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Mark D'Esposito, Department of Psychology, University of California, Berkeley

"Investigating structural-functional relationships between working memory capacity and the anatomy of the intraparietal sulcus"

Abstract:

Working memory (WM) is a form of short-term memory that allows us to plan for the immediate future. WM is a crucial aspect of cognitive abilities but is limited by a small capacity (~2.5-4 visual items on average). It is well-known that activity in the intraparietal sulcus (IPS) in the human brain during WM tasks tracks WM capacity across individuals, but the exact substrates of this WM-related activity are unknown. Understanding these neural mechanisms is important for understanding how neural systems maintain information. For over a year and a half, I have been part of a group that aims to identify a causal relationship between the IPS and WM by using functional magnetic resonance imaging (fMRI) and transcranial magnetic stimulation. For my thesis, I developed an extension of this study to investigate whether individual differences in cortical anatomy may be critical to the WM capacity limits. I am testing whether individual features of cortical anatomy in the IPS constrain functional activation. In order to uncover structural-functional relationships for WM capacity, I have manually labeled the lateral parietal cortex of 20 participants, labeling approximately 600 brain sulci, the indentations that make up over 60% of the human cerebral cortex. The IPS is the largest and deepest sulcus in the lateral parietal region, and the paroccipital IPS (IPS-PO) is a close second. The smallest and shallowest sulci, or tertiary sulci, include the aipsJ, the pips, the sB, and the POF. Unsurprisingly, the IPS and IPS-PO showed the highest fMRI activation. However, the sulcus of Brissaud (sB) also showed remarkably high peak activation, and due to its small surface area, the highest mean activation. This is a surprising result because of the variability in sB across individuals, and this may point to sB as a potential anatomical marker for working memory capacity.

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Mazen Kheirbek, University of California, San Francisco

"Encoding of Associative Learning Task Parameters in Ventral Hippocampus"

Abstract:

The hippocampus is a heavily researched brain structure that has been strongly implicated with learning, declarative memory, and spatial navigation. However, it is unclear how aspects of learning and stimulus associations are neurally encoded and represented. In this study, we sought to understand how the dorsal hippocampus (dHPC) dynamically encodes conditioned stimuli (CSs) that are predictive of differing outcomes across learning through an associative learning paradigm. In collaboration with other lab members, I used a Pavlovian conditioning task in head-fixed mice in which they are presented with a neutral odor (CSs), followed by a two second trace period, and then given one of two unconditioned stimuli (US) depending on the initial CS they received; a positive stimulus (sucrose; CS+ trials) or no stimulus (CS- trials). Simultaneously, we used 2-photon functional calcium imaging to track individual neurons across training sessions to explore how neural representations develop over learning. We found that neural populations are increasingly tuned to respond to the trace period during CS+ trials, but not CS- trials, by both increasing and decreasing firing rates from baseline. Our results suggest that the hippocampus may encode the expectancy of reward. Further research on how the hippocampus encodes learning of emotional associations could ultimately provide therapeutic targets for addiction as well as mood and anxiety disorders such as Post Traumatic Stress Disorder.

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Polina Lishko, Department of Molecular and Cell Biology, University of California, Berkeley

"Regulation of choroid plexus physiology by steroid hormones and its implication in Alzheimer’s disease."

Abstract:

The choroid plexus (CP) is a layer of tightly-connected cuboidal epithelial cells that are situated in the ventricles of the brain. The CP is responsible for the production of cerebrospinal fluid which plays an integral role in providing nutrients and hormones needed for neurogenesis while removing waste products from the brain. Interestingly, the malfunction of the CP has been indicated to negatively affect the progression of Alzheimer’s disease. Previous work in the Lishko Lab has identified Kir7.1, an inward-rectifying potassium channel on the luminal side of the CP epithelium, which has been shown to be the only ion channel in the CP that is potently upregulated by progesterone (P4). Our preliminary data indicate that P4 binds directly to Kir7.1, but the precise steroid-binding domain has not yet been identified. In order to obtain mechanistic insight into how P4 stimulates Kir7.1, we expressed Kir7.1 in HEK cells and incubated them with an ultraviolet (UV) activated P4-biotin probe which is a progesterone molecule that has a UV-photoactivated group that allows the covalent attachment of this probe to a binding partner. Next, the tagged Kir7.1 protein will be purified by electrophoresis and potential binding site(s) will be identified by using mass spectrometry to search for Kir7.1 peptides that are modified by the photoactivated P4 probe. The goals are to determine the Kir7.1 steroid-binding domain, which could be a target for nonsteroidal drug screening, and to determine the molecular mechanism of P4 activation of Kir7.1. Identification of P4 binding site(s) will be crucial not only for understanding the basic principles of this channel’s regulation but will also be helpful for the development of pharmacological tools to alter Kir7.1 activity.

