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1.  Chemical Interrogation of the neuronal kinome using a primary cell-based screening assay 
ACS chemical biology  2013;8(5):10.1021/cb300584e.
A fundamental impediment to functional recovery from spinal cord injury (SCI) and traumatic brain injury is the lack of sufficient axonal regeneration in the adult central nervous system. There is thus a need to develop agents that can stimulate axon growth to re-establish severed connections. Given the critical role played by protein kinases in regulating axon growth and the potential for pharmacological intervention, small molecule protein kinase inhibitors present a promising therapeutic strategy. Here, we report a robust cell-based phenotypic assay, utilizing primary rat hippocampal neurons, for identifying small molecule kinase inhibitors that promote neurite growth. The assay is highly reliable and suitable for medium throughput screening, as indicated by its Z′-factor of 0.73. A focused structurally diverse library of protein kinase inhibitors was screened, revealing several compound groups with the ability to strongly and consistently promote neurite growth. The best performing bioassay hit robustly and consistently promoted axon growth in a postnatal cortical slice culture assay. This study can serve as a jumping-off point for structure activity relationship (SAR) and other drug discovery approaches towards the development of drugs for treating SCI and related neurological pathologies.
doi:10.1021/cb300584e
PMCID: PMC3657311  PMID: 23480631
2.  L1cam Is Crucial for Cell Locomotion and Terminal Translocation of the Soma in Radial Migration during Murine Corticogenesis 
PLoS ONE  2014;9(1):e86186.
L1cam (L1) is a cell adhesion molecule associated with a spectrum of human neurological diseases, the most well-known being X-linked hydrocephalus. Although we recently demonstrated that L1 plays an important role in neuronal migration during cortical histogenesis, the mechanisms of delayed migration have still not been clarified. In this study, we found that cell locomotion in the intermediate zone and terminal translocation in the primitive cortical zone (PCZ) were affected by L1-knockdown (L1-KD). Time-lapse analyses revealed that L1-KD neurons produced by in utero electroporation of shRNA targeting L1 (L1-shRNAs) molecules showed decreased locomotion velocity in the intermediate zone, compared with control neurons. Furthermore, L1-KD neurons showed longer and more undulated leading processes during translocation through the primitive cortical zone. The curvature index, a quantitative index for curvilinearity, as well as the length of the leading process, were increased, whereas the somal movement was decreased in L1-KD neurons during terminal translocation in the PCZ. These results suggest that L1 has a role in radial migration of cortical neurons.
doi:10.1371/journal.pone.0086186
PMCID: PMC3904877  PMID: 24489698
3.  Astrocytes Modulate the Polarization of CD4+ T Cells to Th1 Cells 
PLoS ONE  2014;9(1):e86257.
T-cell characteristics are dynamic and influenced by multiple factors. To test whether cells and the environment in the central nervous system (CNS) can influence T-cells, we tested if culturing mouse CD4+ T-cells on mouse primary astrocytes, compared with standard feeder cells, modified T-cell polarization to Th1 and Treg subtypes. Astrocytes supported the production of Th1 cells and Tregs, which was diminished by inflammatory activation of astrocytes, and glutamate accumulation that may result from impaired glutamate uptake by astrocytes strongly promoted Th1 production. These results demonstrate that astrocytes and the environment in the CNS have the capacity to regulate T-cell characteristics.
doi:10.1371/journal.pone.0086257
PMCID: PMC3904883  PMID: 24489707
4.  MicroRNAs and neuronal development 
Summary
The importance of the involvement of non-protein coding RNAs in biological processes has become evident in recent years along with the identification of the transcriptional regulatory mechanisms that allow them to exert their roles. MicroRNAs (miRNAs) are a novel class of small non-coding RNA that regulates messenger RNA abundance. The capacity of each miRNA to target several transcripts suggests an ability to build a complex regulatory network for fine tuning gene expression; a mechanism by which they are thought to regulate cell fate, proliferation and identity. The brain expresses more distinct miRNAs than any other tissue in vertebrates and it presents an impressive variety of cell types, including many different classes of neurons. Here we review more than 10 years of miRNA research, and discuss the most important findings that have established miRNAs as key regulators of neuronal development.
doi:10.1016/j.siny.2012.07.008
PMCID: PMC3490020  PMID: 22906916
Development; Differentiation; Gene expression; MicroRNA; Neurons
5.  Isoform diversity and its importance for axon regeneration 
Neuropathology  2011;32(4):420-431.
