scholarly journals Purity and Enrichment of Laser-Microdissected Midbrain Dopamine Neurons

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Amanda L. Brown ◽  
Trevor A. Day ◽  
Christopher V. Dayas ◽  
Doug W. Smith
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Dopamine Neuron ◽  
Dopamine Neurons ◽  
Acid Decarboxylase ◽  
Cell Groups ◽  
Midbrain Dopamine ◽  
High Degree ◽  
Midbrain Dopamine Neurons

The ability to microdissect individual cells from the nervous system has enormous potential, as it can allow for the study of gene expression in phenotypically identified cells. However, if the resultant gene expression profiles are to be accurately ascribed, it is necessary to determine the extent of contamination by nontarget cells in the microdissected sample. Here, we show that midbrain dopamine neurons can be laser-microdissected to a high degree of enrichment and purity. The average enrichment for tyrosine hydroxylase (TH) gene expression in the microdissected sample relative to midbrain sections was approximately 200-fold. For the dopamine transporter (DAT) and the vesicular monoamine transporter type 2 (Vmat2), average enrichments were approximately 100- and 60-fold, respectively. Glutamic acid decarboxylase (Gad65) expression, a marker for GABAergic neurons, was several hundredfold lower than dopamine neuron-specific genes. Glial cell and glutamatergic neuron gene expression were not detected in microdissected samples. Additionally, SN and VTA dopamine neurons had significantly different expression levels of dopamine neuron-specific genes, which likely reflects functional differences between the two cell groups. This study demonstrates that it is possible to laser-microdissect dopamine neurons to a high degree of cell purity. Therefore gene expression profiles can be precisely attributed to the targeted microdissected cells.

scholarly journals ImmuSort, a database on gene plasticity and electronic sorting for immune cells

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Pingzhang Wang ◽  
Yehong Yang ◽  
Wenling Han ◽  
Dalong Ma
Keyword(s):  
Gene Expression ◽  
Immune Cells ◽  
Immune Cell ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Experimental Conditions ◽  
Evaluation Scores ◽  
Cell Groups ◽  
Differential Gene ◽  
Disease Associated Genes

Abstract Gene expression is highly dynamic and plastic. We present a new immunological database, ImmuSort. Unlike other gene expression databases, ImmuSort provides a convenient way to view global differential gene expression data across thousands of experimental conditions in immune cells. It enables electronic sorting, which is a bioinformatics process to retrieve cell states associated with specific experimental conditions that are mainly based on gene expression intensity. A comparison of gene expression profiles reveals other applications, such as the evaluation of immune cell biomarkers and cell subsets, identification of cell specific and/or disease-associated genes or transcripts, comparison of gene expression in different transcript variants and probe set quality evaluation. A plasticity score is introduced to measure gene plasticity. Average rank and marker evaluation scores are used to evaluate biomarkers. The current version includes 31 human and 17 mouse immune cell groups, comprising 10,422 and 3,929 microarrays derived from public databases, respectively. A total of 20,283 human and 20,963 mouse genes are available to query in the database. Examples show the distinct advantages of the database. The database URL is http://immusort.bjmu.edu.cn/.

scholarly journals Information topology of gene expression profile in dopaminergic neurons

2017 ◽  
Author(s):  
Mónica Tapia Pacheco ◽  
Pierre Baudot ◽  
Martial A. Dufour ◽  
Christine Formisano-Tréziny ◽  
Simone Temporal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dopaminergic Neurons ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Combinatorial Structure ◽  
Maximum Information ◽  
Midbrain Neurons ◽  
High Degree ◽  
Multivariate Mutual Information ◽  
Gene Expression Levels

SUMMARY PARAGRAPHExtracting high-degree interactions and dependences between variables (pairs, triplets, … k-tuples) is a challenge posed by all omics approaches1, 2. Here we used multivariate mutual information (Ik) analysis3 on single-cell retro-transcription quantitative PCR (sc-RTqPCR) data obtained from midbrain neurons to estimate the k-dimensional topology of their gene expression profiles. 41 mRNAs were quantified and statistical dependences in gene expression levels could be fully described for 21 genes: Ik analysis revealed a complex combinatorial structure including modules of pairs, triplets (up to 6-tuples) sharing strong positive, negative or zero Ik, corresponding to co-varying, clustering and independent sets of genes, respectively. Therefore, Ik analysis simultaneously identified heterogeneity (negative Ik) of the cell population under study and regulatory principles conserved across the population (homogeneity, positive Ik). Moreover, maximum information paths enabled to determine the size and stability of such transcriptional modules. Ik analysis represents a new topological and statistical method of data analysis.

scholarly journals Classification of Midbrain Dopamine Neurons Using Single-Cell Gene Expression Profiling Approaches

2020 ◽  
Vol 43 (3) ◽  
pp. 155-169 ◽  
Author(s):  
Jean-Francois Poulin ◽  
Zachary Gaertner ◽  
Oscar Andrés Moreno-Ramos ◽  
Rajeshwar Awatramani
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Dopamine Neurons ◽  
Cell Gene Expression ◽  
Midbrain Dopamine ◽  
Cell Gene ◽  
Midbrain Dopamine Neurons

