Faculty Bibliography

Digital spatial profiling (DSP) facilitates RNA sequencing (RNA-seq) of small populations of cells, specifically ~20 pyramidal neurons in postmortem formalin-fixed paraffin-embedded (FFPE) human brain tissue. This approach enables precise expression profiling via RNA-seq data linked to spatially characterized samples utilizing tissue-bound probes. We present a comprehensive protocol for manual slide preparation using the GeoMx DSP system as preliminary steps to spatial characterization of lamina-specific pyramidal neurons in human postmortem Brodmann area 9 (BA9) frontal cortex brain tissue.

Nuclear factor I (NFI) misexpressions in humans are associated with severe brain malformations, yet the underlying mechanisms remain poorly understood. Here, we show that NFIs regulate the broad lineage progression and lifespan of radial glial progenitors (RGPs), thereby bidirectionally controlling neocortical development. Human cerebral organoids carrying patient-mimicking NFI mutations exhibit expression-level-dependent bidirectional impairments in RGP temporal development, coinciding with patient phenotypes. In mouse models, selective removal of NFIs leads to a dramatic protraction of RGP lineage progression and lifespan, excessive progeny output, and cortical overgrowth and abnormal folding, whereas overexpression of NFIs accelerates RGP lineage progression, resulting in developmental-stage-dependent precocious production of diverse neural progenies. Moreover, NFIs exhibit positive autoregulation and progressive increase in expression and regulate distinct temporal-specific targets underlying RGP lineage progression. These results suggest that NFIs act as evolutionarily conserved key global temporal regulators of RGP lineage progression and neocortical development.

OBJECTIVES/OBJECTIVE:This study aims to validate vocoders as acoustic models of cochlear implants by determining whether they capture both perceptual sound quality and speech performance. We hypothesize that valid acoustic models of cochlear implants require listener-specific amounts of frequency mismatch between input filters and output tones or noise bands. DESIGN/METHODS:Forty-four adult single-sided deaf cochlear implant users were tested 1 to 5 times for a total of 73 sessions at different time points after initial stimulation. Participants had a cochlear implant in one ear and normal or near-normal hearing in the contralateral ear, allowing within-subject comparisons. In Experiment 1, participants used a method-of-adjustment procedure to select acoustic models most similar to their cochlear implant by adjusting three parameters: low- and high-frequency cutoffs of the acoustic output, and channel interaction (overlap among output sound carriers). In Experiment 2, participants rated the perceptual similarity of five acoustic model types using questionnaires assessing overall similarity and four acoustic dimensions (intelligibility, pleasantness, harshness, and loudness). The five model types included the self-selected model, two all-channel frequency-matched vocoders (tone and noise), and two six-channel frequency-matched vocoders (tone and noise). Frequency-matched acoustic models had output noise bands or tones that were frequency-matched to the analysis filters. In Experiment 3, speech perception was evaluated under six conditions: with the cochlear implant alone and with each of the five acoustic model types presented to the normal hearing ear. RESULTS:Nearly all participants (69 of 73 sessions) selected acoustic models with frequency ranges different from their clinical frequency allocation tables. The low-frequency edge of self-selected models was significantly higher than clinical allocations (456 Hz for Cochlear Ltd. and 266 Hz for MED-EL). Over 80% of selections used minimal channel interaction (tones, nonoverlapping noise bands, or adjacent noise bands). Self-selected models received significantly higher similarity ratings (mean of 6.11, where 6 means "somewhat similar" and 7 "very similar") compared with all frequency-matched models, which were rated around 3 ("not very similar"). Self-selected models were rated most similar to the cochlear implant across multiple acoustic dimensions and were the only models not rated significantly different from the cochlear implant on any dimension. For speech perception, all-channel frequency-matched models significantly overestimated performance compared with the cochlear implant for both words and sentences. Self-selected models provided speech scores closest to cochlear implant performance. Joint analysis of similarity ratings and speech perception scores demonstrated that self-selected models were the only acoustic models achieving both perceptual similarity to the cochlear implant (rating of 6.11 with 7 being "very similar") and comparable speech perception scores (within five percentage points). CONCLUSIONS:Frequency-matched acoustic models fail to replicate the sound of a cochlear implant and all-channel frequency-matched acoustic models also significantly overestimate speech perception. In contrast, self-selected acoustic models incorporating listener-specific perceptual frequency mismatch provide substantially better matches in both subjective sound quality and speech intelligibility. However, variability in similarity ratings across individuals may suggest that additional perceptual components remain unaccounted for in the current parameter set. These findings question the validity of frequency-matched acoustic models of cochlear implants in research applications.