Axon regeneration is a fundamental problem facing neuroscientists and clinicians. Failure of axon regeneration is caused by both extrinsic and intrinsic mechanisms. New techniques to exam gene expression such as Next Generation Sequencing of the Transcriptome (RNA-Seq) drastically increase our knowledge of both gene expression complexity (RNA isoforms) and gene expression regulation. By utilizing RNA-Seq, gene expression can now be defined at the level of isoforms, an essential step for understanding the mechanisms governing cell identity, growth and ultimately cellular responses to injury and disease.
doi:10.1111/j.1440-1789.2011.01280.x
PMCID: PMC3309121  PMID: 22151581
RNA-Seq; axon; regeneration; promoter; isoform; variant; untranslated region; coding DNA sequence; transcription start site
6.  Neuronal Hypoxia Induces Hsp40-Mediated Nuclear Import of Type 3 Deiodinase As an Adaptive Mechanism to Reduce Cellular Metabolism 
The Journal of Neuroscience  2012;32(25):8491-8500.
In neurons, the type 3 deiodinase (D3) inactivates thyroid hormone and reduces oxygen consumption, thus creating a state of cell-specific hypothyroidism. Here we show that hypoxia leads to nuclear import of D3 in neurons, without which thyroid hormone signaling and metabolism cannot be reduced. After unilateral hypoxia in the rat brain, D3 protein level is increased predominantly in the nucleus of the neurons in the pyramidal and granular ipsilateral layers, as well as in the hilus of the dentate gyrus of the hippocampal formation. In hippocampal neurons in culture as well as in a human neuroblastoma cell line (SK-N-AS), a 24 h hypoxia period redirects active D3 from the endoplasmic reticulum to the nucleus via the cochaperone Hsp40 pathway. Preventing nuclear D3 import by Hsp40 knockdown resulted an almost doubling in the thyroid hormone-dependent glycolytic rate and quadrupling the transcription of thyroid hormone target gene ENPP2. In contrast, Hsp40 overexpression increased nuclear import of D3 and minimized thyroid hormone effects in cell metabolism. In conclusion, ischemia/hypoxia induces an Hsp40-mediated translocation of D3 to the nucleus, facilitating thyroid hormone inactivation proximal to the thyroid hormone receptors. This adaptation decreases thyroid hormone signaling and may function to reduce ischemia-induced hypoxic brain damage.
doi:10.1523/JNEUROSCI.6514-11.2012
PMCID: PMC3752066  PMID: 22723689
7.  Formalization, Annotation and Analysis of Diverse Drug and Probe Screening Assay Datasets Using the BioAssay Ontology (BAO) 
PLoS ONE  2012;7(11):e49198.
Huge amounts of high-throughput screening (HTS) data for probe and drug development projects are being generated in the pharmaceutical industry and more recently in the public sector. The resulting experimental datasets are increasingly being disseminated via publically accessible repositories. However, existing repositories lack sufficient metadata to describe the experiments and are often difficult to navigate by non-experts. The lack of standardized descriptions and semantics of biological assays and screening results hinder targeted data retrieval, integration, aggregation, and analyses across different HTS datasets, for example to infer mechanisms of action of small molecule perturbagens. To address these limitations, we created the BioAssay Ontology (BAO). BAO has been developed with a focus on data integration and analysis enabling the classification of assays and screening results by concepts that relate to format, assay design, technology, target, and endpoint. Previously, we reported on the higher-level design of BAO and on the semantic querying capabilities offered by the ontology-indexed triple store of HTS data. Here, we report on our detailed design, annotation pipeline, substantially enlarged annotation knowledgebase, and analysis results. We used BAO to annotate assays from the largest public HTS data repository, PubChem, and demonstrate its utility to categorize and analyze diverse HTS results from numerous experiments. BAO is publically available from the NCBO BioPortal at http://bioportal.bioontology.org/ontologies/1533. BAO provides controlled terminology and uniform scope to report probe and drug discovery screening assays and results. BAO leverages description logic to formalize the domain knowledge and facilitate the semantic integration with diverse other resources. As a consequence, BAO offers the potential to infer new knowledge from a corpus of assay results, for example molecular mechanisms of action of perturbagens.
