Network analysis of adhesion/growth-regulatory galectins and their binding sites in adult chicken retina and choroid

AbstractEnkephalin peptides are present in the retina of several vertebrate species. In the avian retina, enkephalin immunoreactivity is primarily localized to a population of amacrine cells. In the present study, we determined the localization of cells expressing preproenkephalin (PPE) mRNA, which encodes the precursor of enkephalin peptides, in adult as well as in embryonic chicken retinas. The localization of PPE mRNA-expressing cells to the proximal inner nuclear layer (INL) in the adult chicken retina is similar to that of enkephalin-immunoreactive cells observed in previous studies, indicating that amacrine cells expressing PPE mRNA synthesize Met5- and Leu5-enkephalin peptides and related extended forms. Specific hybridization signal is absent in retinas at embryonic day (E) 11, but it is detected in retinas at E 15 and at hatching. PPE mRNA-expressing cells at these ages are located in the proximal INL, and they can be classified as amacrine cells on the basis of their soma size and laminar position. These findings confirm and extend previous observations on the presence of opioid peptides in amacrine cells of the chicken retina. The presence of PPE mRNA at embryonic ages, together with the evidence that enkephalins influence developmental processes, suggests that these peptides modulate retinal maturation in birds.

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MiR-190a Potentially Ameliorates Postoperative Cognitive Dysfunction by Regulating Tiam1

10.21203/rs.2.10148/v3 ◽

2019 ◽

Author(s):

Qiang Liu ◽

Aisheng Hou ◽

Yongyi Zhang ◽

Ying Guo ◽

Jingjing Li ◽

...

Keyword(s):

Network Analysis ◽

Cognitive Dysfunction ◽

Binding Sites ◽

Postoperative Cognitive Dysfunction ◽

The Elderly ◽

Mirna Microarray ◽

Post Surgery ◽

Highly Correlated ◽

Microarray Datasets ◽

Predictive Indicator

Abstract Postoperative cognitive dysfunction (POCD) affects a large number of post-surgery patients, especially for the elderly. However, the etiology of this neurocognitive disorder is largely unknown. Even if several studies have reported a small number of miRNAs as the essential modulatory factors in POCD, these findings are still rather limited. In this study, we used two miRNA microarray datasets to perform differential expression analyses of miRNAs in the hippocampus of POCD model mice. We found that nine miRNAs showed significant associations with POCD in both datasets. Among these miRNAs, mmu-miR-190a-3p was the most significant one. By performing weighted gene co-expression network analysis, we found 25 co-expression modules, of which mmu-miR-190a-3p was significantly anti-correlated with the red module. Moreover, in this red module, 314 genes were significantly enriched in four pathways such as axon guidance and calcium signaling pathway, which are well-documented to be associated with psychiatric disorders and brain development. Also, 169 of the 314 genes were highly correlated with mmu-miR-190a-3p, and four genes (Sphkap, Arhgef25, Tiam1, and Ntrk3) had putative binding sites at 3'-UTR of mmu-miR-190a-3p. Based on protein-protein network analysis, we detected that Tiam1 was a central gene regulated by the mmu-miR-190a-3p. Taken together, we conclude that mmu-miR-190a-3p is involved in the etiology of POCD and may serve as a novel predictive indicator for POCD.

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MiR-190a Potentially Ameliorates Postoperative Cognitive Dysfunction by Regulating Tiam1

10.21203/rs.2.10148/v4 ◽

2019 ◽

Author(s):

Qiang Liu ◽

Aisheng Hou ◽

Yongyi Zhang ◽

Ying Guo ◽

Jingjing Li ◽

...