Somatic mutations accumulate throughout life in every cell, and this process constitutes one of the hallmarks of aging-genomic instability. Caloric restriction (CR) has been shown to extend lifespan across diverse species. Using high-fidelity duplex DNA sequencing of bulk liver, bulk kidney, hepatocytes, and cerebellar neurons, we found that CR in mice reduces genome-wide somatic mutation burdens across multiple tissues and cell types. CR reduced both substitution and insertion/deletion burdens, with the magnitude of these effects varying across sample types. CR also decreased the activity of the enigmatic single-base substitution (SBS) mutational process SBS5 that gives rise to most mutations in mammals. Surprisingly, the mutation burden reduction from CR was greatest in transcriptionally inactive regions. This work illuminates links between diet, aging, and genomic integrity and establishes genomic integrity as a modifiable axis of aging.

Working memory and evidence integration are fundamental components of cognition. Theoretical and behavioral studies argue that both processes are required for plume navigation, a behavior in which animals use stochastic sensory cues to navigate towards an odor source. Here we identify a small population of local neurons in the navigation center of Drosophila that exhibits both theorized processes. During virtual plume navigation, a bump of activity in this population ramps up with successive odor encounters, and can persist for variable intervals after odor loss. While the bump persists, the fly maintains the goal heading it adopted during odor. Silencing these neurons impairs this persistence. Simulations show that the time constant of persistence observed in these neurons optimizes navigation in a turbulent boundary layer plume. Our work localizes working memory and evidence integration to a specific group of neurons, which will facilitate the mechanistic dissection of these building blocks of cognition.

What is a 'natural' behavior? I argue that the study of natural behaviors is often the study of the spontaneous behaviors of animals placed in quantifiably different environments. For behavioral generalists such as rodents, humans, and many other species, there may be no such definable construct as a native habitat or 'natural behavior', due to their successful abilities and needs to rapidly adapt to a wide range of different ecosystems. Instead of prioritizing naturalness, it may be more essential to determine objective outcome measures related to specific behaviors; i.e., which sequences of behaviors and adaptive mechanisms allow animals to survive and reproduce across a range of dynamic or hazardous physical and social environments.

Flying flies can determine ambient wind direction in flight, but what neural representations might support this behavior are unclear. Ambient wind acting on a flying fly creates distinct patterns of airflow and optic flow. Here, we used two-photon imaging to characterize encoding of these two variables across columnar inputs to the fly navigation center, called PFNs. We find tuning for airflow direction and speed across many PFN types but only optic flow direction tuning in limited types. We do not observe tuning to optic flow speed. We build and validate an encoding model that enables simulation of PFN representations during real and simulated flight maneuvers. We show that these representations are sufficient to decode ambient wind direction both theoretically and using a simple feedforward ANN. Our work shows how a compact multisensory representation of self-motion could be used to infer a property of the external world that cannot be directly measured by a single sensory system.

BACKGROUND:Nephrolithiasis recurs after an initial episode within 5 years for 30-50% of stone formers without dietary and/or pharmacological therapy to prevent or reduce stone recurrence. Preventive interventions target increasing urine volume or altering urinary concentration of key risk factors: high calcium, oxalate or uric acid and low urinary citrate. Two strategies for achieving stone prevention involve an untailored generalized approach (empiric therapy) and an approach tailored to results from 24 h urine testing (selective therapy). METHODS:Adults with recurrent kidney stone disease were randomly assigned to empiric (Emp) or selective (Sel) therapy upon completing 24 h urine testing. Participants in the Emp group received standard guideline-based diet and medication therapy. Participants in the Sel group received therapy tailored to their 3 most severe urine abnormalities. Within-group differences in dietary and urinary variables were assessed via the Wilcoxon test and difference between groups in changes from baseline to 8 weeks via general linear modeling. RESULTS:The Emp group had a 33% reduction in dietary oxalic acid intake (p = 0.02), but no significant changes in intakes of water, sodium, animal-based protein, or servings of fruits and vegetables. There were also no significant changes in urine volume or urinary sodium excretion. Overall, Sel participants increased daily intake of water by 17% (p = 0.02), doubled their number of daily fruit/vegetable servings (p = 0.04), and reduced their oxalate (p = 0.04) and sodium (p = 0.05) intakes. Sel participants in the urinary citrate and calcium subgroups showed greater reductions in urinary calcium oxalate supersaturation (-38%) compared to the Emp group (-30%). CONCLUSIONS:The findings suggest that a more personalized approach with a limited number of dietary targets supports improvements that are less likely to occur with empiric therapy which reflects a "one size fits all" method. However, even with tailored therapy, the inter-individual variability in dietary intake and response to treatment must be considered as adherence to dietary recommendations is particularly challenging in a condition that is lifelong. This trial was registered at clinicaltrials. gov NCT05365477.

What is a 'natural' behavior? I argue that the study of natural behaviors is often the study of the spontaneous behaviors of animals placed in quantifiably different environments. For behavioral generalists such as rodents, humans, and many other species, there may be no such definable construct as a native habitat or 'natural behavior', due to their successful abilities and needs to rapidly adapt to a wide range of different ecosystems. Instead of prioritizing naturalness, it may be more essential to determine objective outcome measures related to specific behaviors; i.e., which sequences of behaviors and adaptive mechanisms allow animals to survive and reproduce, across a range of dynamic or hazardous physical and social environments.