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Helen Bateup, Department of Molecular and Cell Biology, University of California, Berkeley

"Conditional knockout of Tsc1 in spiny projection neurons of the striatum results in morphological changes and ASD-associated behavior in mice"

Abstract:

The striatum is a core structure in the brain responsible for motor control and habit learning, and functional changes in this region have been shown to coincide with the restricted, repetitive behaviors (RBBs) observed in Autism Spectrum Disorder (ASD) (Fuccillo 2016). Within the striatum, generally, activation of the direct pathway leads to increased voluntary movement, while indirect pathway activation leads to movement suppression, presenting possible pathway-specific roles in the generation of RRBs (Kravitz et al., 2010). To observe the effect of a loss of function mutation in the ASD-risk gene Tsc1 on striatal spiny projection neurons (SPNs), we used a cell type-specific strategy to knock out Tsc1 in either direct or indirect pathway SPNs in the striatum. Given Tsc1’s role as an inhibitor of mammalian target of rapamycin complex 1 (mTORC1), and mTORC1’s role in cytoskeletal properties, we hypothesize that Tsc1 deletion will lead to morphological alterations. We used super-resolution imaging and image-processing software to quantify somatic, dendritic and axonal morphology in SPNs lacking Tsc1. We also employed expansion microscopy for clearer visualization of axonal arborization and targeting. To determine if Tsc1 deletion in SPNs lead to the presentation of RRBs, we developed a water-mist induced grooming assay. We found no significant differences in SPN dendritic arborization in both direct and indirect Tsc1 KO cells, but we observed changes in SPN soma size. Preliminarily, we found no significant difference in induced grooming behavior in Tsc1 KO animals, but more data is needed to determine if morphological changes in striatal neurons caused by the loss of Tsc1 may coincide with ASD-associated motor behaviors.

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William Jagust, School of Public Health

"The Effect of Amyloid-β and Tau Pathology in Posterior-Medial and Anterior-Temporal Networks on the Hippocampus and Episodic Memory "

Abstract:

There are two distinct cortical pathways responsible for specific characteristics of episodic memory (scene memory and object memory). The PMAT framework defines the two cortical pathways as the posterior medial (PM) and anterior temporal (AT) systems, each of which are both supported by respective anatomy and functional connectivity. The PM system is predominantly responsible for scene memory and includes: medial prefrontal cortex, anterior thalamus, posterior cingulate cortex, retrosplenial cortex, angular gyrus and precuneus. In contrast, the AT system is responsible for processing object memory and includes: amygdala, perirhinal cortex and anterior ventral temporal cortex. In addition, the framework identifies multiple integration regions that assimilate information from both processing networks via the ventromedial prefrontal cortex and hippocampal formation. From past research in the lab, it has been determined the PM and AT systems are uniquely vulnerable to the pathologies of aging and AD, amyloid- and tau. The PM system is selectively vulnerable to amyloid-, whereas the AT system is selectively vulnerable to tau. However, the effect of pathology on these integration regions and cognition is not well known. My project found that Tau in the AT network seemed to be the main driver of structural degeneration in the hippocampus. Furthermore, Tau in both PM and AT regions, not amyloid-β, was negatively related to episodic memory and interestingly, a total measure of combined pathology in the PM and AT regions was no better at predicting episodic memory than AT Tau alone.

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Sheri L. Johnson, Department of Psychology, University of California, Berkeley

"The Search for Transdiagnostic Neuroanatomical Correlates of Emotion-Related Impulsivity"

Abstract:

Emotion-related impulsivity (ERI) is a personality trait defined by tendencies toward loss of self-control in the context of high emotion states. ERI robustly correlates with numerous psychopathologies, making it an important transdiagnostic risk factor. Whereas ERI has been correlated with dysfunction in brain regions such as orbitofrontal cortex (OFC), anterior insula, ventral striatum, and amygdala, no study to date has found a transdiagnostic neuroanatomical correlate of this clinically relevant trait. To fill this gap in knowledge, the present study investigated the relationship between a validated self-report measure of ERI drawn from the Three Factor Impulsivity Index and structural cortical metrics from 100 adult participants enrolled in a larger study. FreeSurfer, a brain imaging software package, was used to first process T1-weighted structural magnetic resonance imaging scans and then extract cortical thickness and local gyrification measurements from two a priori brain regions - OFC and anterior insula.

Three multiple linear regression models were fit, with cortical thickness of the OFC and anterior insula set as the predictor variable and the three factors of the Three Factor Impulsivity Index set as the dependent variables. R2 values for all three models were low and nonsignificant (R2 < 0.05, p > .05 for all models), indicating that the cortical thickness of OFC and anterior insula are not strong predictors of ERI. Additional preregistered analyses will include local Gyrification Index in OFC and anterior insula, as well as gray matter volume in ventral striatum and amygdala, as predictor variables in the models. Due to the large number of predictor variables, a Least Absolute Shrinkage and Selection Operator algorithm will be used to select the strongest neuroanatomical predictor variables. The full model will be cross-validated to test for robustness.

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Mazen Kheirbek, Department of Psychiatry, University of California, San Francisco

"Encoding of Innately Emotional Stimuli in the Ventral Hippocampus"

Abstract:

Although the role of ventral hippocampus (vHPC) in emotional behavior is widely recognized, the coding of valence-related information by vHPC neurons remains unclear. This is important because the ability to appropriately recognize stimuli associated with positive or negative meaning (valence) is foundational for survival and mental health. Preliminary research suggests the possibility of subpopulations of vHPC neurons that respond to aversive environments, while other populations respond to environments that elicit approach. However, the underlying organization of these different subpopulations remains unknown. We hypothesize that there are valence specific subpopulations within the vHPC and sought to evaluate our hypothesis through 2-photon imaging. To appraise neural response properties to emotionally salient events, we imaged calcium dynamics in the vHPC in awake, behaving animals during presentation of various appetitive or aversive stimuli. To assess neural activity in vHPC, the calcium indicator GCaMP6f was expressed in vHPC neurons and a gradient index (GRIN) lens was implanted directly above the vHPC to enable optical access to this deep brain structure. The mice were head-fixed under the 2-photon microscope and exposed to 80 trials of emotionally salient stimuli for two consecutive days. The mice were imaged for two consecutive days in order to evaluate the stability of the neural responses. Afterwards, the imaging data will be analyzed to identify neurons and extract their temporal activity. Our goal is to determine the stability of neural representations to these stimuli and see if there exist ensembles of cells that are valence-specific or valence heterogenous. If we are able to identify the encoding of valence within subpopulations of the vHPC or if valence is not encoded, this information will provide insight on how emotional information may be organized throughout the brain.

