Thomas Newpher | Duke University (original) (raw)

Papers by Thomas Newpher

High-enrollment university courses can be associated with decreased student learning and course s... more High-enrollment university courses can be associated with decreased student learning and course satisfaction. In these large classes, students report feelings of isolation, reduced faculty interaction, and less motivation. Here we address whether team-based learning (TBL), a highly interactive and collaborative form of active learning, can improve the student experience in larger undergraduate neuroscience courses. Specifically, we analyzed student performance on summative assessments, as well as survey responses on measures of the classroom environment from a single TBL course, taught over a range of enrollment sizes (19-103 students). While the higher enrollment course terms had decreased ratings of course quality compared to the lower enrollment terms, we also found that student performance on exams was similar across all course term sizes. Furthermore, we observed no differences across class sizes for most measures of classroom dynamics and course characteristics. Taken together...

Seminars in Cell & Developmental Biology, 2017

Dendritic spines are actin-rich, postsynaptic protrusions that contact presynaptic terminals to f... more Dendritic spines are actin-rich, postsynaptic protrusions that contact presynaptic terminals to form excitatory chemical synapses. These synaptic contacts are widely believed to be the sites of memory formation and information storage, and changes in spine shape are thought to underlie several forms of learning-related plasticity. Both membrane trafficking pathways and the actin cytoskeleton drive activitydependent structural and functional changes in dendritic spines. A key molecular player in regulating these processes is the activity-regulated cytoskeleton-associated protein (Arc), a protein that has diverse roles in expression of synaptic plasticity. In this review, we highlight important findings that have shaped our understanding of Arc's functions in structural and functional plasticity, as well as Arc's contributions to memory consolidation and disease.

Trends in cell biology, 2009

Changes in the molecular composition and signaling properties of excitatory glutamatergic synapse... more Changes in the molecular composition and signaling properties of excitatory glutamatergic synapses onto dendritic spines mediate learning-related plasticity in the mammalian brain. This molecular adaptation serves as the most celebrated cell biological model for learning and memory. Within their micron-sized dimensions, dendritic spines restrict the diffusion of signaling molecules and spatially confine the activation of signal transduction pathways. Much of this local regulation occurs by spatial compartmentalization of glutamate receptors. Here, we review recently identified cell biological mechanisms regulating glutamate receptor mobility within individual dendritic spines. We discuss the emerging functions of glutamate receptors residing within sub-spine microdomains and propose a model for distinct signaling platforms with specialized functions in synaptic plasticity.

Neuron, Jan 22, 2008

Among diverse factors regulating excitatory synaptic transmission, the abundance of postsynaptic ... more Among diverse factors regulating excitatory synaptic transmission, the abundance of postsynaptic glutamate receptors figures prominently in molecular memory and learning-related synaptic plasticity. To allow for both long-term maintenance of synaptic transmission and acute changes in synaptic strength, the relative rates of glutamate receptor insertion and removal must be tightly regulated. Interactions with scaffolding proteins control the targeting and signaling properties of glutamate receptors within the postsynaptic membrane. In addition, extrasynaptic receptor populations control the equilibrium of receptor exchange at synapses and activate distinct signaling pathways involved in plasticity. Here, we review recent findings that have shaped our current understanding of receptor mobility between synaptic and extrasynaptic compartments at glutamatergic synapses, focusing on AMPA and NMDA receptors. We also examine the cooperative relationship between intracellular trafficking and...

Molecular Biology of the Cell, 2002

SCD5 was identified as a multicopy suppressor of clathrin HC-deficient yeast. SCD5 is essential, ... more SCD5 was identified as a multicopy suppressor of clathrin HC-deficient yeast. SCD5 is essential, but anscd5-Δ338 mutant, expressing Scd5p with a C-terminal truncation of 338 amino acids, is temperature sensitive for growth. Further studies here demonstrate that scd5-Δ338affects receptor-mediated and fluid-phase endocytosis and normal actin organization. The scd5-Δ338 mutant contains larger and depolarized cortical actin patches and a prevalence of G-actin bars.scd5-Δ338 also displays synthetic negative genetic interactions with mutations in several other proteins important for cortical actin organization and endocytosis. Moreover, Scd5p colocalizes with cortical actin. Analysis has revealed that clathrin-deficient yeast also have a major defect in cortical actin organization and accumulate G-actin. Overexpression ofSCD5 partially suppresses the actin defect of clathrin mutants, whereas combining scd5-Δ338 with a clathrin mutation exacerbates the actin and endocytic phenotypes. Both ...