doi:10.1371/journal.pone.0049198
PMCID: PMC3498356  PMID: 23155465
8.  Challenges in Small Screening Laboratories: SaaS to the rescue 
The Miami Project to Cure Paralysis, part of the University of Miami Miller School of Medicine, includes a laboratory devoted to High Content Analysis (HCA) of neurons. The goal of the laboratory is to uncover signalling pathways, genes, compounds, or drugs that can be used to promote nerve growth. HCA permits the quantification of neuronal morphology, including the lengths and numbers of axons. HCA screening of various libraries on primary neurons requires a team-based approach, a variety of process steps and complex manipulations of cells and libraries to obtain meaningful results. HCA itself produces vast amounts of information including images, well-based data and cell-based phenotypic measures. Managing experimental workflow and library data, along with the extensive amount of experimental results is challenging.
For academic laboratories generating large data sets from experiments using thousands of perturbagens, a laboratory information management system (LIMS) is the data tracking solution of choice. With both productivity and efficiency as driving rationales, the Miami Project has equipped its HCA laboratory with a Software As A Service (SAAS) LIMS to ensure the quality of its experiments and workflows. The article discusses this application in detail, and how the system was selected and integrated into the laboratory. The advantages of SaaS are described.
PMCID: PMC3289069  PMID: 21631415
Good laboratory practice; High Content Analysis; Laboratory Information Management System; On demand; Software as a Service; Spinal cord injury
9.  In vivo Electroporation and Non-protein Based Screening Assays to Identify Antibodies Against Native Protein Conformations 
Hybridoma  2011;30(5):409-418.
In vivo electroporation has become a gold standard method for DNA immunization. The method assists the DNA entry into cells, results in expression and the display of the native form of antigens to professional cells of the immune system, uses both arms of immune system, has a built-in adjuvant system, is relatively safe, and is cost-effective. However, there are challenges for achieving an optimized reproducible process for eliciting strong humoral responses and for the screening of specific immune responses, in particular, when the aim is to mount humoral responses or to generate monoclonal antibodies via hybridoma technology. Production of monoclonal antibodies demands generation of high numbers of primed B and CD4 T helper cells in lymphoid organs needed for the fusion that traditionally is achieved by a final intravenous antigen injection. The purified antigen is also needed for screening of hundreds of clones obtained upon fusion of splenocytes. Such challenges make DNA vaccination dependent on purified proteins. Here, we have optimized methods for in vivo electroporation, production, and use of cells expressing the antigen and an in-cell Western screening method. These methods resulted in (1) reproducibly mounting robust humoral responses against antigens with different cell localizations, and (2) the ability to screen for antigen eliminating a need for protein/antigen purification. This process includes optimized parameters for in vivo electroporation, the use of transfected cells for final boost, and mild fixation/permeabilization of cells for screening. Using this process, upon two vaccinations via in vivo electroporation (and final boost), monoclonal antibodies against nucleus and cytoplasmic and transmembrane proteins were achieved.
doi:10.1089/hyb.2010.0120
PMCID: PMC3241927  PMID: 22008067
10.  Peripheral Nervous System Genes Expressed in Central Neurons Induce Growth on Inhibitory Substrates 
PLoS ONE  2012;7(6):e38101.