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Rebecca Abergel, Lawrence Berkeley National Lab

"Targeted Alpha Therapy: Characterization and Evaluation of Lysine-based Ac225 Radioimmunoconjugates Against Yersinia Pestis"

Abstract:

Targeted alpha therapy (TAT) is a rapidly advancing subdivision of radioimmunotherapy (RIT) which has shown increasing promise in recent years as a treatment for cellular pathology. As the majority of research into targeted alpha therapy has evaluated the therapeutic efficacy of antibody-drug conjugates (ADC) against a select pool of tumor cell lines, much is left to be discovered with regard to optimal construction and application of radioimmunoconjugates (RIC’s) as treatment for a greater diversity of pathogens. To address these avenues of inquiry, this work investigates refined synthesis and characterization methods for RIC's, as well as the novel application of Ac225 RIC’s against the etiologic agent of the bubonic plague, Yersinia pestis. To achieve the aforementioned objectives, a lysine-based conjugation of antibodies is selected as the ideal method of construction to be investigated, with further discussion on characterization of the resulting ADC’s drug-antibody ratio (DAR), degree of conjugate heterogeneity, and retention of native antibody structure. Following metalation with alpha-emitting radionuclide Ac-225, resulting ADC efficacy was assessed by following growth inhibition of Y. Pestis in an in vitro cell killing (IVK) assay and in vivo depletion of spleen colony-forming units (CFU) in Swiss Webster mice.

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Daniela Kaufer, Helen Wills Neuroscience Institute, University of California, Berkeley. Department of Integrative Biology, University of California, Berkeley.

"The Effects of Juvenile Acute Stress on Prefrontal Cortex Plasticity"

Abstract:

Parvalbumin (PV) is a protein present in GABAergic interneurons of the central nervous system. PV-positive fast-spiking interneuron maturation plays a critical role in triggering the end of the critical period in neural development 5. This maturation is induced partly by perineuronal net (specialized aggregation of extracellular matrices) growth surrounding these neurons, which mediates PV+ neuronal structural plasticity and plays a role in inducing the end of the critical period 1,5,9,13. Interestingly, PV and PNN imbalances are correlated with psychological disorders such as schizophrenia, PTSD, anxiety, and autism spectrum disorders 4,9,11,13. Orthodenticle Homeobox 2 (OTX-2) is a transcription factor that promotes PNN development around PV+ cells by specifically binding to them, and its relationship to the aforementioned psychological disorders is only recently beginning to be explored 2,3,8,10.

In previous studies within the rat animal model, chronic stress during the juvenile period increased PV and PNN levels and an earlier onset of the end of the critical period in regions of the brain such as the hippocampus, sensory cortex, and prefrontal cortex 1,6,7,8,11,12. The prefrontal cortex (PFC) in particular is critical for higher order processing and behavioral decision making in addition to control of stress response. While the impact of chronic stress on the PFC has been extensively studied, analyzing whether PV, PNN, and OTX-2 imbalances can occur as a result of juvenile acute traumatic stress has never been studied before 12,13. Furthermore, it is imperative to investigate whether any structural changes are correlated with behavioral abnormalities following stress. Thus, we are investigating the impact of juvenile acute stress on PNN, PV, and OTX-2 levels in the prefrontal cortex and whether these morphological changes correlate with weight changes, corticosterone levels, fear behavior, and anxiety-like behavior one week following the stressor.

In the current study, juvenile male and female Sprague Dawley rats were exposed to three hours of restraint stress with simultaneous exposure to fox odorant post-natal day 28 (p28), during which blood collections were taken at 0, 30, and 180 minutes. Behavioral testing was then conducted for both stress and control groups (n=32 total. n=16 stress. 8F, 8M. n=16 control. 8F, 8M), after which their brains were removed and sliced via cryostat. Next, PFC brain slices were stained for PV, PNN, and OTX-2 via immunohistochemistry and imaged in 2D using a fluorescent microscope. Counts for PV, PNN, PV-PNN co-labeling and OTX-2 fluorescence intensity were quantified in four specific prefrontal cortex regions— the anterior cingulate cortex (Cg1), prelimbic cortex (PL), infralimbic cortex (IL), and orbitofrontal cortex (OFC).

The results indicate that acute stress in juveniles increases corticosterone levels and leads to less weight gain one week later, suggesting that these physiological changes were correlated with the acute stressor. Interestingly, the behavioral data indicates that while the male juvenile group exhibited increased freezing time during fear behavior testing, the juvenile female stress group freezes less than all other groups during fear behavior testing assays–the statistically significant difference between the time frozen for the juvenile male stress and female stress groups implies that there are sex-specific differences in fear behavior after acute stress. Due to COVID-19 and laboratory closure, only 6 female stress groups animals were imaged and quantified for PV+, PNN+, PV-PNN+ counts and OTX-2+ intensity per PFC subregion. Out of the 6, only 4 were included in the immunohistochemistry data and correlations with behavior because 2 of them were imaged on a different microscope and were outliers with results over 2 SD above the mean.

