scholarly journals Quantitative Profiling of the Human Substantia Nigra Proteome from Laser-capture Microdissected FFPE Tissue

2020 ◽  
Vol 19 (5) ◽  
pp. 839-851 ◽  
Author(s):  
Eva Griesser ◽  
Hannah Wyatt ◽  
Sara Ten Have ◽  
Birgit Stierstorfer ◽  
Martin Lenter ◽  
...  
Keyword(s):  
Substantia Nigra ◽  
Solid Phase ◽  
Neuronal Cell ◽  
Alpha Synuclein ◽  
Ffpe Tissue ◽  
Specific Gene ◽  
Tissue Specimens ◽  
Laser Capture ◽  
Go Terms ◽  
Human Substantia Nigra

Laser-capture microdissection (LCM) allows the visualization and isolation of morphologically distinct subpopulations of cells from heterogeneous tissue specimens. In combination with formalin-fixed and paraffin-embedded (FFPE) tissue it provides a powerful tool for retrospective and clinically relevant studies of tissue proteins in a healthy and diseased context. We first optimized the protocol for efficient LCM analysis of FFPE tissue specimens. The use of SDS containing extraction buffer in combination with the single-pot solid-phase-enhanced sample preparation (SP3) digest method gave the best results regarding protein yield and protein/peptide identifications. Microdissected FFPE human substantia nigra tissue samples (∼3,000 cells) were then analyzed, using tandem mass tag (TMT) labeling and LC-MS/MS, resulting in the quantification of >5,600 protein groups. Nigral proteins were classified and analyzed by abundance, showing an enrichment of extracellular exosome and neuron-specific gene ontology (GO) terms among the higher abundance proteins. Comparison of microdissected samples with intact tissue sections, using a label-free shotgun approach, revealed an enrichment of neuronal cell type markers, such as tyrosine hydroxylase and alpha-synuclein, as well as proteins annotated with neuron-specific GO terms. Overall, this study provides a detailed protocol for laser-capture proteomics using FFPE tissue and demonstrates the efficiency of LCM analysis of distinct cell subpopulations for proteomic analysis using low sample amounts.

scholarly journals Discrimination of Aspergillosis, Mucormycosis, Fusariosis, and Scedosporiosis in Formalin-Fixed Paraffin-Embedded Tissue Specimens by Use of Multiple Real-Time Quantitative PCR Assays

2016 ◽  
Vol 54 (11) ◽  
pp. 2798-2803 ◽  
Author(s):  
Elham Salehi ◽  
Mohammad T. Hedayati ◽  
Jan Zoll ◽  
Haleh Rafati ◽  
Maryam Ghasemi ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Aspergillus Flavus ◽  
Ffpe Tissue ◽  
Content Type ◽  
Real Time Quantitative Pcr ◽  
Tissue Sections ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Tissue Specimens ◽  
Formalin Fixed

In a retrospective multicenter study, 102 formalin-fixed paraffin-embedded (FFPE) tissue specimens with histopathology results were tested. Two 4- to 5-μm FFPE tissue sections from each specimen were digested with proteinase K, followed by automated nucleic acid extraction. Multiple real-time quantitative PCR (qPCR) assays targeting the internal transcribed spacer 2 (ITS2) region of ribosomal DNA, using fluorescently labeled primers, was performed to identify clinically important genera and species of Aspergillus , Fusarium , Scedosporium , and the Mucormycetes . The molecular identification was correlated with results from histological examination. One of the main findings of our study was the high sensitivity of the automated DNA extraction method, which was estimated to be 94%. The qPCR procedure that was evaluated identified a range of fungal genera/species, including Aspergillus fumigatus , Aspergillus flavus , Aspergillus terreus , Aspergillus niger , Fusarium oxysporum , Fusarium solani , Scedosporium apiospermum , Rhizopus oryzae , Rhizopus microsporus , Mucor spp., and Syncephalastrum . Fusarium oxysporum and F. solani DNA was amplified from five specimens from patients initially diagnosed by histopathology as having aspergillosis. Aspergillus flavus , S. apiospermum , and Syncephalastrum were detected from histopathological mucormycosis samples. In addition, examination of four samples from patients suspected of having concomitant aspergillosis and mucormycosis infections resulted in the identification of two A. flavus isolates, one Mucor isolate, and only one sample having both R. oryzae and A. flavus . Our results indicate that histopathological features of molds may be easily confused in tissue sections. The qPCR assay used in this study is a reliable tool for the rapid and accurate identification of fungal pathogens to the genus and species levels directly from FFPE tissues.