Trauma to the spinal cord and brain can result in irreparable loss of function. This failure of recovery is in part due to inhibition of axon regeneration by myelin and chondroitin sulfate proteoglycans (CSPGs). Peripheral nervous system (PNS) neurons exhibit increased regenerative ability compared to central nervous system neurons, even in the presence of inhibitory environments. Previously, we identified over a thousand genes differentially expressed in PNS neurons relative to CNS neurons. These genes represent intrinsic differences that may account for the PNS’s enhanced regenerative ability. Cerebellar neurons were transfected with cDNAs for each of these PNS genes to assess their ability to enhance neurite growth on inhibitory (CSPG) or permissive (laminin) substrates. Using high content analysis, we evaluated the phenotypic profile of each neuron to extract meaningful data for over 1100 genes. Several known growth associated proteins potentiated neurite growth on laminin. Most interestingly, novel genes were identified that promoted neurite growth on CSPGs (GPX3, EIF2B5, RBMX). Bioinformatic approaches also uncovered a number of novel gene families that altered neurite growth of CNS neurons.
doi:10.1371/journal.pone.0038101
PMCID: PMC3368946  PMID: 22701605
11.  Microtubule stabilization reduces scarring and enables axon regeneration after spinal cord injury 
Science (New York, N.y.)  2011;331(6019):928-931.
Hypertrophic scarring and poor intrinsic axon growth capacity constitute major obstacles for spinal cord repair. These processes are tightly regulated by microtubule dynamics. We found that moderate microtubule stabilization decreased scar formation after spinal cord injury (SCI) in rodents via various cellular mechanisms, including dampening of TFG-β signalling. It prevented the accumulation of chondroitin sulfate proteoglycans (CSPGs) and rendered the lesion site permissive for axon regeneration of growth competent sensory neurons. Additionally, microtubule stabilization promoted growth of CNS axons of the Raphe-spinal tract and led to functional improvement. Thus, microtubule stabilization reduces fibrotic scarring and enhances the capacity of axons to grow. Manipulation of microtubules may offer the basis for a multi-targeted therapy after SCI.
doi:10.1126/science.1201148
PMCID: PMC3330754  PMID: 21273450
12.  BioAssay Ontology Annotations Facilitate Cross-Analysis of Diverse High-throughput Screening Data Sets 
Journal of biomolecular screening  2011;16(4):415-426.
High-throughput screening data repositories, such as PubChem, represent valuable resources for the development of small molecule chemical probes and can serve as entry points for drug discovery programs. While the loose data format offered by PubChem allows for great flexibility, important annotations, such as the assay format and technologies employed, are not explicitly indexed. We have previously developed a BioAssay Ontology (BAO) and curated over 350 assays with standardized BAO terms. Here we describe the use of BAO annotations to analyze a large set of assays that employ luciferase- and β-lactamase-based technologies. We identified promiscuous chemotypes pertaining to different sub-categories of assays and specific mechanisms by which these chemotypes interfere in reporter gene assays. Our results show that the data in PubChem can be used to identify promiscuous compounds that interfere non-specifically with particular technologies. Furthermore, we show that BAO is a valuable toolset for the identification of related assays and for the systematic generation of insights that are beyond the scope of individual assays or screening campaigns.
doi:10.1177/1087057111400191
PMCID: PMC3167204  PMID: 21471461
compound promiscuity; assay ontology; reporter gene assays; high-throughput screening data analysis; cheminformatics
13.  Isoform Diversity and Regulation in Peripheral and Central Neurons Revealed through RNA-Seq 
PLoS ONE  2012;7(1):e30417.
To fully understand cell type identity and function in the nervous system there is a need to understand neuronal gene expression at the level of isoform diversity. Here we applied Next Generation Sequencing of the transcriptome (RNA-Seq) to purified sensory neurons and cerebellar granular neurons (CGNs) grown on an axonal growth permissive substrate. The goal of the analysis was to uncover neuronal type specific isoforms as a prelude to understanding patterns of gene expression underlying their intrinsic growth abilities. Global gene expression patterns were comparable to those found for other cell types, in that a vast majority of genes were expressed at low abundance. Nearly 18% of gene loci produced more than one transcript. More than 8000 isoforms were differentially expressed, either to different degrees in different neuronal types or uniquely expressed in one or the other. Sensory neurons expressed a larger number of genes and gene isoforms than did CGNs. To begin to understand the mechanisms responsible for the differential gene/isoform expression we identified transcription factor binding sites present specifically in the upstream genomic sequences of differentially expressed isoforms, and analyzed the 3′ untranslated regions (3′ UTRs) for microRNA (miRNA) target sites. Our analysis defines isoform diversity for two neuronal types with diverse axon growth capabilities and begins to elucidate the complex transcriptional landscape in two neuronal populations.
