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Schwanke S, Jenssen J, Eipert P, Schmitt O. Towards Differential Connectomics with NeuroVIISAS. Neuroinformatics 2019; 17:163-179. [PMID: 30014279 DOI: 10.1007/s12021-018-9389-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The comparison of connectomes is an essential step to identify changes in structural and functional neuronal networks. However, the connectomes themselves as well as the comparisons of connectomes could be manifold. In most applications, comparisons of connectomes are applied to specific sets of data. In many studies collections of scripts are applied optimized for certain species (non-generic approaches) or diseases (control versus disease group connectomes). These collections of scripts have a limited functionality which do not support functional and topographic mappings of connectomes (hemispherical asymmetries, peripheral nervous system). The platform-independent and generic neuroVIISAS framework is built to circumvent limitations that come with variants of nomenclatures, connectivity lists and connectional hierarchies as well as restrictions to structural connectome analyses. A new analytical module is introduced into the framework to compare different types of connectomes and different representations of the same connectome within a unique software environment. As an example a differential analysis of the partial connectome of the laboratory rat that is based on virus tract tracing with the same regions of non-virus tract tracing has been performed. A relatively large connectional coherence between the two different techniques was found. However, some detected connections are described by virus tract-tracing only.
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Affiliation(s)
- Sebastian Schwanke
- Department of Anatomy, University of Rostock, Gertrudenstr. 9, 18057, Rostock, Germany
| | - Jörg Jenssen
- Department of Anatomy, University of Rostock, Gertrudenstr. 9, 18057, Rostock, Germany
| | - Peter Eipert
- Department of Anatomy, University of Rostock, Gertrudenstr. 9, 18057, Rostock, Germany
| | - Oliver Schmitt
- Department of Anatomy, University of Rostock, Gertrudenstr. 9, 18057, Rostock, Germany.
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Joost S, Mikkat S, Wille M, Schümann A, Schmitt O. Membrane Protein Identification in Rodent Brain Tissue Samples and Acute Brain Slices. Cells 2019; 8:cells8050423. [PMID: 31072038 PMCID: PMC6562397 DOI: 10.3390/cells8050423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 02/07/2023] Open
Abstract
Acute brain slices are a sample format for electrophysiology, disease modeling, and organotypic cultures. Proteome analyses based on mass spectrometric measurements are seldom used on acute slices, although they offer high-content protein analyses and explorative approaches. In neuroscience, membrane proteins are of special interest for proteome-based analysis as they are necessary for metabolic, electrical, and signaling functions, including myelin maintenance and regeneration. A previously published protocol for the enrichment of plasma membrane proteins based on aqueous two-phase polymer systems followed by mass spectrometric protein identification was adjusted to the small sample size of single acute murine slices from newborn animals and the reproducibility of the results was analyzed. For this, plasma membrane proteins of 12 acute slice samples from six animals were enriched and analyzed by liquid chromatography-mass spectrometry. A total of 1161 proteins were identified, of which 369 were assigned to membranes. Protein abundances showed high reproducibility between samples. The plasma membrane protein separation protocol can be applied to single acute slices despite the low sample size and offers a high yield of identifiable proteins. This is not only the prerequisite for proteome analysis of organotypic slice cultures but also allows for the analysis of small-sized isolated brain regions at the proteome level.
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Affiliation(s)
- Sarah Joost
- Institute of Anatomy, University Medical Center Rostock, 18057 Rostock, Germany.
| | - Stefan Mikkat
- Core Facility Proteome Analysis, University Medical Center Rostock, 18057 Rostock, Germany.
| | - Michael Wille
- Institute of Anatomy, University Medical Center Rostock, 18057 Rostock, Germany.
| | - Antje Schümann
- Institute of Anatomy, University Medical Center Rostock, 18057 Rostock, Germany.
| | - Oliver Schmitt
- Institute of Anatomy, University Medical Center Rostock, 18057 Rostock, Germany.
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Edwards D, Sommerhage F, Berry B, Nummer H, Raquet M, Clymer B, Stancescu M, Hickman JJ. Comparison of NMDA and AMPA Channel Expression and Function between Embryonic and Adult Neurons Utilizing Microelectrode Array Systems. ACS Biomater Sci Eng 2017; 3:3525-3533. [PMID: 29250595 PMCID: PMC5728088 DOI: 10.1021/acsbiomaterials.7b00596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/13/2017] [Indexed: 12/27/2022]
Abstract
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Microelectrode
arrays (MEAs) are innovative tools used to perform
electrophysiological experiments for the study of electrical activity
and connectivity in populations of neurons from dissociated cultures.
Reliance upon neurons derived from embryonic tissue is a common limitation
of neuronal/MEA hybrid systems and perhaps of neuroscience research
in general, and the use of adult neurons could model fully functional
in vivo parameters more closely. Spontaneous network activity was
concurrently recorded from both embryonic and adult rat neurons cultured
on MEAs for up to 10 weeks in vitro to characterize the synaptic connections
between cell types. The cultures were exposed to synaptic transmission
antagonists against NMDA and AMPA channels, which revealed significantly
different receptor profiles of adult and embryonic networks in vitro.