Preliminary immunohistochemistry findings currently suggest that there is a large number of PV+, PNN+, and PV-PNN+ co-labeled cells in the orbitofrontal cortex (OFC) subregion of the prefrontal cortex, compared to other subregions in the female stress group. The OFC is involved in the cognitive process of decision-making, suggesting that juvenile acute stress may induce PV and PNN imbalances in the region of the brain particularly involved with behavioral decision-making. Lastly, a 2-way ANOVA was conducted with Bonferroni’s post-hoc analysis for multiple comparisons to generate Pearson r values analyzing correlations between PV+, PNN+, PV-PNN+, and OTX-2+ with time frozen during fear behavior sessions. No statistically significant data was yet found in Pearson r values with the four animals analyzed, but preliminary findings suggest a positive correlation between OTX-2 and time frozen during fear behavior sessions in the female stress group.

Finishing imaging and quantification of the data for all animals upon laboratory re-opening will add statistical power to see whether these correlations follow through— perhaps the morphological changes seen in the female stress group can be correlated with their decreased freezing time during fear behavior tests, suggesting that these cellular changes in the OFC may mediate resilience in this female stress group. While both the male and female groups exhibited physiological changes in response to acute stress, the data indicates that the way they process acute stress and behaviorally respond to it may differ in a sex-specific manner.

Overall, this study may further fortify a proposed mechanistic model for how structural changes in the prefrontal cortex can be correlated with psychological disorder-like behavioral changes and resilience. This in turn can potentially provide a foundational knowledge for bio-psychotherapies to leverage for the treatment of such disorders.

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Linda Wilbrecht, Department of Psychology, University of California, Berkeley

"In vivo measures of dopamine and medium spiny neuron activity in the dorsomedial striatum anticipate voluntary shifts in decision making"

Abstract:

Over twenty years ago, evidence was provided suggesting that dopamine neuron activity patterns seem to encode reward prediction errors (Schulz, Dayan, Montague 1997). Since then, a slew of research has implicated dopamine release in motivation, invigoration of actions, as a teaching signal, and more recently, as a general prediction error separable from reward. Our study seeks refine our understanding of dopamine at both the circuit and behavioral level by exploring its modulatory effects on D1R-expressing medium spiny neurons (MSNs) and D2R-MSNs within the dorsomedial striatum (DMS)—a sub-region of the striatum that has been implicated in action selection—while mice perform a probabilistic switching task. Optimal performance within this task requires state inference based on recent experience in order to intuit which of two actions is more likely to lead to reward. Preliminary results suggest that trial by trial changes in dLight signal and MSN CA2+ activity anticipate switching, a major behavioral shift in the task. In discussion, I address 1) possible causal relationships between these signals and 2) cognitive/computational models of uncertainty which may account for this anticipatory activity.

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Kristin Scott, Department of Molecular and Cell Biology, University of California, Berkeley

"Characterization of 2 types of gustatory interneurons in Drosophila melanogaster"

Abstract:

Detection of sugars and water in potential food sources is important for survival across all organisms. In the fruit fly Drosophila melanogaster, neural pathways between taste sensory neurons and feeding motor neurons have not yet been comprehensively elucidated. I and several other lab members have used an EM data set of the whole adult fly brain generated by the Bock group at Janelia Research Campus to reconstruct gustatory receptor neurons (GRNs) at synaptic detail. I then reconstructed two previously uncharacterized interneurons (“Toothless” and “Shisa”) that are immediately downstream of sugar and water sensory cells. Connectivity analysis revealed that these interneurons are part of different circuits. Toothless receives input from one major GRN cell type and provides synaptic input to a proboscis motor neuron while Shisa is part of a complex network of many GRNs and second-order neurons. Their non-overlapping GRN inputs indicate that these interneurons may detect different taste modalities. Thanks to genetic tools developed in the lab, I was able to use a split-Gal4 line specific for Shisa to investigate it further. I used an anion channel rhodopsin to silence Shisa during a temporal consumption assay and found that silencing Shisa does not significantly affect water and sugar consumption. Downstream partners I located using the EM and a trans-synaptic tracing tool suggest that Shisa may participate in other functions such as memory and locomotion. Overall, these studies have given more insight into the role of gustatory interneurons in taste processing and the regulation of feeding behavior.

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Dr. Jamie Cate, Innovative Genomics Institute Building, Berkeley

"eIF3 Mediated Translation Regulation of DUSP2 mRNA"

Abstract:

T cell activation is accompanied by a large increase in protein synthesis that is dependent on increased translation initiation. It has been shown that T cell activation leads to activation of eukaryotic translation initiation factor 3 (eIF3). However, the specific role of eIF3 in mediating the translation burst is not well understood. In this project, I aim to characterize the role of eIF3 in T cell activation by exploring its interactions with dual specificity phosphatase 2 (DUSP2) mRNA. DUSP2 negatively regulates T cell activation by inactivating key MAP kinases. We predict that eIF3 mediates the degradation of DUSP2 mRNA, thereby facilitating T cell activation.

Previously, PAR-CLIP (photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation) analysis from the Cate group found that eIF3 interacts across all regions of DUSP2 mRNA including the 5’-UTR, 3’-UTR and coding region. mRNAs with this unique cross linking pattern are known as “pan-mRNAs.” To further explore this interaction, we performed an immunoprecipitation of eIF3 bound to translating ribosomes in activated Jurkat cells after which we used RT-qPCR to look for pan-mRNAs. This confirmed the presence of eIF3 binding sites on the coding regions of pan-mRNA transcripts. To analyze the interaction of eIF3 with DUSP2 mRNA, I created nanoluciferase reporters containing either the endogenous 3’-UTR regions or those that lacked the eIF3 binding sites. I found that the interaction of the 3’-UTR with eIF3 is important for temporal regulation of DUSP2.

