scholarly journals Comparing the Expression of Genes Related to Serotonin (5-HT) in C57BL/6J Mice and Humans Based on Data Available at the Allen Mouse Brain Atlas and Allen Human Brain Atlas

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
C. A. Acevedo-Triana ◽  
L. A. León ◽  
F. P. Cardenas
Keyword(s):  
Human Brain ◽  
Mouse Brain ◽  
Expression Patterns ◽  
Brain Atlas ◽  
Expression Data ◽  
Expression Of Genes ◽  
High Degree ◽  
The Relationship ◽  
Allen Mouse Brain Atlas

Brain atlases are tools based on comprehensive studies used to locate biological characteristics (structures, connections, proteins, and gene expression) in different regions of the brain. These atlases have been disseminated to the point where tools have been created to store, manage, and share the information they contain. This study used the data published by the Allen Mouse Brain Atlas (2004) for mice (C57BL/6J) and Allen Human Brain Atlas (2010) for humans (6 donors) to compare the expression of serotonin-related genes. Genes of interest were searched for manually in each case (in situ hybridization for mice and microarrays for humans), normalized expression data (z-scores) were extracted, and the results were graphed. Despite the differences in methodology, quantification, and subjects used in the process, a high degree of similarity was found between expression data. Here we compare expression in a way that allows the use of translational research methods to infer and validate knowledge. This type of study allows part of the relationship between structures and functions to be identified, by examining expression patterns and comparing levels of expression in different states, anatomical correlations, and phenotypes between different species. The study concludes by discussing the importance of knowing, managing, and disseminating comprehensive, open-access studies in neuroscience.

scholarly journals Quantitative gene expression profiling of mouse brain regions reveals differential transcripts conserved in human and affected in disease models

2008 ◽  
Vol 33 (2) ◽  
pp. 170-179 ◽  
Author(s):  
Camille Brochier ◽  
Marie-Claude Gaillard ◽  
Elsa Diguet ◽  
Nicolas Caudy ◽  
Carole Dossat ◽  
...  
Keyword(s):  
Gene Expression ◽  
Substantia Nigra ◽  
Mouse Model ◽  
Human Brain ◽  
Mouse Brain ◽  
Wild Type Mouse ◽  
Brain Regions ◽  
Expression Data ◽  
Brain Functions

Using serial analysis of gene expression, we collected quantitative transcriptome data in 11 regions of the adult wild-type mouse brain: the orbital, prelimbic, cingulate, motor, somatosensory, and entorhinal cortices, the caudate-putamen, the nucleus accumbens, the thalamus, the substantia nigra, and the ventral tegmental area. With >1.2 million cDNA tags sequenced, this database is a powerful resource to explore brain functions and disorders. As an illustration, we performed interregional comparisons and found 315 differential transcripts. Most of them are poorly characterized and 20% lack functional annotation. For 78 differential transcripts, we provide independent expression level measurements in mouse brain regions by real-time quantitative RT-PCR. We also show examples where we used in situ hybridization to achieve infrastructural resolution. For 30 transcripts, we next demonstrated that regional enrichment is conserved in the human brain. We then quantified the expression levels of region-enriched transcripts in the R6/2 mouse model of Huntington disease and the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of Parkinson disease and observed significant alterations in the striatum, cerebral cortex, thalamus and substantia nigra of R6/2 mice and in the striatum of MPTP-treated mice. These results show that the gene expression data provided here for the mouse brain can be used to explore pathophysiological models and disclose transcripts differentially expressed in human brain regions.

