Biology subjects

Smith, K. S.

Publications and source records attributed to Smith, K. S..

17 recordsLinked to original sources

bioRxiv2026

Multi-Omic, Multi-Tissue Responses to Acute Exercise in Sedentary Adults: Findings from the Molecular Transducers of Physical Activity Consortium

Regular physical activity represents one of the greatest mechanisms for maintaining human health, yet the underlying molecular transducers of these benefits remain incompletely understood. Multi-omic assays now provide new opportunities to study the coordinated molecular responses of body tissues to different exercise modalities. The Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to address this need by creating a molecular map of the response to physical activity. Described here is the first human cohort of MoTrPAC: sedentary adults enrolled prior to study suspension during the COVID-19 pandemic (N=175) randomized to either endurance or resistance exercise, or non-exercise control. From these participants, we detail their global acute molecular response in skeletal muscle, adipose tissue, and blood, integrated at multiple levels: tissue, exercise modality, timepoint, and omic category. These analyses characterize key molecular pathways, identify central regulators, and implicate novel candidate exerkines in mediating multi-organ exercise effects.

systems biology↗

bioRxiv2025

Phasic dopamine encodes persistent attraction to reward cues

Reward-predictive cues can become attractive themselves due to incentive salience attribution. This manifests as persistent engagement with cues, known as sign-tracking. Cue-evoked phasic dopamine in the nucleus accumbens core (NAc) is critical for sign-tracking and cue-evoked reward craving, yet is also known to follow learning rules requiring outcome value updating. Would cue-evoked dopamine track incentive salience persistence, or change in accord with reward value alteration while failing to encode persistent behaviors? We assessed NAc dopamine activity using fiber photometry in sign-tracking rats during an omission task, in which physical cue interaction cancels reward. Animals adapted to reward loss while maintaining non-physical cue interaction reflective of persistent incentive salience. Cue-evoked dopamine remained unchanged during omission, mirroring robust incentive salience but not behavioral adaptations occurring with learning. In contrast, outcome-related dopamine reflected reward gain or loss. Therefore, cue-related dopamine encodes persistence of cue value, independent of outcome-related dopamine signals tracking reward occurrence.

neuroscience↗

bioRxiv2025

A catastrophic marine mortality event caused by a complex algal bloom including the novel brevetoxin producer, Karenia cristata (Dinophyceae)

Harmful algal blooms of Karenia brevis (Dinophyceae) are a global anomaly, occurring in one location worldwide, causing severe marine and acute human impacts via brevetoxins (BTX). During 2025 an unprecedented, currently ongoing, mass marine mortality occurred in South Australia, across an area of [~]20,000 km2, persisting for >6 months, resulting in the deaths of [~]106 marine animals of >550 taxa, with human health impacts. Using custom metabarcoding, long-read sequencing and targeted quantitative PCR, we characterized the microalgal assemblage. Karenia cristata dominated over the sampling area, in an assemblage with four other Karenia species with varied abundances spatially and temporally. High abundances of K. cristata appeared in the austral autumn, and hydrodynamic processes appear to have entrained cells coastward in the semi-enclosed seas. We isolated the species and characterized it using light and electron microscopy, liquid chromatography mass spectrometry and toxicity assays. We show for the first time that the rare and little known K. cristata produces significant BTX with a profile (BTX-2, -3, -B5), differing from K. brevis, with toxicological effects. These findings reveal a novel, significant BTX-producing Karenia, which considering its substantial detrimental marine ecosystem impacts, is an emerging international threat with unknown consequences in changing ocean conditions.

ecology↗

bioRxiv2024

Habit learning shapes activity dynamics in the central nucleus of the amygdala

As animals perform instrumental tasks, they may develop a habit response with extended experience. Habits are automatic, inflexible, outcome value insensitive behaviors that are regulated by a network of brain regions including the central nucleus of the amygdala (CeA). Prior work has demonstrated that the CeA governs motivational pursuit and is necessary for habit formation. However, the behavioral features that CeA neurons encode in habit formation remain relatively unknown. To address this, we first used male and female Long-Evans rats to quantify CeA cFos expression after performance of a maze task. There, we found that animals with extended training show elevated cFos expression. Then, we implanted animals with drivable silicon probes to record in-vivo single unit electrophysiological activity from the CeA as animals developed habit responding on the maze. We observed significant activity during outcome consumption late in training while also observing elevated unit activity when animals consumed outcomes of larger magnitudes. Outcome related activity did not persist during probe tests following outcome devaluation, despite animals continuing to perform the task. Together, these data add to growing evidence that suggests that the CeA is involved in motivational processes that contribute to the development of habit formation.