doi:10.1371/journal.pone.0030417
PMCID: PMC3260295  PMID: 22272348
14.  A modifier locus on chromosome 5 contributes to L1 cell adhesion molecule X-linked hydrocephalus in mice 
Neurogenetics  2009;11(1):53-71.
Humans with L1 cell adhesion molecule (L1CAM) mutations exhibit X-linked hydrocephalus, as well as other severe neurological disorders. L1-6D mutant mice, which are homozygous for a deletion that removes the sixth immunoglobulin-like domain of L1cam, seldom display hydrocephalus on the 129/Sv background. However, the same L1-6D mutation produces severe hydrocephalus on the C57BL/6J background. To begin to understand how L1cam deficiencies result in hydrocephalus and to identify modifier loci that contribute to X-linked hydrocephalus by genetically interacting with L1cam, we conducted a genome-wide scan on F2 L1-6D mice, bred from L1-6D 129S2/SvPasCrlf and C57BL/6J mice. Linkage studies, utilizing chi-square tests and quantitative trait loci mapping techniques, were performed. Candidate modifier loci were further investigated in an extension study. Linkage was confirmed for a locus on chromosome 5, which we named L1cam hydrocephalus modifier 1 (L1hydro1), p = 4.04 × 10−11.
doi:10.1007/s10048-009-0203-3
PMCID: PMC2863031  PMID: 19565280
L1cam; Hydrocephalus; Modifier; Linkage analysis; QTL
15.  L1-Mediated Branching Is Regulated by Two Ezrin–Radixin–Moesin (ERM)-Binding Sites, the RSLE Region and a Novel Juxtamembrane ERM-Binding Region 
We investigated how the neural cell adhesion molecule L1 mediates neurite outgrowth through L1–L1 homophilic interactions. Wild-type L1 and L1 with mutations in the cytoplasmic domain (CD) were introduced into L1 knock-out neurons, and transfected neurons were grown on an L1 substrate. Neurite length and branching were compared between wild-type L1 and L1CD mutations. Surprisingly, the L1CD is not required for L1-mediated neurite outgrowth but plays a critical role in neurite branching, through both the juxtamembrane region and the RSLE region. We demonstrate that both regions serve as ezrin–moesin–radixin-binding sites. A truncation mutant that deletes 110 of 114 amino acids of the L1CD still supports neurite outgrowth on an L1 substrate, suggesting that a coreceptor binds to L1 in cis and mediates neurite outgrowth and that L1–ankyrin interactions are not essential for neurite initiation or outgrowth. These data are consistent with a model in which L1 can influence L1-mediated neurite outgrowth and branching through both the L1CD and a coreceptor.
doi:10.1523/JNEUROSCI.4097-04.2005
PMCID: PMC2860578  PMID: 15647482
IL1CAM; neurite outgrowth; ERM proteins; axon branching; juxtamembrane; ankyrin; adhesion
16.  ETHANOL INHIBITS L1 CELL ADHESION MOLECULE TYROSINE PHOSPHORYLATION AND DEPHOSPHORYLATION AND ACTIVATION OF PP60SRC 
Journal of neurochemistry  2009;110(3):779-790.