Further bioinformatic analysis from the Cate group found that the interaction of eIF3 with certain mRNAs occurs at conserved sequence motifs. Interestingly, the same motifs are also bound by the human YTH domain protein 2 (YTHDF2), which regulates mRNA degradation. We explored this link by performing an immunoprecipitation of eIF3 followed by Western blot and mass spectrometry analysis to show that eIF3 interacts with YTHDF2.

Through this project, I attempt to understand how eIF3 regulates the translation of DUSP2 during T cell activation. Elucidating the mechanism of translation during T cell activation is useful for improving cancer therapies that rely on T cell activation.

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Stephen P. Hinshaw, Department of Psychology, University of California, Berkeley

"Adverse childhood events and onset of sexual activity in young women with and without histories of ADHD"

Abstract:

Research suggests that adverse childhood events (ACEs) are associated with a variety of negative health outcomes. Little research has examined how ACEs may relate to sexual behavior among women with childhood-diagnosed attention-deficit/hyperactivity disorder (ADHD). We investigated associations between (a) any ACE as well as specific categories of ACEs and (b) age at first sexual intercourse and early sexual initiation (before age 15) in a sample of young women (ages 17-24) with and without childhood diagnoses of ADHD.

The Berkeley Girls with ADHD Longitudinal Study (BGALS) is a prospective, longitudinal investigation of the developmental trajectories and outcomes of a sample of young women with (N=140) and without (N=88) a childhood diagnosis of ADHD. In this study, self-report data on age at first intercourse and adverse childhood events were collected at Waves 3 and 4 (average age 20 and 26, respectively) via the Social Relationships Interview and at Wave 4 via the Adverse Childhood Events Scale.

Among women with ADHD, those who experienced any ACE (96/123) reported a significantly younger age at first sexual intercourse and higher percentage of early sexual initiation relative to women who did not experience any ACE (15.9 vs. 17.2, p=0.011; 21.9% vs. 3.7%, p=0.030). Among women without ADHD, those who experienced any ACE (57/85) did not report a significantly younger age at first sexual intercourse or higher percentage of early sexual initiation relative to women who did not experience any ACE.

These findings suggest that ACEs may be associated with risky sexual behavior among women with ADHD. Specifically, a combination of childhood ADHD and the experience of any ACE predicted a younger age at first sexual intercourse and early sexual initiation among our sample of women. These findings have important implications for the sexual behavior and reproductive health of young women with histories of childhood ADHD.

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Helen Bateup, Department of Molecular & Cell Biology, University of California, Berkeley

"The Role of SynGAP in Striatal Dependent Behaviors"

Abstract:

Mutations in the SYNGAP1 gene, which encodes for the protein SynGAP, result in a complex neurodevelopmental disorder associated with intellectual disability, autism spectrum disorder, and motor impairments. In the cortex and hippocampus, loss of SynGAP leads to increased AMPAR insertion, enlarged dendritic spines, accelerated synaptic maturation, and impaired synaptic plasticity. While this prior work strongly implicates SynGAP as a regulator of glutamatergic synaptic transmission, very little is known about its functions outside of these brain regions. Notably, SynGAP is strongly expressed in the striatum, the primary input structure of the basal ganglia, which is responsible for a variety of motor-related functions including action selection and instrumental learning. Two classes of striatal projection neurons (SPNs) exert selective and often opposing influence over behavior: the direct (or striatonigral) pathway and the parallel indirect (or striatopallidal) pathway. How SynGAP deletion results in altered striatal circuit function and the behavioral manifestations associated with SYNGAP1 disorder is unknown. Here I investigate whether selective disruption of SynGAP expression in specific striatal neuron populations is sufficient to impact behaviors relevant for SYNGAP1 disorder. To do so, I food restricted and trained mice to self-administer food pellets under a random ratio schedule of reinforcement, which biases towards goal-directed responding. Following this schedule, I tested these mice on an outcome devaluation test to probe whether their actions were goal-directed or habitual. The results from this behavioral assay indicate that global Syngap1 heterozygous mice, which model haploinsufficiency in SYNGAP1 patients, have reduced goal-directed behavior. Furthermore, mice in which Syngap1 is conditionally deleted in indirect pathway SPNs replicate these results. This suggests that loss of SynGAP in indirect pathway SPNs is sufficient to reduce goal-directed behavior in favor of habitual actions. Such an outcome may be a contributor to the restricted, repetitive behaviors observed in individuals with SYNGAP1 disorder. Future experiments will test if these behavioral alterations can be rescued using cell type-specific gene restoration in constitutive heterozygous Syngap1 mice.

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Mark D'Esposito, Department of Psychology, University of California, Berkeley

"Frontoparietal network connectivity and working memory performance following targeted network disruption: compensation or global impairment?"