Applied Optics, 2010

We apply a wide-field quantitative phase microscopy technique based on parallel two-step phase-sh... more We apply a wide-field quantitative phase microscopy technique based on parallel two-step phase-shifting on-axis interferometry to visualize live biological cells and microorganism dynamics. The parallel on-axis holographic approach is more efficient with camera spatial bandwidth consumption compared to previous off-axis approaches and thus can capture finer sample spatial details, given a limited spatial bandwidth of a specific digital camera. Additionally, due to the parallel acquisition mechanism, the approach is suitable for visualizing rapid dynamic processes, permitting an interferometric acquisition rate equal to the camera frame rate. The method is demonstrated experimentally through phase microscopy of neurons and unicellular microorganisms.

Journal of Undergraduate Neuroscience Education, 2023

The start of the COVID-19 pandemic forced an unprecedented shift from face-to-face (F2F) instruct... more The start of the COVID-19 pandemic forced an unprecedented shift from face-to-face (F2F) instruction to emergency remote teaching (ERT) for over one billion learners worldwide. Studies from K-12 and higher education have begun to address the impact of ERT on student learning and well-being. The lessons learned from ERT will likely shape the response to future public health emergencies and inform the design and implementation of remote courses. As such, it will be important to identify teaching practices in ERT that promoted student engagement and learning. Here, we address whether undergraduate collaborative learning courses were able to support student content knowledge outcomes at similar levels in ERT as compared to F2F classroom environments. Specifically, we tracked student performance in three different team-based undergraduate neuroscience courses. These courses were all taught by the same instructor during the academic years 2020-2021 and 2021-2022. Importantly, we found that student scores on individual and team assessments as well as measures of course satisfaction were similar between ERT and F2F. Taken together, our data suggest that the virtual collaborative learning environment in these courses was not associated with a decrease in student or team performance when compared to a traditional F2F classroom.

Journal of Visualized Experiments

ARTICLES DISCUSSED: Pekarek, B. T., Hunt, P. J., Belfort, B. D. W., Liu, G., Arenkiel, B. R. Imag... more ARTICLES DISCUSSED: Pekarek, B. T., Hunt, P. J., Belfort, B. D. W., Liu, G., Arenkiel, B. R. Imaging and quantification of intact neuronal dendrites via CLARITY tissue clearing. Journal of Visualized Experiments: JoVE. (170), e62532 (2021). Frankfurt, M., Bowman, R. Rapid Golgi stain for dendritic spine visualization in hippocampus and prefrontal cortex. Journal of Visualized Experiments: JoVE. (178), e63404 (2021). Śliwińska, M. A., Cały, A., Szymański, J., Radwańska, K. Serial Block-Face Scanning Electron Microscopy (SBEM) for the study of dendritic spines. Journal of Visualized Experiments: JoVE. (176), e62712 (2021). Chan, U., Gautam, D., West, A. E. Utilizing in vivo postnatal electroporation to study cerebellar granule neuron morphology and synapse development. Journal of Visualized Experiments: JoVE. (172), e62568 (2021). Cuentas-Condori, A., Miller III, D. M. Imaging dendritic spines in Caenorhabditis elegans. Journal of Visualized Experiments: JoVE. (175), e62676 (2021).

