Faculty Bibliography

The interstitial space (ISS) component of brain extracellular space resembles an unconsolidated porous medium. Previous analysis of the diffusion of small molecules in this domain shows that the typical porosity is 0.2 and typical tortuosity 1.6. An ensemble of cubic cells separated by uniform sheets of ISS cannot generate the measured tortuosity, even if some of the tortuosity value is attributed to interstitial viscosity, so more complex models are needed. Here two models are analysed: the corner cubic void (CCV) and the edge tunnel void (ETV). Both models incorporate dead spaces formed from local expansions of the ISS to increase geometrical tortuosity. Using Monte Carlo simulation of diffusion it is found that in the range of normal porosities, the square of the tortuosity is a linear function of the ratio of void to sheet volumes for the CCV model and this model can generate the experimentally observed tortuosities. For abnormally high porosities, however, the linear relation fails. The ETV model shows a quartic functional relation and can only generate the observed tortuosity if interstitial viscosity is present. The CCV model is used to analyse the recently described changes in porosity between asleep and awake brain states.

A well-accepted strategy to prevent kidney stones is to increase urine volume by increasing oral intake of fluids, especially water, to lower supersaturation of the relevant, relatively insoluble salts, and thereby lower the risk of precipitation. Randomized controlled trials have shown that this strategy works. It is inexpensive, safe, and intuitively attractive to patients. However, although any beverage can increase urine volume, and citrus juices can increase urine citrate content and pH, no beverage other than water has been clearly shown by randomized controlled trial to prevent kidney stones. We designed an innovative, palatable, low-calorie, high alkali citrate beverage to prevent kidney stones, called Moonstone. One packet of Moonstone powder, mixed in 500 ml of water, contains 24.5 meq of alkali citrate. We administered one packet twice a day to ten calcium stone formers. Moonstone resulted in an increase in mean 24-h urine citrate and urine pH, and a decrease in supersaturation of calcium oxalate in calcium stone formers compared to an equal volume of water. These changes, comparable to those seen in a prior study of a similar amount of (potassium-magnesium) citrate, will likely be associated with a clinically meaningful reduction in kidney stone burden in patients with calcium stones. The effect to increase urine pH would also be expected to benefit patients with uric acid and cystine stones, groups that we hope to study in a subsequent study. The study preparation was well tolerated and was selected as a preferred preventative strategy by about half the participants. Moonstone is an alternative, over-the-counter therapy for kidney stone prevention.

One major question in neuroscience is how to relate connectomes to neural activity, circuit function, and learning. We offer an answer in the peripheral olfactory circuit of the Drosophila larva, composed of olfactory receptor neurons (ORNs) connected through feedback loops with interconnected inhibitory local neurons (LNs). We combine structural and activity data and, using a holistic normative framework based on similarity-matching, we formulate biologically plausible mechanistic models of the circuit. In particular, we consider a linear circuit model, for which we derive an exact theoretical solution, and a nonnegative circuit model, which we examine through simulations. The latter largely predicts the ORN [Formula: see text] LN synaptic weights found in the connectome and demonstrates that they reflect correlations in ORN activity patterns. Furthermore, this model accounts for the relationship between ORN [Formula: see text] LN and LN-LN synaptic counts and the emergence of different LN types. Functionally, we propose that LNs encode soft cluster memberships of ORN activity, and partially whiten and normalize the stimulus representations in ORNs through inhibitory feedback. Such a synaptic organization could, in principle, autonomously arise through Hebbian plasticity and would allow the circuit to adapt to different environments in an unsupervised manner. We thus uncover a general and potent circuit motif that can learn and extract significant input features and render stimulus representations more efficient. Finally, our study provides a unified framework for relating structure, activity, function, and learning in neural circuits and supports the conjecture that similarity-matching shapes the transformation of neural representations.