Abstract:

Substantial neuroimaging research has found evidence of coactivation of the prefrontal cortex (PFC) and superior intraparietal sulcus (IPS) during working memory (WM) tasks, leading to the recognition of a frontoparietal network involved in WM. However, the differential roles of these regions and the effect of their connection on WM performance is still not completely understood. This study combines fMRI and transcranial magnetic stimulation (TMS) to elucidate the role of PFC, IPS and the frontoparietal network in WM. Participants performed a continuous report WM task in which they viewed varying numbers of colored squares and, after a WM delay, reported the color of a randomly chosen square by scrolling through a continuous color wheel. This task was completed in the MRI scanner and later in TMS sessions which targeted IPS, PFC, and a primary somatosensory control site on separate days. Functional MRI revealed activity that scaled with load in both PFC and IPS during the WM delay. In order to estimate the importance of frontoparietal connectivity in WM, we performed a connectivity analysis using resting sate fMRI data from 85 subjects and compared each subject’s level of frontoparietal connectivity to their WM precision. The results revealed no significant correlation between PFC-IPS connectivity and WM precision. Next, we used TMS to evaluate the necessity of the frontoparietal network in precise WM by comparing each participant’s TMS impairment in PFC and IPS to their level of connectivity. We found no significant effect of PFC-IPS connectivity on TMS impairment. These results suggest that the frontoparietal network may not be the seat of WM storage, and instead may be involved in top-down control of WM representations in other brain regions.

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Dr. Deborah Dean, Children's Hospital Oakland Research Institute (CHORI)

"Identification of Putative Chi sites in the Chlamydia trachomatis Genome"

Abstract:

Chlamydia trachomatis is an obligate intracellular pathogen of humans. It causes urogenital, ocular and rectal diseases that are typically treated with azithromycin for uncomplicated infections or doxycycline, a tetracycline antibiotic. C. trachomatis has close genomic homology with the swine pathogen Chlamydia suis. Many C. suis strains contain a tetracycline resistance [tet(C)] cassette acquired through homologous recombination with other gut bacteria—a consequence of lacing pig feed with antibiotics. Since swine are a major global livestock with significant contact with humans, they pose a potential significant health risk if the cassette is transferred to C. trachomatis. In an effort to understand the molecular basis of where and how tetC may be transferred to C. trachomatis, my project aims to identify the C. trachomatis Chi (crossover hotspot instigator) site(s),at which homologous recombination might occur with a high probability. RMES and Python Parser software programs were used to identify putative Chi sites in the C. trachomatis genome using criteria such as frequency, overrepresentation in the genome, skew, and skew significance. I aim to confirm these Chi sites through transformation of C. trachomatis with recombinant plasmids containing the putative Chi motif sequences. In order to facilitate transformation into C. trachomatis, I cured C. trachomatis strain L2 of its natural plasmid using repeated treatments with Novobiocin. Using a plaque assay to segregate clonal populations of L2, I identified a clone that was 92.7% cured of its natural plasmid. We are currently developing plasmid constructs with the putative Chi sites through restriction enzyme digests, ligations, transformation into E. coli and maxiprep DNA purification. After creating these plasmid constructs, I will transform L2 with each independently and propagate the bacteria, thus allowing the plasmid to replicate. A qPCR of the strain containing the “true” Chi motif will have the highest levels of HMW (high molecular weight) accumulated DNA–since Chi sites act to prevent DNA degradation–compared to insertion of a scrambled, non-functional Chi motif.

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David Ackerly, Department of Integrative Biology, University of California, Berkeley

"Metagenomics of Oaks: Patterns of fungal diversity in and on the leaves of California oaks"

Abstract:

Although not much can be seen with the naked eye, the leaves of oak trees harbor immense bacterial, viral, and fungal diversity. Here we focus on the fungal community, which may include pathogenic fungi that cause leaf rot, commensal epiphytic fungi, as well as a largely unexplored type of fungi known as endophytes which are thought to be mutualistic. This project seeks to understand the impact of factors such as collection time of year and site of collection on the diversity of fungal genera present in and on the oak leaf. Oak leaf samples were collected from 47 sites across California over the span of four years and were classified as both samples and fungal communities. DNA was extracted from the leaf samples and sequenced using double digest RAD Seq. All the returned sequence reads that aligned to the oak reference genome were removed and consensus sequences were generated for the remaining reads. Consensus sequences were BLASTed to GenBank fungal sequence databases to match each locus to a fungal OTU (genus). The BLAST results returned a list of 57 fungal genera present in 130 different communities. Genera found ranged from parasitic fungi of insects such as Chordyceps (possibly present as dormant spores) and potentially mutualistic fungi such as Epicoccum, and a dominant signal of epiphytic mold. Each community contained anywhere from 3 to 20 different fungal genera. In order to explain differences between fungal communities we performed an NMDS community ordination. Collection site explains 37% of the variation and includes many different factors such as, wind patterns, precipitation patterns, surrounding vegetation, and season. Further analyses show that date of collection explains 20% and oak species explains 16% of the variation.

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Dan Feldman, Department of Molecular & Cell Biology, University of California, Berkeley

"Localizing in-vivo silicon probe recording sites using immunohistochemistry approaches with analysis on the spatial and temporal effect of astrocyte activation"

Abstract:

Multi-site silicon recording electrodes are widely used in neuroscience research to record neuronal signals extracellularly in live animals. Recording locations are coarsely selected with reference to stereotaxic coordinates or functional imaging, but for more precise localization, recording penetrations must be reconstructed post-hoc, e.g. by applying fluorescent dye to the electrode and visualizing it postmortem through histological slices. In this thesis, I investigated whether penetrations can be accurately reconstructed by immunostaining for glial fibrillary acidic protein (GFAP), a marker for activated astrocytes. Electrode penetration and similar acute brain trauma activate astrocytes. GFAP is upregulated when astrocytes are active. I explored the spatial and temporal pattern of GFAP response to electrode penetration in mouse’s somatosensory cortex and established a correlation between time and radius of GFAP signal surrounding the silicon probe recording site. I also explored the optimal timing to use GFAP to discriminate recordings in closeby columns. Results demonstrate that GFAP staining enables accurate localization of recording penetrations without applying fluorescent dye on the electrode. This method relies on intrinsic protein expression in the brain and prevented the potential problems of using an external dye.