Traffic, 2006

Clathrin is a major vesicle coat protein involved in receptor-mediated endocytosis. In yeast and ... more Clathrin is a major vesicle coat protein involved in receptor-mediated endocytosis. In yeast and higher eukaryotes, clathrin is recruited to the plasma membrane during the early stage of endocytosis along with clathrin-associated adaptors. As coated pits undergo maturation, a burst of actin polymerization accompanies and helps drive vesicle internalization. Here, we investigate the dynamics of clathrin relative to the early endocytic patch protein Sla2p. We find that clathrin is recruited to the cortex prior to Sla2p. In the absence of clathrin, normal numbers of Sla2p patches form, but many do not internalize or are dramatically delayed in completion of endocytosis. Patches that do internalize receive Sla1p late, which is followed by Abp1, which appears near the end of Sla2p lifetime. In addition, clathrin mutants develop actin comet tails, suggesting an important function in actin patch organization/dynamics. Similar to its mammalian counterparts, the light chain (LC) subunit of yeast clathrin interacts directly with the coiled-coil domain of Sla2p. A mutant of Sla2p that no longer interacts with LC (sla2Δ376-573) results in delayed progression of endocytic patches and aberrant actin dynamics. These data demonstrate an important role for clathrin in organization and progression of early endocytic patches to the late stages of endocytosis.

The EMBO Journal, 2010

Myosins-I are conserved proteins that bear an N-terminal motor head followed by a Tail Homology 1... more Myosins-I are conserved proteins that bear an N-terminal motor head followed by a Tail Homology 1 (TH1) lipidbinding domain. Some myosins-I have an additional C-terminal extension (C ext) that promotes Arp2/3 complexdependent actin polymerization. The head and the tail are separated by a neck that binds calmodulin or calmodulinrelated light chains. Myosins-I are known to participate in actin-dependent membrane remodelling. However, the molecular mechanisms controlling their recruitment and their biochemical activities in vivo are far from being understood. In this study, we provided evidence suggesting the existence of an inhibitory interaction between the TH1 domain of the yeast myosin-I Myo5 and its C ext. The TH1 domain prevented binding of the Myo5 C ext to the yeast WIP homologue Vrp1, Myo5 C ext-induced actin polymerization and recruitment of the Myo5 C ext to endocytic sites. Our data also indicated that calmodulin dissociation from Myo5 weakened the interaction between the neck and TH1 domains and the C ext. Concomitantly, calmodulin dissociation triggered Myo5 binding to Vrp1, extended the myosin-I lifespan at endocytic sites and activated Myo5-induced actin polymerization.

Molecular Biology of the Cell, 2006

Clathrin-mediated endocytosis is a major pathway for uptake of lipid and protein cargo at the pla... more Clathrin-mediated endocytosis is a major pathway for uptake of lipid and protein cargo at the plasma membrane. The lattices of clathrin-coated pits and vesicles are comprised of triskelions, each consisting of three oligomerized heavy chains (HC) bound by a light chain (LC). In addition to binding HC, LC interacts with members of the Hip1/R family of endocytic proteins, including the budding yeast homologue, Sla2p. Here, using in vivo analysis in yeast, we provide novel insight into the role of this interaction. We find that overexpression of LC partially restores endocytosis to cells lacking clathrin HC. This suppression is dependent on the Sla2p binding region of LC. Using live cell imaging techniques to visualize endocytic vesicle formation, we find that the N-terminal Sla2p binding region of LC promotes the progression of arrested Sla2p patches that form in the absence of HC. We propose that LC binding to Sla2p positively regulates Sla2p for efficient endocytic vesicle formation.

Journal of Cell Science, 2012

Phosphorylation regulates assembly and disassembly of proteins during endocytosis. In yeast, Prk1... more Phosphorylation regulates assembly and disassembly of proteins during endocytosis. In yeast, Prk1/Ark1 phosphorylate factors after vesicle internalization leading to coat disassembly. Scd5, a protein phosphatase-1 (PP1) targeting subunit, is proposed to regulate dephosphorylation of Prk1/Ark1 substrates to promote new rounds of endocytosis. In this study we analyzed scd5-PP1Δ2, a mutation causing impaired PP1 binding. scd5-PP1Δ2 caused hyperphosphorylation of several Prk1 endocytic targets. Live cell imaging of 15 endocytic components in scd5-PP1Δ2 revealed most factors arriving before invagination/actin had delayed lifetimes. Severely affected were early factors and Sla2 (Hip1R homologue), whose lifetime was extended nearly 4-fold. In contrast, the lifetime of Sla1, a Prk1 target, was extended less than 2-fold, but its cortical recruitment was significantly reduced. Delayed Sla2 dynamics caused by scd5-PP1Δ2 were suppressed by SLA1 overexpression. This was dependent on Sla1's L...