Marked microglial reaction in normal aging human substantia nigra: correlation with extraneuronal neuromelanin pigment deposits

2007 ◽  
Vol 114 (4) ◽  
pp. 419-424 ◽  
Author(s):  
Thomas G. Beach ◽  
Lucia I. Sue ◽  
Douglas G. Walker ◽  
Lih Fen Lue ◽  
Donald J. Connor ◽  
...  
Keyword(s):  
Substantia Nigra ◽  
Normal Aging ◽  
Human Substantia Nigra

scholarly journals Anatomical and functional organization of the human substantia nigra and its connections

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Yu Zhang ◽  
Kevin Michel-Herve Larcher ◽  
Bratislav Misic ◽  
Alain Dagher
Keyword(s):  
Substantia Nigra ◽  
Functional Organization ◽  
Impulsive Choice ◽  
Behavioral Measures ◽  
Human Connectome Project ◽  
Motor Impulsivity ◽  
Cortical Regions ◽  
Value Coding ◽  
Decisional Impulsivity ◽  
Human Substantia Nigra

We investigated the anatomical and functional organization of the human substantia nigra (SN) using diffusion and functional MRI data from the Human Connectome Project. We identified a tripartite connectivity-based parcellation of SN with a limbic, cognitive, motor arrangement. The medial SN connects with limbic striatal and cortical regions and encodes value (greater response to monetary wins than losses during fMRI), while the ventral SN connects with associative regions of cortex and striatum and encodes salience (equal response to wins and losses). The lateral SN connects with somatomotor regions of striatum and cortex and also encodes salience. Behavioral measures from delay discounting and flanker tasks supported a role for the value-coding medial SN network in decisional impulsivity, while the salience-coding ventral SN network was associated with motor impulsivity. In sum, there is anatomical and functional heterogeneity of human SN, which underpins value versus salience coding, and impulsive choice versus impulsive action.

Nucleolin in Neurons of the Human Substantia Nigra

2018 ◽  
Vol 12 (2) ◽  
pp. 205-208
Author(s):  
D. A. Sufieva ◽  
V. V. Guselnikova ◽  
D. E. Korzhevskii
Keyword(s):  
Substantia Nigra ◽  
Human Substantia Nigra

scholarly journals High sensitivity sanger sequencing detection of BRAF mutations in metastatic melanoma FFPE tissue specimens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lauren Y. Cheng ◽  
Lauren E. Haydu ◽  
Ping Song ◽  
Jianyi Nie ◽  
Michael T. Tetzlaff ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Limit Of Detection ◽  
False Negative ◽  
High Sensitivity ◽  
Ffpe Tissue ◽  
Braf Mutations ◽  
Tissue Samples ◽  
Ffpe Samples ◽  
Droplet Pcr ◽  
Tissue Specimens

AbstractMutations in the BRAF gene at or near the p. V600 locus are informative for therapy selection, but current methods for analyzing FFPE tissue DNA generally have a limit of detection of 5% variant allele frequency (VAF), or are limited to the single variant (V600E). These can result in false negatives for samples with low VAFs due to low tumor content or subclonal heterogeneity, or harbor non-V600 mutations. Here, we show that Sanger sequencing using the NuProbe VarTrace BRAF assay, based on the Blocker Displacement Amplification (BDA) technology, is capable of detecting BRAF V600 mutations down to 0.20% VAF from FFPE lymph node tissue samples. Comparison experiments on adjacent tissue sections using BDA Sanger, immunohistochemistry (IHC), digital droplet PCR (ddPCR), and NGS showed 100% concordance among all 4 methods for samples with BRAF mutations at ≥ 1% VAF, though ddPCR did not distinguish the V600K mutation from the V600E mutation. BDA Sanger, ddPCR, and NGS (with orthogonal confirmation) were also pairwise concordant for lower VAF mutations down to 0.26% VAF, but IHC produced a false negative. Thus, we have shown that Sanger sequencing can be effective for rapid detection and quantitation of multiple low VAF BRAF mutations from FFPE samples. BDA Sanger method also enabled detection and quantitation of less frequent, potentially actionable non-V600 mutations as demonstrated by synthetic samples.

P3 THE EFFECT OF PARAQUAT ON ALPHA-SYNUCLEIN EXPRESSION IN THE SUBSTANTIA NIGRA OF THE RAT BRAIN

2006 ◽  
Vol 17 (5-6) ◽  
pp. 542
Author(s):  
M. ??mia??owska ◽  
J.M. Wiero??ska ◽  
B. Zi??ba ◽  
K. Kuter ◽  
T. Lenda ◽  
...  
Keyword(s):  
Substantia Nigra ◽  
Rat Brain ◽  
Alpha Synuclein

scholarly journals Histomorphological Effects of Nicotine on Selected Parts of the Brain of Adult Wistar Rats

2018 ◽  
Vol 25 (2) ◽  
Author(s):  
John Chukwuma Oyem ◽  
Emmanuel Igho Odokuma
Keyword(s):  
Substantia Nigra ◽  
Cell Count ◽  
Wistar Rats ◽  
Neuronal Cell ◽  
Oral Exposure ◽  
Control Group ◽  
Cell Diameter ◽  
Dependent Manner ◽  
Histological Techniques ◽  
Group 1