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Gary D. Richards, Department of Biomedical Sciences, University of Pacific

"Impacts of endocranial and ectocranial shape on middle meningeal arteriovenous pattern in 6-8.0 year old humans"

Abstract:

The meningeal arteriovenous system supplies or drains blood from the cranial vault bones and dura. In juveniles aged 6-8.0, complexity of middle meningeal patterns varies bilaterally, by developmental age, and by the configuration of the main rami. We employ geometric morphometric analysis to discern potential relationships between the neurovascular bundle and endocranial shape differences.

Forty crania, developmentally aged from 5.8-7.9 years, were CT-scanned. Tooth calcification patterns were employed to determine developmental age. Middle meningeal neurovascular patterns were mapped on isosurfaces and evaluated for complexity, bilateralism, age differences and Adachi types. We collected 33 3D endocranial landmarks from CT-scans. Principal Component Analysis (PCA) was performed on Procrustes aligned shape variables in Morphologica to assess endocranial shape differences.

We found that Shape variation along PC1showed a shift from brachycephaly to dolichocephaly. Individuals with Type II middle meningeal patterns clustered within –PC2 but were randomly distributed on PC2. Bilateral complexity analysis shows that right-dominant complexity clustered around the mean of PC1-PC2, but not in the left. The Adachi types varied in their distribution bilaterally.

The association between the neurovascular pattern and endocranial shape in relation to complexity is based on endocranial length-breadth differences. Dolichocephalic endocrania exhibit less complex branching. Right-dominated patterns correlate with shape while left patterns are randomly distributed. Although the correlation between the meningeal neurovascular bundle and endocranial shape appears unclear, specific pattern are emerging. Further work is required to elucidate causative factors for pattern differences.

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Bethanie R. Edwards, Department of Earth and Planetary Sciences, University of California, Berkeley

"Ethanol Alters Growth Rate and Lipidome of Chlorella vulgaris"

Abstract:

Chlorella vulgaris (C. vulgaris) was cultured in media containing a range of low ethanol, methanol, and isopropanol concentrations. Growth rate was not appreciably altered by low concentrations of methanol or isopropanol, although higher concentrations were toxic. However, concentrations of 0.005% and 0.01% volume/volume (v/v) ethanol robustly increased the growth rate of C. vulgaris whereas the 0.05% v/v treatment exhibited slower growth. Concentrations above 0.05% v/v led to strong inhibition of growth. Ultra High Performance Liquid Chromatography-High Resolution Accurate Mass Mass Spectrometry (UPLC-HRAM MS) was used to characterize changes in the relative concentration of lipids in the algae when grown mixotrophically with ethanol. Changes in the lipidome are apparent at time point 15 day (T15day) as well as T21day. Relative concentrations of a variety of lipid species, including phospholipids, free fatty acids, and glycolipids are altered in a dose dependent fashion in the faster growing samples. The lipidome of the 0.05% v/v treatment was significantly different from the other treatments, indicating a stress response to ethanol. Importantly, the 0.05% v/v treatment showed robust increases in production of long chain free fatty acids and oxylipins of pharmaceutical interest. These results indicate that the changes in growth in the presence of low ethanol concentrations are not simply due to increased availability of biologically utilizable carbon. Possible causes of this relatively large increase in growth rate, such as changes in the metabolism of C. vulgaris induced by the presence of ethanol, require further investigation.

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Robert Knight, Helen Helen Wills Neuroscience Institute University of California, Berkeley

"Scalp EEG Reveals Signed and Unsigned Prediction Error Components Underlying Performance Monitoring ERPs"

Abstract:

A key component of goal-directed behavior is the ability to respond and adapt to feedback. In EEG data, the feedback-related negativity (FRN), a fronto-central event related potential (ERP) that occurs after the presentation of feedback, is often used as a marker of this process. Recent studies have suggested that the FRN is modulated by expectation, rather than valence, of feedback, as was classically thought. However, few studies account for the potentially confounding effects of the P300, a large ERP that overlaps with the FRN temporally and is similarly modulated by the valence and likelihood of feedback. To decouple the contributions of valence and expectation to the FRN’s amplitude, we collected EEG data during an interval timing task that utilized differences in task difficulty to dissociate the role of expectation and valence. Using a single trial regression analysis in the time, frequency and spatial dimensions, we have found that the FRN is indicative of a signed prediction error component, while an unsigned rediction error component underlies the P300.

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Tony M. Keaveny

Department of Biochemistry, University of California, Berkeley

"The Effect of Ribose-Induced Crosslinks on Bone Material and Mechanical Properties"

More than 422 million individuals are living with diabetes worldwide, making diabetes among the most common chronic diseases. In addition to the many adverse health effects caused by blood sugar fluctuations in diabetics, there is a significant reported increase in the number of cases of bone fractures. Research suggests that exposure to reducing sugars, such as ribose, leads to the development of non-enzymatic collagen crosslinks through a process known as non-enzymatic glycation (NEG) of bone collagen. These non-enzymatic crosslinks, in high numbers, are suspected to decrease bone’s ability to resist fracture. This study evaluates the effect of ribose induced NEG on the microarchitecture, material, and mechanics of murine femurs by utilizing an in vitro crosslinking assay, a three-point bending mechanical test, and a total fluorescence assay for crosslinking quantification.