neuroscience↗

bioRxiv2023

Transcriptomics and chromatin accessibility in multiple African population samples

Mapping the functional human genome and impact of genetic variants is often limited to European-descendent population samples. To aid in overcoming this limitation, we measured gene expression using RNA sequencing in lymphoblastoid cell lines (LCLs) from 599 individuals from six African populations to identify novel transcripts including those not represented in the hg38 reference genome. We used whole genomes from the 1000 Genomes Project and 164 Maasai individuals to identify 8,881 expression and 6,949 splicing quantitative trait loci (eQTLs/sQTLs), and 2,611 structural variants associated with gene expression (SV-eQTLs). We further profiled chromatin accessibility using ATAC-Seq in a subset of 100 representative individuals, to identity chromatin accessibility quantitative trait loci (caQTLs) and allele-specific chromatin accessibility, and provide predictions for the functional effect of 78.9 million variants on chromatin accessibility. Using this map of eQTLs and caQTLs we fine-mapped GWAS signals for a range of complex diseases. Combined, this work expands global functional genomic data to identify novel transcripts, functional elements and variants, understand population genetic history of molecular quantitative trait loci, and further resolve the genetic basis of multiple human traits and disease.

genomics↗

bioRxiv2023

A thin-film optogenetic visual prosthesis

Retinitis pigmentosa and macular degeneration lead to photoreceptor death and loss of visual perception. Despite recent progress, restorative technologies for photoreceptor degeneration remain largely unavailable. Here, we describe a novel optogenetic visual prosthesis (FlexLED) based on a combination of a thin-film retinal display and optogenetic activation of retinal ganglion cells (RGCs). The FlexLED implant is a 30 {micro}m thin, flexible, wireless {micro}LED display with 8,192 pixels, each with an emission area of 66 {micro}m2. The display is affixed to the retinal surface, and the electronics package is mounted under the conjunctiva in the form factor of a conventional glaucoma drainage implant. In a rabbit model of photoreceptor degeneration, optical stimulation of the retina using the FlexLED elicits activity in visual cortex. This technology is readily scalable to hundreds of thousands of pixels, providing a route towards an implantable optogenetic visual prosthesis capable of generating vision by stimulating RGCs at near-cellular resolution.

neuroscience↗

bioRxiv2023

Task history dictates how the dorsolateral striatum controls action strategy and vigor

The dorsolateral striatum (DLS) is linked to the learning and honing of action routines. However, the DLS is also important for performing behaviors that have been successful in the past. The learning function can be thought of as prospective, helping to plan ongoing actions to be efficient and often optimal. The performance function is more retrospective, helping the animal continue to behave in a way that had worked previously. How the DLS manages this all is curious. What happens when a learned behavior becomes sub-optimal due to environment changes. In this case, the prospective function of the DLS would cause animals to (adaptively) learn and plan more optimal actions. In contrast, the retrospective function would cause animals to (maladaptively) favor the old behavior. Here we find that, during a change in learned task rules, DLS inhibition causes animals to adjust less rapidly to the new task (and to behave less vigorously) in a maladaptive way. Yet, when the task is changed back to the initially learned rules, DLS inhibition instead causes a rapid and vigorous adjustment of behavior in an adaptive way. These results show that inhibiting the DLS biases behavior towards initially acquired strategies, implying a more retrospective outlook in action selection when the DLS is offline. Thus, an active DLS could encourage planning and learning action routines more prospectively. Moreover, the DLS control over behavior can appear to be either advantageous/flexible or disadvantageous/inflexible depending on task context, and its control over vigor can change depending on task context. Significant StatementBasal ganglia networks aid behavioral learning (a prospective planning function) but also favor the use of old behaviors (a retrospective performance function), making it unclear what happens when learned behaviors become suboptimal. Here we inhibit the dorsolateral striatum (DLS) as animals encounter a change in task rules, and again when they shift back to those learned task rules. DLS inhibition reduces adjustment to new task rules (and reduces behavioral vigor), but it increases adjustment back to the initially learned task rules later (and increases vigor). Thus, in both cases, DLS inhibition favored the use of the initially learned behavioral strategy, which could appear either maladaptive or adaptive. We suggest that the DLS might promote a prospective orientation of action control.