Keyword(s):

Network Analysis ◽

Cognitive Dysfunction ◽

Binding Sites ◽

Postoperative Cognitive Dysfunction ◽

The Elderly ◽

Mirna Microarray ◽

Post Surgery ◽

Highly Correlated ◽

Microarray Datasets ◽

Predictive Indicator

Abstract Postoperative cognitive dysfunction (POCD) affects a large number of post-surgery patients, especially for the elderly. However, the etiology of this neurocognitive disorder is largely unknown. Even if several studies have reported a small number of miRNAs as the essential modulatory factors in POCD, these findings are still rather limited. In this study, we used two miRNA microarray datasets to perform differential expression analyses of miRNAs in the hippocampus of POCD model mice. We found that nine miRNAs showed significant associations with POCD in both datasets. Among these miRNAs, mmu-miR-190a-3p was the most significant one. By performing weighted gene co-expression network analysis, we found 25 co-expression modules, of which mmu-miR-190a-3p was significantly anti-correlated with the red module. Moreover, in this red module, 314 genes were significantly enriched in four pathways such as axon guidance and calcium signaling pathway, which are well-documented to be associated with psychiatric disorders and brain development. Also, 169 of the 314 genes were highly correlated with mmu-miR-190a-3p, and four genes (Sphkap, Arhgef25, Tiam1, and Ntrk3) had putative binding sites at 3'-UTR of mmu-miR-190a-3p. Based on protein-protein network analysis, we detected that Tiam1 was a central gene regulated by the mmu-miR-190a-3p. Taken together, we conclude that mmu-miR-190a-3p is involved in the etiology of POCD and may serve as a novel predictive indicator for POCD.

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Characterization of the C-protein from posterior latissimus dorsi muscle of the adult chicken: heterogeneity within a single sarcomere.

The Journal of Cell Biology ◽

10.1083/jcb.96.1.297 ◽

1983 ◽

Vol 96 (1) ◽

pp. 297-300 ◽

Cited By ~ 36

Author(s):

F C Reinach ◽

T Masaki ◽

D A Fischman

Keyword(s):

Binding Sites ◽

Latissimus Dorsi ◽

Protein Isoforms ◽

Fiber Types ◽

Adult Chicken ◽

C Protein ◽

Molecular Weights ◽

Anterior Latissimus Dorsi ◽

Fast Twitch

Specific isoforms of myofibrillar proteins are expressed in different muscles and in various fiber types within a single muscle. We have isolated and characterized monoclonal antibodies against C-proteins from slow tonic (anterior latissimus dorsi, ALD) and fast twitch (pectoralis major) muscles of the chicken. Although the antibody against "fast" C-protein (MF-1) did not bind to the "slow" isoform and the antibody to the "slow" C-protein (ALD-66) did not bind to the "fast" isoform, we observed that both antibodies bound C-protein from the posterior latissimus dorsi (PLD) muscle. Here we demonstrate that in the PLD muscle the binding sites of these two antibodies reside in two different C-protein isoforms which have different molecular weights and can be separated by hydroxylapatite column chromatography. Since we have shown previously that both these antibodies stain all myofibers and myofibrils derived from PLD muscle, we conclude that all myofibers in this muscle contain both isoforms with all sarcomeres.

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Immunolocalization of TRPC channel subunits 1 and 4 in the chicken retina

Visual Neuroscience ◽

10.1017/s0952523803204107 ◽

2003 ◽

Vol 20 (4) ◽

pp. 453-463 ◽

Cited By ~ 22

Author(s):

SCOTT CROUSILLAC ◽

MICHELLE LEROUGE ◽

MICHELE RANKIN ◽

EVANNA GLEASON

Keyword(s):