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Andreas Stahl, Department of Nutritional Sciences and Toxicology. University of California, Berkeley.

"Mechanosensitive transcriptional co-activators Yap and Taz produce differential effects on the thermogenic capacity of brown and beige adipose tissues"

Abstract:

In response to cold exposure, brown and beige adipose tissues (BAT) generate heat through the activity of uncoupling protein 1 (UCP1). UCP1 catalyzes mitochondrial proton leak, dissociating the electron transport chain from ATP synthesis to dissipate energy as heat in a process known as non-shivering thermogenesis. Previous research in the lab has indicated a mechanosensitive role of the transcriptional co-activators, yes-associated protein 1 (Yap) and WW domain-containing transcription regulator protein 1 (Taz), in mediating BAT thermogenic activity. Specifically, Yap and Taz heterozygote knockout animals showed reduced BAT thermogenic activity, resulting in increased body weight and reduced glucose tolerance. To clarify the individual roles of Yap and Taz in both brown and beige adipose tissues, we used a Cre/Lox system driven by the UCP1 promoter to generate single knockout mice. Here we show that Yap and Taz produce differential effects on the thermogenic capacity of BAT. Yap knockout mice have increased fat mass, reduced glucose tolerance, and impaired metabolic respiration. Conversely, Taz knockout mice resulted in no changes in body mass, glucose tolerance, or metabolic respiration compared to controls. To further characterize these animals, I measured gene expression and protein abundance to probe the effects of knockouts on specific adipogenic and thermogenic markers. To supplement my findings, I used an in vitro subcutaneous white adipose tissue (sWAT) model and found that verteporfin-induced Yap inhibition disrupts UCP1 expression during differentiation without affecting general adipogenesis marker FABP4. These results demonstrate an early developmental role of Yap in the differentiation of beige adipose tissue and will serve as a starting point for further investigation into the functions of Yap/Taz in disorders such as metabolic syndrome.

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Doris Bachtrog, Department of Integrative Biology, University of California, Berkeley

"The Effect of Large Y-chromosome on Male Aging"

Abstract:

Aging is an intriguing phenomenon that has been widely studied for many years. Recent studies have shown that transposable elements (TEs), mobile DNA segments, increases during aging that this may be sex-specific. However, we still do not know how the amount of TEs in the genome can affect the aging process within a sex.

In my research, I investigated how the abundance of TEs on the Y chromosome affects aging of Drosophila pseudoobscura. TEs are a main constituent of the repressed DNA region and forms a large proportion of the Y chromosome. Therefore, I conducted lifespan assays on two Drosophila strains where the only difference is that one male has an additional 24Mb of Y chromosome DNA. Contrary to expected, there were no significant differences in aging between the two strains.

I also collected RNA-seq data from the aged males to see how genes and TEs were differentially expressed. RNA-seq analysis showed that at the level of gene expression, we can observe an overexpression of TEs in the aged male bearing a large Y. I observed a 36% increase of TE expression in males with a large Y compared to a 11% reduction in males with a small Y. While 29 TEs were significantly upregulated in males carrying a large Y, only 10 TEs were in males carrying a small Y. The fact the small Y males did not show such upregulation suggests that there could be a higher loss of TE suppression in the large Y.

This result is important as it suggests the size of Y could affect global regulation and expression of TEs. While there are differences in TE expression, interestingly it does not correspond to differences in aging. This could suggest a more complex relationship between gene regulation and expression. Future experiments can focus on conducting more trials to confirm the aging results, and also conducting qPCR to confirm the TE expression.

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Andrew Dillin, Department of Molecular & Cell Biology, University of California, Berkeley

"Novel regulators of mitochondrial health uncovered by synthetic lethality screen in C. elegans"

Abstract:

Several neurodegenerative diseases such as Parkinson’s and Alzheimer’s are reported to be a result of a decline in protein homeostasis as organisms age. Mitochondria, a vital organelle in the cell, is especially susceptible and thought to be a sensor of proteotoxic stress. Understanding how mitochondria communicate stress and recover homeostasis is therefore fundamental in developing novel treatments for age-onset human diseases. One way that mitochondria communicate stress is through the Mitochondrial Unfolded Protein Response (mtUPR), a protective transcriptional program activated by the stress signal ATFS-1. However, ATFS-1-deficient animals show development with full functions despite with a slight delay, suggesting that there are other cellular pathways conferring organismal health in the absence of ATFS-1, and very little is known about these alternative cellular pathways. To identify novel regulators that interact with ATFS-1, together with my lab members, we performed a genome-wide screen on ATFS-1 loss-of-function mutant C. elegans and identified 42 primary genes that when RNAi KD, made ATFS-1 mutant sick, but did not affect the health of wildtype worms. I rescreened the primary genes and found 5 genes that showed the strongest lethal phenotypes. Out of the 5 genes, we found that gpb-1 KD activates mtUPR specifically and modifies mitochondrial response to paraquat, a toxin that induces mitochondrial stress, suggesting a potential role of gpb-1 in regulating mitochondrial health. gpb-1 encodes for the beta subunit of the G protein in C. elegans, and we observed similar mtUPR activation in gpc-2 KD, a gene encoding for the gamma subunit of the G protein heterotrimer. Moreover, GPB-1 has a known mammalian ortholog, GNB2/4, mutations of which are implicated in Charcot-Marie-Tooth disease. Therefore, characterizing how GPB-1 interacts with ATFS-1 to regulate mitochondrial health will illuminate our understanding on neurodegenerative diseases characterized by mitochondrial dysfunction and provide insights on the development of novel treatments.