A Shared Gene-Expression Signature in Innate-Like Lymphocytes.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3903-3903
Author(s):  
Tetsuya Yamagata ◽  
Christophe Benoist ◽  
Diane Mathis
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Gene Expression Signature ◽  
Cell Types ◽  
Self Recognition ◽  
Distinct Cell ◽  
Invariant Structures ◽  
Small Set ◽  
High Degree

Abstract Innate and adaptive immunity are the two major arms of the immune system. They rely on very distinct cell-types, primarily distinguished by the source of diversity for non-self recognition, of germline or somatic origin. There exists, however, a subset of lymphocytes whose receptors require rearrangement but result in semi-invariant structures with a high degree of self-specificity. We hypothesized that these innate-like lymphocytes might share a common gene transcription signature. To test this notion, we made pair-wise comparisons of the gene-expression profiles of innate-like lymphocytes and closely paired adaptive system counterparts (NKT vs. CD4T, CD8ααT vs. CD8αβT, B1 vs. B2), and bioinformatically extracted common features and common genes distinguishing innate from adaptive cell-types. A statistically significant “innate signature” was indeed distilled, composed of a small set of genes over- and under-expressed in innate vs. adaptive lymphocytes. Particularly intriguing was the high representation of interferon-inducible GTPases crucial for resistance against intracellular pathogens, and of small G proteins involved in intracellular vacuole maturation and trafficking. Overall, this combined expression pattern can thus be designated as an “innate signature” among lymphocytes.

scholarly journals In vivo patch-clamp recordings reveal distinct subthreshold signatures and threshold dynamics of midbrain dopamine neurons

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Kanako Otomo ◽  
Jessica Perkins ◽  
Anand Kulkarni ◽  
Strahinja Stojanovic ◽  
Jochen Roeper ◽  
...  
Keyword(s):  
Membrane Potential ◽  
Action Potential ◽  
Dopamine Neuron ◽  
Dopamine Neurons ◽  
Firing Patterns ◽  
Action Potential Threshold ◽  
Midbrain Dopamine ◽  
Potential Threshold ◽  
Midbrain Dopamine Neurons

AbstractThe in vivo firing patterns of ventral midbrain dopamine neurons are controlled by afferent and intrinsic activity to generate sensory cue and prediction error signals that are essential for reward-based learning. Given the absence of in vivo intracellular recordings during the last three decades, the subthreshold membrane potential events that cause changes in dopamine neuron firing patterns remain unknown. To address this, we established in vivo whole-cell recordings and obtained over 100 spontaneously active, immunocytochemically-defined midbrain dopamine neurons in isoflurane-anaesthetized adult mice. We identified a repertoire of subthreshold membrane potential signatures associated with distinct in vivo firing patterns. Dopamine neuron activity in vivo deviated from single-spike pacemaking by phasic increases in firing rate via two qualitatively distinct biophysical mechanisms: 1) a prolonged hyperpolarization preceding rebound bursts, accompanied by a hyperpolarizing shift in action potential threshold; and 2) a transient depolarization leading to high-frequency plateau bursts, associated with a depolarizing shift in action potential threshold. Our findings define a mechanistic framework for the biophysical implementation of dopamine neuron firing patterns in the intact brain.

scholarly journals Subthreshold repertoire and threshold dynamics of midbrain dopamine neuron firing in vivo

2020 ◽  
Author(s):  
Kanako Otomo ◽  
Jessica Perkins ◽  
Anand Kulkarni ◽  
Strahinja Stojanovic ◽  
Jochen Roeper ◽  
...  
Keyword(s):  
Action Potential ◽  
Prediction Error ◽  
Dopamine Neuron ◽  
Dopamine Neurons ◽  
Threshold Dynamics ◽  
Action Potential Threshold ◽  
Midbrain Dopamine ◽  
Potential Threshold ◽  
Midbrain Dopamine Neurons

AbstractThe firing pattern of ventral midbrain dopamine neurons is controlled by afferent and intrinsic activity to generate prediction error signals that are essential for reward-based learning. Given the absence of intracellular in vivo recordings in the last three decades, the subthreshold membrane potential events that cause changes in dopamine neuron firing patterns remain unknown. By establishing stable in vivo whole-cell recordings of >100 spontaneously active midbrain dopamine neurons in anaesthetized mice, we identified the repertoire of subthreshold membrane potential signatures associated with distinct in vivo firing patterns. We demonstrate that dopamine neuron in vivo activity deviates from a single spike pacemaker pattern by eliciting transient increases in firing rate generated by at least two diametrically opposing biophysical mechanisms: a transient depolarization resulting in high frequency plateau bursts associated with a reactive, depolarizing shift in action potential threshold; and a prolonged hyperpolarization preceding slower rebound bursts characterized by a predictive, hyperpolarizing shift in action potential threshold. Our findings therefore illustrate a framework for the biophysical implementation of prediction error and sensory cue coding in dopamine neurons by tuning action potential threshold dynamics.

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