The relationship between cell proliferation and the transcription of the nuclear oncogenes c-myc, c-myb and c-ets-1 during feather morphogenesis in the chick embryo

Development ◽  
1991 ◽  
Vol 111 (3) ◽  
pp. 699-713 ◽  
Author(s):  
X. Desbiens ◽  
C. Queva ◽  
T. Jaffredo ◽  
D. Stehelin ◽  
B. Vandenbunder
Keyword(s):  
Cell Proliferation ◽  
Endothelial Cells ◽  
Spatial Distribution ◽  
Chick Embryo ◽  
Expression Patterns ◽  
S Phase ◽  
Skin Morphogenesis ◽  
Dermal Cells ◽  
The Relationship

We have described the expression of three nuclear protooncogenes, c-myc, c-myb and c-ets-1 during feather morphogenesis in the chick embryo. In parallel with the expression patterns obtained by in situ hybridization, we have mapped the spatial distribution of S-phase cells by monitoring the incorporation of 5-bromodeoxyuridine. We do not detect c-myc or c-myb transcripts during the early stages when S-phase cells are scattered in the dermis and in the epidermis. Rather c-ets-1 transcripts are abundant in the dermal cells which divide and accumulate under the uniform epidermis. At the onset of the formation of the feather bud, cells within each rudiment cease DNA replicative activities and c-myc transcripts are detected both in the epidermis and in the underlying dermis. This expression precedes the reentry into the S phase. The transcription of c-myb, which has been previously tightly linked to hemopoietic cells is also detected in the developing skin. This expression is essentially located in proliferating epidermal cells on and after the beginning of feather outgrowth. As feather outgrowth proceeds, the distribution of c-myc and c-myb transcripts is restricted to the highly proliferating epidermis. In contrast c-ets-1 transcripts are never detected in the epidermis. During the later stages of skin morphogenesis, the transcription of c-ets-1 is restricted to the endothelial cells of blood vessels, as previously described. We suggest that the differential expression of these nuclear oncogenes reflects the activation of different mitotic controlling pathways during the development of the skin.

scholarly journals Differential Expression of the Carbonic Anhydrase Genes for CA VII (Car7) And CA-RP VIII (Car8) in Mouse Brain

1997 ◽  
Vol 45 (5) ◽  
pp. 657-662 ◽  
Author(s):  
Maha M. Lakkis ◽  
K. Sue O'Shea ◽  
Richard E. Tashian
Keyword(s):  
Carbonic Anhydrase ◽  
Mouse Brain ◽  
Expression Patterns ◽  
Granular Cell ◽  
Cortical Layer ◽  
Cell Layers ◽  
High Level ◽  
The Brain ◽  
Lower Expression

The spatial expression patterns of the two α-carbonic anhydrase genes, CA VII and CA-RP VIII (called Car7 and Car8 in the mouse) were examined in the mouse brain by in situ hybridization. These two genes are the most highly conserved evolutionarily among the mammalian α-CAs. Both genes showed a similarly wide expression pattern in the brain. In the cerebrum, mRNA expression was detected in the pia, choroid plexus, and neurons of the cortical layer, thalamus, and medial habenulae. A high level of expression appeared in the pyramidal and granular cells of the hippocampus. In the cerebellum, both Car7 and Car8 were transcribed to different degrees in the Purkinje cells, and a lower expression level occured in the molecular and granular cell layers. Transcription signals for both genes were excluded from the white matter regions.

scholarly journals NeuroD2 and neuroD3: distinct expression patterns and transcriptional activation potentials within the neuroD gene family.

1996 ◽  
Vol 16 (10) ◽  
pp. 5792-5800 ◽  
Author(s):  
M B McCormick ◽  
R M Tamimi ◽  
L Snider ◽  
A Asakura ◽  
D Bergstrom ◽  
...  
Keyword(s):  
Nervous System ◽  
Transcriptional Activation ◽  
Expression Patterns ◽  
Predicted Amino Acid Sequence ◽  
Helix Loop Helix ◽  
Related Family ◽  
New Genes ◽  
Bhlh Proteins ◽  
High Degree

