sexual pelvic thrusting changes with body size. By analyzing films of copulating mammals, from mice Mus musculus to elephants Elephantidae, we find that bigger animals thrust slower. The rate of pelvic thrusting decreases from 6 Hz for the pocket mouse Pergonathus to 1.3-1.8 Hz for humans to an absence of thrusting for the rhino Rhinocerotidae and elephant Elephantidae families. To understand this dependence on body size, we consider the spring-like behavior of the legs, which is associated with the elasticity of the body's muscles, tendons, and ligaments. For both running and thrusting, a maximum amplitude and great energy savings can be achieved if the system is oscillated at its resonant or natural frequency. Resonant frequencies, as measured through previous studies of running in dogs Canis familiaris and horses Equus ferus caballus, show good agreement with sexual thrusting frequencies. Running and sexual thrusting have nothing in common from a behavioral perspective, but from a physical perspective, they are both constrained by the same musculoskeletal systems, and both take advantage of resonance. Our findings may provide improved treatments for human sexual dysfunction as well as improving breeding strategies for domestic mammals.