animal behavior and cognition↗

bioRxiv2023

Multiomic identification of key transcriptional regulatory programs during endurance exercise training

Transcription factors (TFs) play a key role in regulating gene expression. We conducted an integrated analysis of chromatin accessibility, DNA methylation, mRNA expression, protein abundance and phosphorylation across eight tissues in fifty rats of equally represented sexes following endurance exercise training (EET) to identify coordinated epigenomic and transcriptional changes and determine key TFs involved. We uncovered tissue-specific EET associated changes and TF motif enrichment across differentially expressed genes (DEGs), accessible regions (DARs), and methylated regions (DMRs). We discovered distinct routes of EET-induced regulation through either epigenomic alterations providing better access for TFs to affect target genes, or via changes in TF expression or activity enabling target gene responses. We identified TF motifs enriched among correlated epigenomic and transcriptomic alterations, DEGs correlated with exercise-related phenotypic and cell type composition changes, and EET-induced activity changes of TFs whose target genes are enriched for DEGs. This analysis elucidates the unique gene regulatory mechanisms mediating diverse transcriptional responses to EET across tissues.

genomics↗

bioRxiv2022

Nucleus accumbens acetylcholine receptors modulate the balance of flexible and inflexible cue-directed motivation

Sign-tracking is a conditioned response where animals interact with reward-predictive cues and can be used as a means to approximate a cues motivational value. The nucleus accumbens core (NAc) has been highly implicated in mediating the sign-tracking response. Additionally, acetylcholine (ACh) transmission throughout the striatum broadly has been attributed to both incentive motivation and behavioral flexibility. Here, we show that sign-tracking responses are indeed flexible in the face of a contingency change in the form of an omission schedule, and that this flexibility is mediated by NAc ACh. Using behavioral and pharmacological methods, we show that blockade of NAc nicotinic receptors (nAChRs) augmented sign-tracking persistence, while blockade of muscarinic receptors (mAChRs) enhanced response flexibility following introduction of the omission schedule. Further, we detail how mAChR or nAChR antagonism impacted the microstructure of sign-tracking responses. These results indicate that NAc ACh receptors have opposing roles in the regulation of sign-tracking response flexibility without altering the motivational value of the cue.

neuroscience↗

bioRxiv2022

Treg cells drive MYCN-mediated immunosuppression and tumor aggressiveness in high-risk neuroblastoma

Solid tumors, especially those with aberrant MYCN activation, harbor an immunosuppressive microenvironment to fuel malignant growth and trigger treatment resistance1,2, yet the underlying mechanisms are elusive and effective strategies to tackle this challenge are lacking. Here we demonstrated the crucial role of T regulatory (Treg) cells in MYCN-mediated immune repression and tumor aggression using high-risk neuroblastoma (NB) as a model system. Human MYCN-activated NB attracts CD4+ Treg cells, which are also found enriched in MYCN-high primary patient samples. Zebrafish MYCN-overexpressing neural crests recruit Cd4+ cells before tumor formation and induce an immunosuppressive microenvironment, thereby promoting tumor onset and progression. Strikingly, disruption of Treg cells through depletion of forkhead box protein 3a restores anti-tumor immunity and impairs NB development. Together, our studies establish Treg cells as the key driver of MYCN-mediated immunosuppression and tumor aggressiveness, providing mechanistic insights and therapeutic implications.