Transient Receptor Potential ◽

Trp Channels ◽

Expression Patterns ◽

Plexiform Layer ◽

Cell Types ◽

Retinal Cell ◽

Inner Plexiform Layer ◽

Double Labeling ◽

Adult Chicken ◽

Chicken Retina

In the vertebrate retina, multiple cell types express G protein-coupled receptors linked to the IP3 signaling pathway. The signaling engendered by activation of this pathway can involve activation of calcium permeable transient receptor potential (TRP) channels. To begin to understand the role of these channels in the retina, we undertake an immunocytochemical localization of two TRP channel subunits. Polyclonal antibodies raised against mammalian TRPC1 and TRPC4 are used to localize the expression of these proteins in sections of the adult chicken retina. Western blot analysis indicates that these antibodies recognize avian TRPC1 and TRPC4. TRPC1 labeling is almost completely confined to the inner plexiform layer (IPL) where it labels a subset of processes that ramify in three broad stripes. Occasionally, cell bodies are labeled. These can be found in the inner nuclear layer (INL) proximal to the IPL, the IPL, and the ganglion cell layer (GCL). Double-labeling experiments using a polyclonal antibody that recognizes brain nitric oxide synthase (bNOS) in the chicken indicate that many of the TRPC1-positive processes and cell bodies also express bNOS. Labeling with the TRPC4 antibody was much more widespread with some degree of labeling found in all layers of the retina. TRPC4 immunoreactivity was found in the photoreceptor layer, in the outer plexiform layer (OPL), in radially oriented cells in the INL, diffusely in the IPL, and in vertically oriented elements below the GCL. Double-labeling experiments with a monoclonal antibody raised against vimentin indicate that the TRPC4-positive structures in the INL and below the GCL are Müller cells. Thus, TRPC1 and TRPC4 subunits have unique expression patterns in the adult chicken retina. The distributions of these two subunits indicate that different retinal cell types express TRP channels containing different subunits.

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MiR-190a Potentially Ameliorates Postoperative Cognitive Dysfunction by Regulating Tiam1

10.21203/rs.2.10148/v2 ◽

2019 ◽

Author(s):

Qiang Liu ◽

Aisheng Hou ◽

Yongyi Zhang ◽

Ying Guo ◽

Jingjing Li ◽

...

Keyword(s):

Network Analysis ◽

Cognitive Dysfunction ◽

Binding Sites ◽

Postoperative Cognitive Dysfunction ◽

The Elderly ◽

Mirna Microarray ◽

Post Surgery ◽

Highly Correlated ◽

Microarray Datasets ◽

Predictive Indicator

Abstract Postoperative cognitive dysfunction (POCD) affects a large number of post-surgery patients, especially for the elderly. However, the etiology of this neurocognitive disorder is largely unknown. Even if several studies have reported a small number of miRNAs as the essential modulatory factors in POCD, these findings are still rather limited. In this study, we used two miRNA microarray datasets to perform differential expression analyses of miRNAs in the hippocampus of POCD model mice. We found that nine miRNAs showed significant associations with POCD in both datasets. Among these miRNAs, mmu-miR-190a-3p was the most significant one. By performing weighted gene co-expression network analysis, we found 25 co-expression modules, of which mmu-miR-190a-3p was significantly anti-correlated with the red module. Moreover, in this red module, 314 genes were significantly enriched in four pathways such as axon guidance and calcium signaling pathway, which are well-documented to be associated with psychiatric disorders and brain development. Also, 169 of the 314 genes were highly correlated with mmu-miR-190a-3p, and four genes (Sphkap, Arhgef25, Tiam1, and Ntrk3) had putative binding sites at 3'-UTR of mmu-miR-190a-3p. Based on protein-protein network analysis, we detected that Tiam1 was a central gene regulated by the mmu-miR-190a-3p. Taken together, we conclude that mmu-miR-190a-3p is involved in the etiology of POCD and may serve as a novel predictive indicator for POCD.

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A Derived Network-Based Interferon-Related Signature of Human Macrophages Responding toMycobacterium tuberculosis

BioMed Research International ◽

10.1155/2014/713071 ◽

2014 ◽

Vol 2014 ◽

pp. 1-16 ◽

Cited By ~ 2

Author(s):

Kang Wu ◽

Hai Fang ◽

Liang-Dong Lyu ◽

Douglas B. Lowrie ◽

Ka-Wing Wong ◽

...