We have identified two new genes, neuroD2 and neuroD3, on the basis of their similarity to the neurogenic basic-helix-loop-helix (bHLH) gene neuroD. The predicted amino acid sequence of neuroD2 shows a high degree of homology to neuroD and MATH-2/NEX-1 in the bHLH region, whereas neuroD3 is a more distantly related family member. neuroD3 is expressed transiently during embryonic development, with the highest levels of expression between days 10 and 12. neuroD2 is initially expressed at embryonic day 11, with persistent expression in the adult nervous system. In situ and Northern (RNA) analyses demonstrate that different regions of the adult nervous system have different relative amounts of neuroD and neuroD2 RNA. Similar to neuroD, expression of neuroD2 in developing Xenopus laevis embryos results in ectopic neurogenesis, indicating that neuroD2 mediates neuronal differentiation. Transfection of vectors expressing neuroD and neuroD2 into P19 cells shows that both can activate expression through simple E-box-driven reporter constructs and can activate a reporter driven by the neuroD2 promoter region, but the GAP-43 promoter is preferentially activated by neuroD2. The noncongruent expression pattern and target gene specificity of these highly related neurogenic bHLH proteins make them candidates for conferring specific aspects of the neuronal phenotype.

scholarly journals PubAnatomy 3D: Integrating Medline Exploration with the Allen Mouse Brain Atlas

2013 ◽  
Vol 7 ◽  
Author(s):  
Yang Gang ◽  
Dai Manhong ◽  
Song Jean ◽  
Mirel BarBara ◽  
Meng Fan
Keyword(s):  
Mouse Brain ◽  
Brain Atlas ◽  
Allen Mouse Brain Atlas

scholarly journals Circulating Clonally Expanded T Cells Reflect Functions of Tumor Infiltrating T Cells

2020 ◽  
Author(s):  
Liliana Lucca ◽  
Pierre-Paul Axisa ◽  
Benjamin Lu ◽  
Brian Harnett ◽  
Shlomit Jessel ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Metastatic Melanoma ◽  
Cell Function ◽  
Expression Patterns ◽  
Immune Monitoring ◽  
T Cell Response ◽  
Circulating T Cells ◽  
High Degree ◽  
The Relationship

AbstractUnderstanding the relationship between tumor and peripheral immune environments could allow longitudinal immune monitoring in cancer. Here, we examined whether T cells that share the same TCRαβ and are found in both tumor and blood can be interrogated to gain insight into the ongoing tumor T cell response. Paired transcriptome and TCRαβ repertoire of circulating and tumor-infiltrating T cells were analyzed from matched tumor and blood from patients with metastatic melanoma at the single cell level. We found that in circulating T cells matching clonally expanded tumor-infiltrating T cells (circulating TILs), gene signatures of effector functions, but not terminal exhaustion, reflect those observed in the tumor. In contrast, features of exhaustion are displayed predominantly by T cells present only in tumor. Finally, genes associated with a high degree of blood-tumor TCR sharing were overexpressed in tumor tissue after immunotherapy. These data demonstrate that circulating TILs, identified by TCRs shared with T cells in tumors, have unique transcriptional expression patterns that may have utility for the interrogation of T cell function in cancer immunotherapy.SummaryCombining transcriptomic and TCRαβ repertoire analysis of circulating and tumor-infiltrating CD8 T cells from patients with metastatic melanoma, we identify a blood-based population with effector properties that reflect those of clonally related tumor-resident T cells.

scholarly journals SpaGE: Spatial Gene Enhancement using scRNA-seq

2020 ◽  
Vol 48 (18) ◽  
pp. e107-e107 ◽  
Author(s):  
Tamim Abdelaal ◽  
Soufiane Mourragui ◽  
Ahmed Mahfouz ◽  
Marcel J T Reinders
Keyword(s):  
Spatial Information ◽  
Spatial Configuration ◽  
Single Cells ◽  
Large Datasets ◽  
Brain Atlas ◽  
Hybridization Data ◽  
Transcriptome Expression ◽  
Whole Transcriptome ◽  
Allen Mouse Brain Atlas

Abstract Single-cell technologies are emerging fast due to their ability to unravel the heterogeneity of biological systems. While scRNA-seq is a powerful tool that measures whole-transcriptome expression of single cells, it lacks their spatial localization. Novel spatial transcriptomics methods do retain cells spatial information but some methods can only measure tens to hundreds of transcripts. To resolve this discrepancy, we developed SpaGE, a method that integrates spatial and scRNA-seq datasets to predict whole-transcriptome expressions in their spatial configuration. Using five dataset-pairs, SpaGE outperformed previously published methods and showed scalability to large datasets. Moreover, SpaGE predicted new spatial gene patterns that are confirmed independently using in situ hybridization data from the Allen Mouse Brain Atlas.