Developmental Cell, 2005

Newly forming clathrin-coated pits accumulate dy-1 Department of Molecular Biology and Microbiolo... more Newly forming clathrin-coated pits accumulate dy-1 Department of Molecular Biology and Microbiology namin and AP-2 in parallel with clathrin. Recruitment or Case Western Reserve University capture of cargo may be important for stabilizing early Cleveland, Ohio 44106 pits so that they continue to grow and complete coated 2 Miami Project to Cure Paralysis vesicle formation (Ehrlich et al., 2004). Also, the size of 3 Department of Molecular and Cellular Pharmacology the cargo influences the size and length of time it takes University of Miami to form a CCV. Coated pits that do not stabilize undergo Miami, Florida 33101 collapse and uncoat without budding. Finally, vesicle release is accompanied by a burst of dynamin recruitment, followed by transient actin polymerization, which Summary is thought to propel vesicles away from the surface (Ehrlich et al., 2004; Merrifield et al., 2002). Additionally, Clathrin-mediated transport is a major pathway for actin is implicated at other stages of endocytosis, inendocytosis. However, in yeast, where cortical actin cluding organization of sites of coated pit formation, patches are essential for endocytosis, plasma memcoated pit assembly, and constriction and/or scission brane-associated clathrin has never been observed. of CCVs (Bennett et al., 2001; Engqvist-Goldstein et al., Using live cell imaging, we demonstrate cortical 2004; Gaidarov et al., 1999; Yarar et al., 2005). clathrin in association with the actin-based endocytic In Saccharomyces cerevisiae, a dynamic actin cytomachinery in yeast. Fluorescently tagged clathrin is skeleton plays a central role in endocytosis (Engqvistfound in highly mobile internal trans-Golgi/endoso-Goldstein and Drubin, 2003). Treatment of yeast with mal structures and in smaller cortical patches. Total actin polymerization inhibitors dramatically blocks ininternal reflection fluorescence microscopy showed ternalization (Ayscough, 2000; Lappalainen and Drubin, that cortical patches are likely endocytic sites, as 1997). In addition, many factors required for proper clathrin is recruited prior to a burst of intensity of the cortical actin organization are also important for enactin patch/endocytic marker, Abp1. Clathrin also acdocytosis and are homologs of proteins involved in cumulates at the cortex with internalizing ␣ factor reclathrin-mediated uptake in other organisms (Engqvistceptor, Ste2p. Cortical clathrin localizes with epsins Goldstein and Drubin, 2003). These include the ep-Ent1/2p and AP180s, and its recruitment to the sursins Ent1p and Ent2p, the EH domain proteins End3p face is dependent upon these adaptors. In contrast, and Eps15-related Pan1p, amphiphysins Rvs161p and Sla2p, End3p, Pan1p, and a dynamic actin cytoskele-Rvs167p, the intersectin-like Sla1p, the Hip1/R homoton are not required for clathrin assembly or exlog Sla2p, and kinases such as Ypk1/2, related to PKB change but are required for the mobility, maturation, and SGK, and actin-regulating kinases Ark1 and Prk1 and/or turnover of clathrin-containing endocytic homologs of animal AAK1 and GAK (Engqvist-Goldstein structures. and Drubin, 2003). Many of these proteins associate transiently with cortical actin patches, which are be-Introduction lieved to form at sites of endocytosis (Engqvist-Goldstein and Drubin, 2003; Huckaba et al., 2004; Jonsdottir and Li, Clathrin is a major vesicle coat protein involved in re-2004; Kaksonen et al., 2003). ceptor-mediated endocytosis (RME) (Brodsky et al., Recent real-time microscopy of fluorescently labeled 2001). Sorting into clathrin-coated pits (CCP) and forendocytic/cortical patch proteins has provided novel mation of clathrin-coated vesicles (CCV) are mediated insight into the dynamics of these factors during endothrough adaptors, which directly bind cargo or bridge cytosis in yeast (Huckaba et al., 2004; Jonsdottir and interactions of clathrin to other endocytic factors and Li, 2004; Kaksonen et al., 2003). Initially Sla1p, Sla2p, inositol phospholipid-containing membrane. The globular Pan1p, and Las17p are recruited to cortical sites. This N-terminal domain (TD) of clathrin heavy chain (HC) is is followed by the assembly of actin, Arp2/3 complexes, important for binding to membrane-associated adapand Abp1. As vesicles/patches appear to pinch off, the tors, including AP-2, AP180/CALM, amphiphysin, epsin, early patch proteins are released and actin/Abp1 Hip1, ARH, and Dab2 (Traub, 2003). Also, actin and actinpatches move rapidly away from the cortex (Kaksonen associated factors play a role in the clathrin-mediated enet al., 2003). This late event is accompanied by recruitdocytosis (Engqvist-Goldstein and Drubin, 2003). ment of type I myosins, Myo3p and Myo5p, which are Recent studies in animal cells using components of hypothesized to function in vesicle fission (Jonsdottir the endocytic machinery tagged with green fluorescent and Li, 2004). Finally, internalized vesicles labeled with protein (GFP) derivatives have allowed examination of the lipophilic dye FM 4-64 and containing Abp1 have the dynamics of clathrin-mediated endocytosis in vivo, been observed moving from the bud cortex into the including measurements of the timing of endocytic mother cell along actin cables (Huckaba et al., 2004). events and the order of machinery and cargo recruit-Though details of the dynamics of endocytosis are emerging from yeast and animal studies, in yeast the role of clathrin in endocytosis remains unclear. Previous