Genomic alterations (GA) in NF2 tumor-suppressor gene have been associated with aggressive behavior in kidney tumors. We used comprehensive genomic profiling (CGP) to evaluate the frequencies of NF2 GA in histologic subtypes of kidney tumors and co-occurring GA in other genes and biomarkers. Advanced kidney tumors included 1875 clear cell (ccRCC), 405 papillary (pRCC), 108 chromophobe (chRCC), 171 sarcomatoid (sRCC), 61 collecting duct (cdRCC), 49 medullary (mRCC), 134 unclassified (uRCC), 906 urothelial carcinoma of renal pelvis (UC), and 147 Wilms tumors underwent hybrid-capture based CGP to evaluate all classes of GA. 192 (4.9%) of kidney tumors featured NF2 GA which were predominantly structural variant mutations (89%), followed by copy number alterations (9%). Gender and age were similar between NF2-mutant (NF2mut) and NF2-wild type (NF2wt) cohorts with male preponderance. NF2 GA frequency was highest in cdRCC (30%), sRCC (21%), uRCC (15%), and pRCC (12%) while lowest in ccRCC (3%), UC (3%) Wilms tumor (1%), and chRCC (0%). NF2 mutational status was associated with loss of Ch 22 (P < .001). NF2mut RCC harbored co-occurring GA including CDKN2A, CDKN2B, SETD2, and BAP1. VHL, PBRM1, PTEN, and FGFR3 GA were significantly more frequent in NF2wt than in NF2mut tumors. MTOR pathway GAs were uncommon in NF2mut tumors. No NF2 mutated RCC featured MSI-high or high TMB. sRCC was associated with high PD-L1 expression. PD-L1 SP142 tumoral (P = .04) and immune cells (P = .013) were more frequent in NF2mut as compared to NF2wt group. Among histologic subtypes of RCC, cdRCC, sRCC, pRCC, and uRCC are enriched in NF2 GA. Co-occurrent GA in CDKN2A/B, SETD2, and BAP1 may represent potential therapeutic targets. Higher level of PD-L1 expression in NF2mut cohort suggests that these tumors might be sensitive to immune checkpoint inhibitor therapies.

BACKGROUND/UNASSIGNED:Prefrontal cortical neurons play essential roles in performing rule-dependent tasks and working memory-based decision making. METHODS/UNASSIGNED:Motivated by PFG recordings of task-performing mice, we developed an excitatory-inhibitory spiking recurrent neural network (SRNN) to perform a rule-dependent two-alternative forced choice (2AFC) task. We imposed several important biological constraints onto the SRNN, and adapted spike frequency adaptation (SFA) and SuperSpike gradient methods to train the SRNN efficiently. RESULTS/UNASSIGNED:The trained SRNN produced emergent rule-specific tunings in single-unit representations, showing rule-dependent population dynamics that resembled experimentally observed data. Under varying test conditions, we manipulated the SRNN parameters or configuration in computer simulations, and we investigated the impacts of rule-coding error, delay duration, recurrent weight connectivity and sparsity, and excitation/inhibition (E/I) balance on both task performance and neural representations. CONCLUSIONS/UNASSIGNED:Overall, our modeling study provides a computational framework to understand neuronal representations at a fine timescale during working memory and cognitive control, and provides new experimentally testable hypotheses in future experiments.

Oxytocin (OT), a peptide hormone and neuromodulator, is involved in diverse physiological and pathophysiological processes in the central nervous system and the periphery. However, the regulation and functional sequences of spatial OT release in the brain remain poorly understood. We describe a genetically encoded G-protein-coupled receptor activation-based (GRAB) OT sensor called GRAB_OT1.0. In contrast to previous methods, GRAB_OT1.0 enables imaging of OT release ex vivo and in vivo with suitable sensitivity, specificity and spatiotemporal resolution. Using this sensor, we visualize stimulation-induced OT release from specific neuronal compartments in mouse brain slices and discover that N-type calcium channels predominantly mediate axonal OT release, whereas L-type calcium channels mediate somatodendritic OT release. We identify differences in the fusion machinery of OT release for axon terminals versus somata and dendrites. Finally, we measure OT dynamics in various brain regions in mice during male courtship behavior. Thus, GRAB_OT1.0 provides insights into the role of compartmental OT release in physiological and behavioral functions.