cancer biology↗

bioRxiv2021

Multiple Causal Variants Underlie Genetic Associations in Humans

The majority of associations between genetic variation and human traits and diseases are non-coding and in strong linkage disequilibrium (LD) with surrounding genetic variation. In these cases, a single causal variant is often assumed to underlie the association, however no systematic assessment of the number of causal variants has been performed. In this study, we applied a massively parallel reporter assay (MPRA) in lymphoblastoid cells to functionally evaluate 49,256 allelic pairs, representing 30,893 genetic variants in high, local linkage disequilibrium for 744 independent cis-expression quantitative trait loci (eQTL) and assessed each for colocalization across 114 traits. We identified 8,502 allele-independent regulatory regions containing 1,264 allele-specific regulatory variants, and found that 17.7% of eQTL contained more than one significant allelic effect. We show that detected regulatory variants are highly and specifically enriched for activating chromatin structures and allelic transcription factor binding, for which ETS-domain family members are a large driver. Integration of MPRA profiles with eQTL/complex trait colocalizations identified causal variant sets for associations with blood cell measurements, Asthma, Multiple Sclerosis, Inflammatory Bowel Disease, and Crohns Disease. These results demonstrate that a sizable number of association signals are manifest through multiple, tightly-linked causal variants requiring high-throughput functional assays for fine-mapping.

genetics↗

bioRxiv2019

Genetic dysregulation of gene expression and splicing during a ten-year period of human aging

Molecular and cellular changes are intrinsic to aging and age-related diseases. Prior cross-sectional studies have investigated the combined effects of age and genetics on gene expression and alternative splicing; however, there has been no long-term, longitudinal characterization of these molecular changes, especially in older age. We performed RNA sequencing in whole-blood from the same individuals from the PIVUS study at ages 70 and 80 to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging. We observe that individuals are more similar to their own expression profiles later in life than profiles of other individuals their own age; 93% of samples cluster with their own measurement at another age, and there is a strong correlation of genetic effects on expression between the two ages (median{rho} G = 0.96). Despite this, we identify 1,291 and 294 genes differentially expressed and alternatively spliced with age, as well as 529 genes with outlying individual trajectories of aging. Further, 7.8% and 9.6% of tested genes show a reduction in genetic associations with expression and alternative splicing in older age, with impacted genes enriched in DNA repair pathways. Together these findings indicate that, although gene expression and alternative splicing and their genetic regulation are mostly stable late in life, a small subset of genes is dynamic and is characterized by changes in expression and splicing and a reduction in genetic regulation.

genomics↗

bioRxiv2018

Explorations with conditioned stimuli in autoshaping procedures

Sign-tracking is a form of autoshaping where by animals reliably develop conditioned responses toward stimuli that predict an outcome. While the assignment of some value to a predictive cue may be adaptive (i.e., to be alerted to food and water sources), the attribution of value to predictive cues can be maladaptive as seen in behaviors elicited during addiction. Here we test if responding to the predictive cue changes in the context of other cues that are only partially predictive (Experiment 1). Previous work on sequential cues leading to reward have shown a bias in responding toward the first cue in the sequence over learning (Smedley and Smith 2018a, 2018b). Here we test if this effect is unique to discrete cues or if a bias in responding can be seen in a single, long cue (Experiment 2). Finally, we investigate if sign-tracking responses can reliably develop towards a cue that arrives after the delivery of reward (backwards conditioning, Experiment 3). Together, we aim to address various gaps in knowledge about the nature of the sign-tracking response.

animal behavior and cognition↗

bioRxiv2018

Circuit directionality for motivation: lateral accumbens-pallidum, but not pallidum-accumbens, connections regulate motivational attraction to reward cues

Sign-tracking behavior, in which animals interact with a cue that predicts reward, provides an example of how incentive salience can be attributed to cues and elicit motivation. The nucleus accumbens (NAc) and ventral pallidum (VP) are two regions involved in cue-driven motivation. The VP, and subregions of the NAc including the medial shell and core, are critical for sign-tracking, and connections between the medial shell and VP are known to participate in sign-tracking and other motivated behaviors. The NAc lateral shell (NAcLSh) is a distinct and understudied subdivision of the NAc, and its contribution to the process by which reward cues acquire value remains unclear. The NAcLSh has been implicated in reward-directed behavior, and has reciprocal connections with the VP, suggesting that NAcLSh and VP interactions could be important mechanisms for incentive salience. Here, we use DREADDs (Designer Receptors Exclusively Activated by Designer Drugs) and an intersectional viral delivery strategy to produce a biased inhibition of NAcLSh neurons projecting to the VP, and vice versa. We find that disruption of connections from NAcLSh to VP reduces sign-tracking behavior while not affecting consumption of food rewards. In contrast, VP to NAcLSh disruption affected neither sign-tracking nor reward consumption, but did produce a greater shift in animals behavior more towards the reward source when it was available. These findings indicate that the NAcLSh[->]VP pathway plays an important role in guiding animals towards reward cues, while VP[->]NAcLSh back-projections may not and may instead bias motivated behavior towards rewards.