Fetal alcohol syndrome(Abel, 2000) is a leading cause of mental retardation. The neuropathology found in fetal alcohol syndrome is similar to the phenotypes expressed in diseases caused by mutations in the gene for L1 cell adhesion molecule. L1 has a crucial role in the developing nervous system, acting in cell-cell adhesion, neuronal guidance, and growth. We have previously shown that L1 mediated neurite outgrowth and L1 activation of ERK1/2 is exquisitely sensitive to ethanol (Tang, He, O'Riordan, Farkas, Buck, Lemmon, and Bearer, 2006). One possible mechanism for this effect is through disruption of a tyrosine based sorting signal, Y(1176)RSLE, on the cytoplasmic domain of L1. Our goal was to determine if ethanol inhibited the sorting signal or its phosphorylation state. Ethanol had no effect on L1 distribution to the growth cone or its ability to be expressed on the cell surface. Clustering of L1 resulted in increased dephosphorylation of Y(1176), increased L1 tyrosine phosphorylation, and an increase in the activation of pp60src, all of which were inhibited by 25 mM ethanol. Inhibition of pp60src inhibited increases in L1 tyrosine and ERK1/2 phosphorylation, and Y(1176) dephosphorylation. We conclude that ethanol disrupts L1 trafficking/signaling following its expression on the surface of the growth cone, and prior to its activation of pp60src.
doi:10.1111/j.1471-4159.2009.06143.x
PMCID: PMC2730836  PMID: 19457108
Ethanol; L1 cell adhesion molecule; distribution; fetal alcohol syndrome; tyrosine phosphorylation; tyrosine dephosphorylation; pp60src; axonal sorting; lipid rafts
17.  The Role of Endocytosis in Regulating L1-mediated Adhesion* 
The Journal of biological chemistry  2001;276(2):1285-1290.
L1 is a neural cell adhesion molecule critical for neural development. Full-length L1 (L1FL) contains an alternatively spliced cytoplasmic sequence, RSLE, which is absent in L1 expressed in nonneuronal cells. The RSLE sequence follows a tyrosine, creating an endocytic motif that allows rapid internalization via clathrin-mediated endocytosis. We hypothesized that L1FL would internalize more rapidly than L1 lacking the RSLE sequence (L1ΔRSLE) and that internalization might regulate L1-mediated adhesion. L1 internalization was measured by immunofluorescence microscopy and by uptake of 125I-anti-rat-L1 antibody, demonstrating that L1FL is internalized 2–3 times faster than L1ΔRSLE. Inhibition of clathrin-mediated endocytosis slowed internalization of L1FL but did not affect initial uptake of L1ΔRSLE. To test whether L1 endocytosis regulates L1 adhesion, cell aggregation rates were tested. L1ΔRSLE cells aggregated two times faster than L1FL cells. Inhibition of clathrin-mediated endocytosis increases the aggregation rate of the L1FL cells to that of L1ΔRSLE cells. Our results demonstrate that rapid internalization of L1 dramatically affects L1 adhesion.
doi:10.1074/jbc.M006658200
PMCID: PMC2426744  PMID: 11035015
18.  Characterization of the Neuron-Specific L1-CAM Cytoplasmic Tail: Naturally Disordered in Solution It Exercises Different Binding Modes for Different Adaptor Proteins† 
Biochemistry  2008;47(13):4160-4168.
L1, a highly conserved transmembrane glycoprotein member of the immunoglobulin superfamily of cell adhesion molecules, mediates many developmental processes in the nervous system. Here we present the biophysical characterization and the binding properties of the least structurally defined part of this receptor: its cytoplasmic tail (CT). We have shown by analytical ultracentrifugation and dynamic light scattering experiments that it is mostly monomeric and unstructured in aqueous solution. We have defined by nuclear magnetic resonance the molecular details of L1-CT binding to two major targets: a membrane-cytoskeletal linker (MCL), ezrin, and an endocytosis mediator, AP2. Surprisingly, in addition to the two previously identified ezrin binding motifs, the juxtamembrane and the 1176YRSLE regions, we have discovered a third one, a part of which has been previously associated with binding to another MCL, ankyrin. For the L1 interaction with AP2 we have determined the precise interaction region surrounding the 1176YRSLE binding site and that this overlaps with the second ezrin binding site. In addition, we have shown that the juxtamembrane region of L1-CT has some binding affinity to AP2-μ2, although the specificity of this interaction needs further investigation. These data indicate that L1-CT belongs to the class of intrinsically disordered proteins. Endogenous flexibility of L1-CT might play an important role in dynamic regulation of intracellular signaling: the ability of cytoplasmic tails to accommodate different targets has the potential to fine-tune signal transduction via cell surface receptors.