285 VIABILITY AND GENE EXPRESSION OF MESENCHYMAL STEM CELLS CRYOPRESERVED WITH DIFFERENT CRYOPROTECTANTS

2008 ◽  
Vol 20 (1) ◽  
pp. 222 ◽  
Author(s):  
M. K. Kim ◽  
S. A. Ock ◽  
B. G. Jeon ◽  
J. H. Cho ◽  
G. J. Rho
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Expression Patterns ◽  
Long Term Storage ◽  
Expression Of Genes ◽  
Cell Tissue ◽  
Fetal Bovine

Long-term storage of stem cells with self-renewal plays a pivotal role in cell tissue engineering, which could be a novel option for improving regenerative diseases. However, the choice of a selective cryoprotectant is still to be addressed. Dimethyl sulfoxide (DMSO), which in current practice is the most widely used as a cryoprotectant for cell freezing, is known to have toxic side effects (Wang et al. 2007 Cryobiology 55, 60–65). In this study, therefore, the effect of two different cryoprotectants, used alone or in combination, on frozen–thawed porcine mesenchymal stem cells (MSCs) was investigated by evaluating their viability, apoptosis, and gene expression patterns. MSCs isolated from bone marrow were cultured in advanced Dulbecco's modified Eagle medium (ADMEM) supplemented with 10% fetal bovine serum (FBS) and characterized by the expression of alkaline phosphatase (AP) activity and cell-surface antigen profiles (CD105 as positive, CD45 and CD133 as negative markers). Subconfluent cultures of MSCs (1 � 106 cells mL–1) at 4–5 passages were equilibrated in different cryoprotectants: (1)ADMEM supplemented with 10% DMSO, (2) ADMEM supplemented with 1.5 m ethylene glycol (EG), and (3) ADMEM supplemented with 0.75 m EG and 5% DMSO, and frozen in a programmable freezer. The straws were cooled at –4�C min–1 from 25�C to –7�C. After being seeded, the straws were further cooled to –35�C at a –0.6�C min–1 ramp rate, and then immediately plunged into LN2 and stored at least a week. After thawing at 37�C in a water bath, viability and apoptosis of cells were analyzed by flow cytometry using an In Situ Cell Death Detection kit (Roche, Mannheim, Germany). Expression of HSP70, Nanog, and β-actin was analyzed by Western blotting and quantitative real-time polymerase chain reaction (qRT-PCR), and compared to that of non-cryopreserved MSCs. Doubling time of cryopreserved MSCs was higher than for non-cryopreserved MSCs. There were no significant differences among cryopreserved groups. The rates of viability and apoptosis of non-cryopreserved MSCs (91% and 4.71%, respectively) was significantly (P < 0.05) higher than for MSCs cryopreserved with 10% DMSO, 1.5 m EG, or the 0.75 m EG and 5% DMSO mixture (71.78% and 3.45%, 70.09% and 3.22%, 68.97% and 2.42%, respectively), but the rates among different cryopreserved treatments did not differ. After thawing, expression of HSP70, Nanog, and β-actin in cryopreserved MSCs showed patterns similar to those of non-cryopreserved MSCs. In conclusion, the present study indicates that EG is an alternative cryoprotectant for cryopreservation of porcine MSCs. Further studies are needed to evaluate the possible effects on the expression of genes related to viability and apoptosis in MSCs cryopreserved with different cryoprotectants.

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