Keyword(s):

Network Analysis ◽

Binding Sites ◽

Direct Interaction ◽

Host Responses ◽

Human Macrophage ◽

Human Macrophages ◽

Transcriptional Signature ◽

Highly Expressed Genes ◽

Induced Genes ◽

Human Infections

Network analysis of transcriptional signature typically relies on direct interaction between two highly expressed genes. However, this approach misses indirect and biological relevant interactions through a third factor (hub). Here we determine whether a hub-based network analysis can select an improved signature subset that correlates with a biological change in a stronger manner than the original signature. We have previously reported an interferon-related transcriptional signature (THP1r2Mtb-induced) fromMycobacterium tuberculosis(M. tb)-infected THP-1 human macrophage. We selected hub-connected THP1r2Mtb-induced genes into the refined network signature TMtb-iNet and grouped the excluded genes into the excluded signature TMtb-iEx. TMtb-iNet retained the enrichment of binding sites of interferon-related transcription factors and contained relatively more interferon-related interacting genes when compared to THP1r2Mtb-induced signature. TMtb-iNet correlated as strongly as THP1r2Mtb-induced signature on a public transcriptional dataset of patients with pulmonary tuberculosis (PTB). TMtb-iNet correlated more strongly in CD4+and CD8+T cells from PTB patients than THP1r2Mtb-induced signature and TMtb-iEx. When TMtb-iNet was applied to data during clinical therapy of tuberculosis, it resulted in the most pronounced response and the weakest correlation. Correlation on dataset from patients with AIDS or malaria was stronger for TMtb-iNet, indicating an involvement of TMtb-iNet in these chronic human infections. Collectively, the significance of this work is twofold: (1) we disseminate a hub-based approach in generating a biologically meaningful and clinically useful signature; (2) using this approach we introduce a new network-based signature and demonstrate its promising applications in understanding host responses to infections.

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MiR-190a Potentially Ameliorates Postoperative Cognitive Dysfunction by Regulating Tiam1

10.21203/rs.2.10148/v5 ◽

2019 ◽

Author(s):

Qiang Liu ◽

Aisheng Hou ◽

Yongyi Zhang ◽

Ying Guo ◽

Jingjing Li ◽

...

Keyword(s):

Network Analysis ◽

Cognitive Dysfunction ◽

Binding Sites ◽

Postoperative Cognitive Dysfunction ◽

The Elderly ◽

Mirna Microarray ◽

Post Surgery ◽

Highly Correlated ◽

Microarray Datasets ◽

Predictive Indicator

Abstract Postoperative cognitive dysfunction (POCD) affects a large number of post-surgery patients, especially for the elderly. However, the etiology of this neurocognitive disorder is largely unknown. Even if several studies have reported a small number of miRNAs as the essential modulatory factors in POCD, these findings are still rather limited. In this study, we used two miRNA microarray datasets to perform differential expression analyses of miRNAs in the hippocampus of POCD model mice. We found that nine miRNAs showed significant associations with POCD in both datasets. Among these miRNAs, mmu-miR-190a-3p was the most significant one. By performing weighted gene co-expression network analysis, we found 25 co-expression modules, of which mmu-miR-190a-3p was significantly anti-correlated with the red module. Moreover, in this red module, 314 genes were significantly enriched in four pathways such as axon guidance and calcium signaling pathway, which are well-documented to be associated with psychiatric disorders and brain development. Also, 169 of the 314 genes were highly correlated with mmu-miR-190a-3p, and four genes (Sphkap, Arhgef25, Tiam1, and Ntrk3) had putative binding sites at 3'-UTR of mmu-miR-190a-3p. Based on protein-protein network analysis, we detected that Tiam1 was a central gene regulated by the mmu-miR-190a-3p. Taken together, we conclude that mmu-miR-190a-3p is involved in the etiology of POCD and may serve as a novel predictive indicator for POCD.

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