doi:10.1021/bi702433q
PMCID: PMC2426742  PMID: 18321067
19.  Disrupted Schwann cell–axon interactions in peripheral nerves of mice with altered L1-integrin interactions 
The cell adhesion molecule L1 is important for peripheral nerve development. Mice lacking the 6th Ig domain of L1 (L1-6D mice) lose L1 homophilic binding and RGD dependent L1-integrin binding [Itoh, K., Cheng, L., Kamei, Y., Fushiki, S., Kamiguchi, H., Gutwein, P., Stoeck, A., Arnold, B., Altevogt, P., Lemmon, V., 2004. Brain development in mice lacking L1-L1 homophilic adhesion. J. Cell Biol. 165, 145–154]. We examined the ultrastructure of sciatic nerves from L1-6D at postnatal day 7 and 8 weeks. Unmyelinated axons frequently detached at the edge of Schwann cells, and naked axons were observed. Myelin was thinner in L1-6D and abnormal, multiple axons wrapped in a single myelin sheath were routinely observed. Previous work has shown that L1 on axons interacts with a heterophilic binding partner on Schwann cells to facilitate normal peripheral nerve formation. Taken together, it is likely that L1 on axons binds integrins on Schwann cells, resulting in interactions between axons and Schwann cells that are essential for ensheathment and myelination.
doi:10.1016/j.mcn.2005.06.006
PMCID: PMC2424132  PMID: 16456929
20.  RanBPM is an L1-interacting protein that regulates L1-mediated mitogen-activated protein kinase activation 
Journal of neurochemistry  2005;94(4):1102-1110.
A yeast two-hybrid screen using the last 28 amino acids of the cytoplasmic domain of the neural cell adhesion molecule L1 identified RanBPM as an L1-interacting protein. RanBPM associates with L1 in vivo and the N-terminal region of RanBPM (N-RanBPM), containing the SPRY domain, is sufficient for the interaction with L1 in a glutathione S-transferase pulldown assay. L1 antibody patching dramatically changes the subcellular localization of N-RanBPM in transfected COS cells. Overexpression of N-RanBPM in COS cells reduces L1-triggered extracellular signal-regulated kinase 1/2 activation by 50% and overexpression of N-RanBPM in primary neurons inhibits L1-mediated neurite outgrowth and branching. These data suggest that RanBPM is an adaptor protein that links L1 to the extracellular signal-regulated kinase/MAPK pathway
doi:10.1111/j.1471-4159.2005.03254.x
PMCID: PMC2424128  PMID: 16000162
adhesion molecule adaptor; axon extension; Ig superfamily
21.  96-Well electroporation method for transfection of mammalian central neurons 
BioTechniques  2006;41(5):619-624.
Manipulating gene expression in primary neurons has been a goal for many scientists for over 20 years. Vertebrate central nervous system neurons are classically difficult to transfect. Most lipid reagents are inefficient and toxic to the cells, and time-consuming methods such as viral infections are often required to obtain better efficiencies. We have developed an efficient method for the transfection of cerebellar granule neurons and hippocampal neurons with standard plasmid vectors. Using 96-well electroporation plates, square-wave pulses can introduce 96 different plasmids into neurons in a single step. The procedure results in greater than 20% transfection efficiencies and requires only simple solutions of nominal cost. In addition to enabling the rapid optimization of experimental protocols with multiple parameters, this procedure enables the use of high content screening methods to characterize neuronal phenotypes.
doi:10.2144/000112279
PMCID: PMC2424126  PMID: 17140120
22.  EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries 
BMC Bioinformatics  2008;9:186.
Background
Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds.
Results
We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples) produced by subtractive hybridization.