neuroscience↗

bioRxiv2018

The dorsolateral striatum regulates habits by way of performance vigor when actions are initiated

Despite clear evidence linking basal ganglia control to habits, it remains unclear through what mechanisms this control occurs. Here, we demonstrate that a key function of the dorsolateral striatum (DLS) is to regulate the vigor of a learned behavior at the moment of initiation in a habit-promoting manner. Shifts in vigor by phasic DLS perturbations coincide closely with how outcome-insensitive (i.e., habitual) the behaviors are in both response-based and cue-based task situations. Surprisingly, the control over habit strength by way of changes in vigor occurs without consistent changes in accuracy, suggesting that mechanisms controlling habit and vigor are dissociable from performance governed task rules. Finally, we show that increased DLS activity improves vigor preferentially when learned outcome values are stable, while reduced DLS activity dampens vigor preferentially when outcome values change. These data indicate that improving action vigor could be a principle route by which the basal ganglia facilitate habits.

animal behavior and cognition↗

bioRxiv2018

Identification of rare-disease genes in diverse undiagnosed cases using whole blood transcriptome sequencing and large control cohorts

RNA sequencing (RNA-seq) is a complementary approach for Mendelian disease diagnosis for patients in whom exome-sequencing is not informative. For both rare neuromuscular and mitochondrial disorders, its application has improved diagnostic rates. However, the generalizability of this approach to diverse Mendelian diseases has yet to be evaluated. We sequenced whole blood RNA from 56 cases with undiagnosed rare diseases spanning 11 diverse disease categories to evaluate the general application of RNA-seq to Mendelian disease diagnosis. We developed a robust approach to compare rare disease cases to existing large sets of RNA-seq controls (N=1,594 external and N=31 family-based controls) and demonstrated the substantial impacts of gene and variant filtering strategies on disease gene identification when combined with RNA-seq. Across our cohort, we observed that RNA-seq yields a 8.5% diagnostic rate. These diagnoses included diseases where blood would not intuitively reflect evidence of disease. We identified RARS2 as an under-expression outlier containing compound heterozygous pathogenic variants for an individual exhibiting profound global developmental delay, seizures, microcephaly, hypotonia, and progressive scoliosis. We also identified a new splicing junction in KCTD7 for an individual with global developmental delay, loss of milestones, tremors and seizures. Our study provides a broad evaluation of blood RNA-seq for the diagnosis of rare disease.

genomics↗

bioRxiv2017

A computational framework for detecting signatures of accelerated somatic evolution in cancer genomes

By accumulation of somatic mutations, cancer genomes evolve, diverging away from the genome of the host. It remains unclear to what extent somatic evolutionary divergence is comparable across different regions of the cancer genome versus concentrated in specific genomic elements. We present a novel computational framework, SASE-mapper, to identify genomic regions that show signatures of accelerated somatic evolution (SASE) in a subset of samples in a cohort, marked by accumulation of an excess of somatic mutations compared to that expected based on local, context-aware background mutation rates in the cancer genomes. Analyzing tumor whole genome sequencing data for 365 samples from 5 cohorts we detect recurrent SASE at a genome-wide scale. The SASEs were enriched for genomic elements associated with active chromatin, and regulatory regions of several known cancer genes had SASE in multiple cohorts. Regions with SASE carried specific mutagenic signatures and often co-localized within the 3D nuclear space suggesting their common basis. A subset of SASEs was frequently associated with regulatory changes in key cancer pathways and also poor clinical outcome. While the SASE-associated mutations were not necessarily recurrent at base-pair resolution, the SASEs recurrently targeted same functional regions, with similar consequences. It is likely that regulatory redundancy and plasticity promote prevalence of SASE-like patterns in the cancer genomes.

bioinformatics↗