The DsRed fusion of the clathrin light chain LCa was provided by Jim Keen and used as

Journal of Visualized Experiments (JoVE), 2022

ARTICLES DISCUSSED: Pekarek, B. T., Hunt, P. J., Belfort, B. D. W., Liu, G., Arenkiel, B. R. Ima... more ARTICLES DISCUSSED:

Pekarek, B. T., Hunt, P. J., Belfort, B. D. W., Liu, G., Arenkiel, B. R. Imaging and quantification of intact neuronal dendrites via CLARITY tissue clearing. Journal of Visualized Experiments: JoVE. (170), e62532 (2021).

Frankfurt, M., Bowman, R. Rapid Golgi stain for dendritic spine visualization in hippocampus and prefrontal cortex. Journal of Visualized Experiments: JoVE. (178), e63404 (2021).

Śliwińska, M. A., Cały, A., Szymański, J., Radwańska, K. Serial Block-Face Scanning Electron Microscopy (SBEM) for the study of dendritic spines. Journal of Visualized Experiments: JoVE. (176), e62712 (2021).

Chan, U., Gautam, D., West, A. E. Utilizing in vivo postnatal electroporation to study cerebellar granule neuron morphology and synapse development. Journal of Visualized Experiments: JoVE. (172), e62568 (2021).

Cuentas-Condori, A., Miller III, D. M. Imaging dendritic spines in Caenorhabditis elegans. Journal of Visualized Experiments: JoVE. (175), e62676 (2021).

Journal of undergraduate neuroscience education : JUNE : a publication of FUN, Faculty for Undergraduate Neuroscience, 2020

Team-based learning (TBL) is a special form of collaborative learning that involves the use of pe... more Team-based learning (TBL) is a special form of collaborative learning that involves the use of permanent working teams throughout the semester. In this highly structured and interactive teaching method, students perform preparatory activities outside of class to gain factual knowledge and understand basic concepts. In class, students collaborate with peers to apply content, analyze findings, and synthesize new ideas. To better understand the learning outcomes specific to TBL courses, we analyzed end-of-semester course evaluations from an undergraduate neuroscience course taught using either a moderate structure active learning or TBL format. Our analysis reveals that the TBL taught classes had significantly higher levels of self-reported learning in the areas of gaining, understanding, and synthesizing knowledge. We propose that these gains are driven by the TBL readiness assurance process and peer evaluations. Both of these structural components are expected to increase student acc...

Journal of Undergraduate Neuroscience Education, 2021