Conclusion
EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.
doi:10.1186/1471-2105-9-186
PMCID: PMC2322989  PMID: 18402700
23.  Dephosphorylation and internalization of cell adhesion molecule L1 induced by theta burst stimulation in rat hippocampus 
The neural cell adhesion molecule L1 may participate in initiating and maintaining synaptic changes during learning in the hippocampus. One prominent form of synaptic change in the hippocampus is long-term potentiation (LTP) that occurs following specific patterns of synaptic activity. We present evidence that Y1176 of the YRSL motif within L1 cytoplasmic domain is dephosphorylated in LTP-induced hippocampus. The dephosphorylated L1 is associated with AP-2 and AP180 that are required for clathrin-mediated internalization of L1. These data suggest that clathrin-mediated recycling of L1 at presynaptic sites is enhanced by certain kinds of neural activity, and that maintenance of LTP-induced synaptic changes is regulated by L1 recycling.
doi:10.1016/j.mcn.2005.02.014
PMCID: PMC1382274  PMID: 15911348
24.  Recycling of the Cell Adhesion Molecule L1 in Axonal Growth Cones 
The cell adhesion molecule (CAM) L1 plays crucial roles in axon growth in vitro and in the formation of major axonal tracts in vivo. It is generally thought that CAMs link extracellular immobile ligands with retrogradely moving actin filaments to transmit force that pulls the growth cone forward. However, relatively little is known about the fate of CAMs that have been translocated into the central (C)-domain of the growth cone. We have shown previously that L1 is preferentially endocytosed at the C-domain. In the present study, we further analyze the subcellular distribution of endocytic organelles containing L1 at different time points and demonstrate that internalized L1 is transported into the peripheral (P)-domain of growth cones advancing via an L1-dependent mechanism. Internalized L1 is found in vesicles positioned along microtubules, and the centrifugal transport of these L1-containing vesicles is dependent on dynamic microtubules in the P-domain. Furthermore, we show that endocytosed L1 is reinserted into the plasma membrane at the leading edge of the P-domain. Monitoring recycled L1 reveals that it moves retrogradely on the cell surface into the C-domain. In contrast, the growth cone advancing independently of L1 internalizes and recycles L1 within the C-domain. For the growth cone to advance, the leading edge needs to establish strong adhesive interactions with the substrate while attachments at the rear are released. Recycling L1 from the C-domain to the leading edge provides an effective way to create asymmetric L1-mediated adhesion and therefore would be critical for L1-based growth cone motility.
PMCID: PMC1237010  PMID: 10804209
neural cell adhesion molecule; L1; axonal growth cone; endocytosis; recycling; microtubule
25.  A Neuronal Form of the Cell Adhesion Molecule L1 Contains a Tyrosine-Based Signal Required for Sorting to the Axonal Growth Cone 
The neural cell adhesion molecule L1, which is present on axons and growth cones, plays a crucial role in the formation of major axonal tracts such as the corticospinal tract and corpus callosum. L1 is preferentially transported to axons and inserted in the growth cone membrane. However, how L1 is sorted to axons remains unclear. Tyr1176 in the L1 cytoplasmic domain is adjacent to a neuron-specific alternatively spliced sequence, RSLE (Arg-Ser-Leu-Glu). The resulting sequence of YRSLE conforms to a tyrosine-based consensus motif (YxxL) for sorting of integral membrane proteins into specific cellular compartments. To study a possible role of the YRSLE sequence in L1 sorting, chick DRG neurons were transfected with human L1 cDNA that codes for full-length L1 (L1FL ), a non-neuronal form of L1 that lacks the RSLE sequence (L1ΔRSLE), mutant L1 with a Y1176A substitution (L1Y1176A ), or L1 truncated immediately after the RSLE sequence (L1ΔC77). L1FL and L1ΔC77, both of which possess the YRSLE sequence, were expressed in the axonal growth cone and to a lesser degree in the cell body. In contrast, expression of both L1ΔRSLE and L1Y1176A was restricted to the cell body and proximal axonal shaft. We also found that L1ΔRSLE and L1Y1176A were integrated into the plasma membrane in the cell body after missorting. These data demonstrate that the neuronal form of L1 carries the tyrosine-based sorting signal YRSLE, which is critical for sorting L1 to the axonal growth cone.
PMCID: PMC1226933  PMID: 9570805
neural cell adhesion molecule; L1; axon; growth cone; protein sorting; tyrosine-based sorting signal

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