Glycine receptors in the striatum, globus pallidus, and substantia nigra of the human brain: An immunohistochemical study

2007 ◽  
Vol 502 (6) ◽  
pp. 1012-1029 ◽  
Author(s):  
Henry J. Waldvogel ◽  
Kristin Baer ◽  
Kathryn L. Allen ◽  
Mark I. Rees ◽  
Richard L.M. Faull
Keyword(s):  
Substantia Nigra ◽  
Human Brain ◽  
Globus Pallidus ◽  
Immunohistochemical Study ◽  
Glycine Receptors

scholarly journals DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation

2017 ◽  
Author(s):  
Elizabeth Nacheva ◽  
Katya Mokretar ◽  
Aynur Soenmez ◽  
Alan M Pittman ◽  
Colin Grace ◽  
...  
Keyword(s):  
Substantia Nigra ◽  
Human Brain ◽  
Frontal Cortex ◽  
Genome Sequencing ◽  
Copy Number ◽  
Dna Isolation ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Whole Genome ◽  
Salting Out

AbstractPotential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under different conditions, and salting-out. We first analysed DNA using array CGH, which revealed a striking wave pattern suggesting primarily GC-rich cerebellar losses, even against matched frontal cortex DNA, with a similar pattern on a SNP array. The aCGH changes varied with the isolation protocol. Droplet digital PCR of two genes also showed protocol-dependent losses. Whole genome sequencing showed GC-dependent variation in coverage with spin column isolation from cerebellum. We also extracted and sequenced DNA from substantia nigra using salting-out and phenol / chloroform. The mtDNA copy number, assessed by reads mapping to the mitochondrial genome, was higher in substantia nigra when using phenol / chloroform. We thus provide evidence for significant method-dependent bias in DNA isolation from human brain, as reported in rat tissues. This may contribute to array “waves”, and could affect copy number determination, particularly if mosaicism is being sought, and sequencing coverage. Variations in isolation protocol may also affect apparent mtDNA abundance.

scholarly journals A pH-eQTL interaction at the RIT2-SYT4 Parkinson's disease risk locus in the substantia nigra

2020 ◽  
Author(s):  
Sejal Patel ◽  
Derek Howard ◽  
Leon French
Keyword(s):  
Gene Expression ◽  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Substantia Nigra ◽  
Human Brain ◽  
Disease Risk ◽  
Brain Regions ◽  
Dopamine Neurons ◽  
Postmortem Human Brain ◽  
Increased Risk

BACKGROUND: Parkinson's disease (PD) causes severe motor and cognitive disabilities that result from the progressive loss of dopamine neurons in the substantia nigra. The rs12456492 variant in the RIT2 gene has been repeatedly associated with increased risk for Parkinson's disease. From a transcriptomic perspective, a meta-analysis found that RIT2 gene expression is correlated with pH in the human brain. OBJECTIVE: To assess pH associations at the RIT2-SYT4 locus. METHODS: Linear models to examine two datasets that assayed rs12456492, gene expression, and pH in the postmortem human brain. RESULTS: Using the BrainEAC dataset, we replicate the positive correlation between RIT2 gene expression and pH in the human brain. Furthermore, we found that the relationship between expression and pH is influenced by rs12456492. When tested across ten brain regions, this interaction is specifically found in the substantia nigra. A similar association was found for the co-localized SYT4 gene. In addition, SYT4 associations are stronger in a combined model with both genes, and the SYT4 interaction appears to be specific to males. In the GTEx dataset, the pH associations involving rs12456492 and expression of either SYT4 and RIT2 was not seen. This null finding may be due to the short postmortem intervals (PMI) of the GTEx tissue samples. In the BrainEAC data, we tested the effect of PMI and only observed the interactions in the longer PMI samples. CONCLUSIONS: These previously unknown associations suggest novel mechanistic roles for rs12456492, RIT2, and SYT4 in the regulation of pH in the substantia nigra.

An immunohistochemical study of pro-somatostatin-derived peptides in the human brain

Neuroscience ◽  
1987 ◽  
Vol 22 (3) ◽  
pp. 781-800 ◽  
Author(s):  
C. Bouras ◽  
P.J. Magistretti ◽  
J.H. Morrison ◽  
J. Constantinidis
Keyword(s):  
Human Brain ◽  
Immunohistochemical Study

Subthalamo-Pallidal Circuit

2017 ◽  
pp. 143-150
Author(s):  
Charles J. Wilson
Keyword(s):  
Basal Ganglia ◽  
Substantia Nigra ◽  
Globus Pallidus ◽  
Subthalamic Nucleus ◽  
Substantia Nigra Pars Reticulata ◽  
Modern Methods

The subthalamo-pallidal system constitutes the second layer of circuitry in the basal ganglia, downstream of the striatum. It consists of four nuclei. Two of them, the external segment of the globus pallidus (GPe) and subthalamic nucleus (STN), make their connections primarily within the basal ganglia. The others, the internal segment of the globus pallidus (GPi) and the substantia nigra pars reticulata (SNr), are the output nuclei of the basal ganglia. Collectively, their axons distribute collaterals to all the targets of the basal ganglia. Rare interneurons have been reported in each of them from studies of Golgi-stained preparations, but they have not so far been confirmed using more modern methods. The circuit as described here is based primarily on studies of the axonal arborizations of neurons stained individually by intracellular or juxtacellular labeling.

Preliminary observations of transverse relaxation rates obtained at 3 Tesla from the substantia nigra of adult normal human brain

1995 ◽  
Vol 8 (1) ◽  
pp. 25-27 ◽  
Author(s):  
J. A. Helpern ◽  
J. M. Gorell ◽  
J. C. Deniau ◽  
K. M. A. Welch ◽  
R. J. Ordidge
Keyword(s):  
Substantia Nigra ◽  
Human Brain ◽  
3 Tesla ◽  
Relaxation Rates ◽  
Transverse Relaxation ◽  
Normal Human Brain ◽  
Normal Human
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