Nicotine has been defined as a potent parasympathomimetic alkaloid that accumulates in the roots and leaves of Nightshade family of plants Aim: This study was aimed at evaluating the effects of orally ingested nicotine in the histology of hippocampus, substantia nigra and cerebellum.Materials and Methods: Twenty four adult male Wistar rats (100g – 200g) were randomly divided into 4 groups (group 1 – group 4). Group 1 served as the control group, while groups 2 - 4 were the treated groups. Nicotine was diluted in water and 1ml of the different dosage (2mg/kg/day, 4mg/kg/day and 6mg/kg/day) were administered to the treated groups respectively with the aid of orogastric cannula for 42 days. Animals were euthanized by cervical dislocation at the end of 7, 21 and 42 days so as to demonstrate the dose and time dependant effect of this agent. Brain tissues were harvested, processed and stained using Haematoxylin and eosin according to standard histological techniques. Stained tissue images were captured using digital micrometer eyepiece and cell count was determined using stereological technique.Statistical analysis: Data obtained were subjected to statistical analysis with the use of statistical package for social sciences (SPSS version 20). Significant differences were obtained using One Way Analysis of Variance with a probability of  0.05 (95% confidence limit) and Tukeys post hoc  test was further used to determine the mean significant differences between specific groups.Results: Histological findings showed mild, moderate and severe hyperplasia in a dose and time dependant manner. However, observations from quantitative analysisalso revealed a dose and time dependant significant increase in neuronal cell count and cell diameter of the hippocampus, Substantia nigra and cerebellum.Conclusion: This study has demonstrated that oral exposure of Nicotine in rats display proliferative adaptive changes on the hippocampus, substantia nigra and cerebellum in a dose/time dependent manner.

scholarly journals Evaluation of the Xpert MTB/RIF Performance on Tissues: Potential Impact on Airborne Infection Isolation at a Tertiary Cancer Care Center

2018 ◽  
Vol 39 (4) ◽  
pp. 462-466 ◽  
Author(s):  
Tracy McMillen ◽  
Shauna C. Usiak ◽  
Liang Hua Chen ◽  
Luz Gomez ◽  
Peter Ntiamoah ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Limit Of Detection ◽  
Tertiary Care ◽  
Ffpe Tissue ◽  
Cancer Center ◽  
Oncology Patients ◽  
Tissue Samples ◽  
Airborne Infection ◽  
Potential Impact ◽  
Tissue Specimens

OBJECTIVESIn this study, we sought to evaluate the performance of the Xpert MTB/RIF (Cepheid) assay for the detection of Mycobacterium tuberculosis (MTB) complex DNA on fresh and formalin-fixed, paraffin-embedded (FFPE) tissue specimens from oncology patients in an area with a low prevalence of tuberculosis. We also aimed to retrospectively assess the potential impact of Xpert MTB/RIF on the duration of airborne infection isolation (AII).SETTINGA 473-bed, tertiary-care cancer center in New York City.DESIGNA total of 203 tissue samples (101 FFPE and 102 fresh) were tested using Xpert MTB/RIF, including 133 pulmonary tissue samples (65.5%) and 70 extrapulmonary tissue samples (34.5%). Acid-fast bacilli (AFB) culture was used as the diagnostic gold standard. The limit of detection (LOD) and reproducibility were also evaluated for both samples types using contrived specimens. The potential impact of the Xpert MTB PCR assay on tissue samples from AII patients on AII duration was retrospectively assessed.RESULTSUsing the Xpert MTB/RIF for fresh tissue specimens, the sensitivity was 50% (95% CI, 1.3%–98.7%) and the specificity was 99% (95% CI, 94.5%–99.9%). For FFPE tissue specimens, the sensitivity was 100% (95% CI, 63.1%–100%) and the specificity was 98.3% (95% CI, 95.5%–100%. The LOD was 103 colony-forming units (CFU)/mL for both fresh and FFPE tissue specimens, and the Xpert MTB/RIF was 100% reproducible at concentrations 10 times that of the LOD. With an expected turnaround time of 24 hours, the Xpert MTB PCR could decrease the duration of AII from a median of 8 days to a median of 1 day.CONCLUSIONSThe Xpert MTB/RIF assay offers a valid option for ruling out Mycobacterium tuberculosis complex (MTBC) on tissue samples from oncology patients and for minimizing AII resource utilization.Infect Control Hosp Epidemiol 2018;39:462–466

Distribution of [3H]SCH 23390 Binding Sites in the Human Substantia Nigra

1991 ◽  
pp. 93-94
Author(s):  
F. Thibaut ◽  
E.C. Hirsch ◽  
R. Raisman ◽  
F. Javoy-Agid ◽  
Y. Agid
Keyword(s):  
Substantia Nigra ◽  
Binding Sites ◽  
Sch 23390 ◽  
Human Substantia Nigra
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