In addition, both embryonic and adult neurons were evaluated for NMDA
and AMPA channel subunit expression over five weeks in vitro. The
results established that neurons derived from embryonic tissue did
not express mature synaptic channels for several weeks in vitro under
defined conditions. Consequently, the embryonic response to synaptic
antagonists was significantly different than that of neurons derived
from adult tissue sources. These results are especially significant
because most studies reported with embryonic hippocampal neurons do
not begin at two to four weeks in culture. In addition, the utilization
of MEAs in lieu of patch-clamp electrophysiology avoided a large-scale,
labor-intensive study. These results establish the utility of this
unique hybrid system derived from adult hippocampal tissue in combination
with MEAs and offer a more appropriate representation of in vivo function
for drug discovery. It has application for neuronal development and
regeneration as well as for investigations into neurodegenerative
disease, traumatic brain injury, and stroke.
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Affiliation(s)
- Darin Edwards
- NanoScience Technology Center, University of Central Florida, 12424 Research Parkway, Orlando, Florida 32826, United States.,The Burnett School of Biomedical Sciences, University of Central Florida, UCF College of Medicine, 6850 Lake Nona Blvd, Orlando, Florida 32827, United States
| | - Frank Sommerhage
- NanoScience Technology Center, University of Central Florida, 12424 Research Parkway, Orlando, Florida 32826, United States
| | - Bonnie Berry
- NanoScience Technology Center, University of Central Florida, 12424 Research Parkway, Orlando, Florida 32826, United States.,The Burnett School of Biomedical Sciences, University of Central Florida, UCF College of Medicine, 6850 Lake Nona Blvd, Orlando, Florida 32827, United States
| | - Hanna Nummer
- NanoScience Technology Center, University of Central Florida, 12424 Research Parkway, Orlando, Florida 32826, United States
| | - Martina Raquet
- NanoScience Technology Center, University of Central Florida, 12424 Research Parkway, Orlando, Florida 32826, United States
| | - Brad Clymer
- NanoScience Technology Center, University of Central Florida, 12424 Research Parkway, Orlando, Florida 32826, United States
| | - Maria Stancescu
- NanoScience Technology Center, University of Central Florida, 12424 Research Parkway, Orlando, Florida 32826, United States
| | - James J Hickman
- NanoScience Technology Center, University of Central Florida, 12424 Research Parkway, Orlando, Florida 32826, United States.,The Burnett School of Biomedical Sciences, University of Central Florida, UCF College of Medicine, 6850 Lake Nona Blvd, Orlando, Florida 32827, United States
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Baghel MS, Thakur MK. Differential proteome profiling in the hippocampus of amnesic mice. Hippocampus 2017; 27:845-859. [PMID: 28449397 DOI: 10.1002/hipo.22735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 04/06/2017] [Accepted: 04/12/2017] [Indexed: 12/20/2022]
Abstract
Amnesia or memory loss is associated with brain aging and several neurodegenerative pathologies including Alzheimer's disease (AD). This can be induced by a cholinergic antagonist scopolamine but the underlying molecular mechanism is poorly understood. This study of proteome profiling in the hippocampus could provide conceptual insights into the molecular mechanisms involved in amnesia. To reveal this, mice were administered scopolamine to induce amnesia and memory impairment was validated by novel object recognition test. Using two-dimensional gel electrophoresis coupled with MALDI-MS/MS, we have analyzed the hippocampal proteome and identified 18 proteins which were differentially expressed. Out of these proteins, 11 were downregulated and 7 were upregulated in scopolamine-treated mice as compared to control. In silico analysis showed that the majority of identified proteins are involved in metabolism, catalytic activity, and cytoskeleton architectural functions. STRING interaction network analysis revealed that majority of identified proteins exhibit common association with Actg1 cytoskeleton and Vdac1 energy transporter protein. Furthermore, interaction map analysis showed that Fascin1 and Coronin 1b individually interact with Actg1 and regulate the actin filament dynamics. Vdac1 was significantly downregulated in amnesic mice and showed interaction with other proteins in interaction network. Therefore, we silenced Vdac1 in the hippocampus of normal young mice and found similar impairment in recognition memory of Vdac1 silenced and scopolamine-treated mice. Thus, these findings suggest that Vdac1-mediated disruption of energy metabolism and cytoskeleton architecture might be involved in scopolamine-induced amnesia.
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Affiliation(s)
- Meghraj Singh Baghel
- Department of Zoology, Biochemistry and Molecular Biology Laboratory, Centre of Advanced Study, Banaras Hindu University, Varanasi, 221005, India
| | - Mahendra Kumar Thakur
- Department of Zoology, Biochemistry and Molecular Biology Laboratory, Centre of Advanced Study, Banaras Hindu University, Varanasi, 221005, India
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