Using odors to find food and mates is one of the most ancient and highly conserved behaviors. Arthropods from flies to moths to crabs use broadly similar strategies to navigate toward odor sources-such as integrating flow information with odor information, comparing odor concentration across sensors, and integrating odor information over time. Because arthropods share many homologous brain structures-antennal lobes for processing olfactory information, mechanosensors for processing flow, mushroom bodies (or hemi-ellipsoid bodies) for associative learning, and central complexes for navigation, it is likely that these closely related behaviors are mediated by conserved neural circuits. However, differences in the types of odors they seek, the physics of odor dispersal, and the physics of locomotion in water, air, and on substrates mean that these circuits must have adapted to generate a wide diversity of odor-seeking behaviors. In this review, we discuss common strategies and specializations observed in olfactory navigation behavior across arthropods, and review our current knowledge about the neural circuits subserving this behavior. We propose that a comparative study of arthropod nervous systems may provide insight into how a set of basic circuit structures has diversified to generate behavior adapted to different environments.

Despite advances in uncovering the mechanisms that underlie neuroinflammation and neurodegenerative disease, therapies that prevent neuronal loss remain elusive. Targeting of disease-defining markers in conditions such as Alzheimer disease (amyloid-β and tau) or Parkinson disease (α-synuclein) has been met with limited success, suggesting that these proteins do not act in isolation but form part of a pathological network. This network could involve phenotypic alteration of multiple cell types in the CNS, including astrocytes, which have a major neurosupportive, homeostatic role in the healthy CNS but adopt reactive states under acute or chronic adverse conditions. Transcriptomic studies in human patients and disease models have revealed the co-existence of many putative reactive sub-states of astrocytes. Inter-disease and even intra-disease heterogeneity of reactive astrocytic sub-states are well established, but the extent to which specific sub-states are shared across different diseases is unclear. In this Review, we highlight how single-cell and single-nuclei RNA sequencing and other 'omics' technologies can enable the functional characterization of defined reactive astrocyte states in various pathological scenarios. We provide an integrated perspective, advocating cross-modal validation of key findings to define functionally important sub-states of astrocytes and their triggers as tractable therapeutic targets with cross-disease relevance.

PURPOSE/OBJECTIVE:-weighted radial stack-of-stars 3D gradient echo (GRE) sequence with comparable image quality to conventional MP-RAGE and to demonstrate how the radial acquisition scheme can be utilized for additional retrospective motion correction to improve robustness to head motion. METHODS:The proposed sequence, named MP-RAVE, has been derived from a previously described radial stack-of-stars 3D GRE sequence (RAVE) and includes a 180° inversion recovery pulse that is generated once for every stack of radial views. The sequence is combined with retrospective 3D motion correction to improve robustness. The effectiveness has been evaluated in phantoms and healthy volunteers and compared to conventional MP-RAGE acquisition. RESULTS:MP-RAGE and MP-RAVE anatomical images were rated "good" to "excellent" in overall image quality, with artifact level between "mild" and "no artifacts", and with no statistically significant difference between methods. During head motion, MP-RAVE showed higher inherent robustness with artifacts confined to local brain regions. In combination with motion correction, MP-RAVE provided noticeably improved image quality during different head motion and showed statistically significant improvement in image sharpness. CONCLUSION/CONCLUSIONS:MP-RAVE provides comparable image quality and contrast to conventional MP-RAGE with improved robustness to head motion. In combination with retrospective 3D motion correction, MP-RAVE can be a useful alternative to MP-RAGE, especially in non-cooperative or pediatric patients.

Systems-level assessments of protein-protein interaction (PPI) network dysfunctions are currently out-of-reach because approaches enabling proteome-wide identification, analysis, and modulation of context-specific PPI changes in native (unengineered) cells and tissues are lacking. Herein, we take advantage of chemical binders of maladaptive scaffolding structures termed epichaperomes and develop an epichaperome-based 'omics platform, epichaperomics, to identify PPI alterations in disease. We provide multiple lines of evidence, at both biochemical and functional levels, demonstrating the importance of these probes to identify and study PPI network dysfunctions and provide mechanistically and therapeutically relevant proteome-wide insights. As proof-of-principle, we derive systems-level insight into PPI dysfunctions of cancer cells which enabled the discovery of a context-dependent mechanism by which cancer cells enhance the fitness of mitotic protein networks. Importantly, our systems levels analyses support the use of epichaperome chemical binders as therapeutic strategies aimed at normalizing PPI networks.