scholarly journals Regulated necrosis-related molecule mRNA expression in humans and mice and in murine acute tissue injury and systemic autoimmunity leading to progressive organ damage, and progressive fibrosis

2016 ◽  
Vol 36 (6) ◽  
Author(s):  
Mohsen Honarpisheh ◽  
Jyaysi Desai ◽  
Julian A. Marschner ◽  
Marc Weidenbusch ◽  
Maciej Lech ◽  
...  
Keyword(s):  
Tissue Injury ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Tumour Necrosis Factor Receptor ◽  
Tissue Remodelling ◽  
Specific Expression ◽  
Systemic Autoimmunity ◽  
Regulated Necrosis ◽  
Apoptosis Protein ◽  
Species Specific

The species-specific, as well as organ-specific expression of regulated necrosis (RN)-related molecules, is not known. We determined the expression levels of tumour necrosis factor receptor-1 (TNFR1), receptor activated protein kinase (RIPK)1, RIPK3, mixed lineage kinase domain-like (MLKL), CASP8, Fas-associated protein with death domain (FADD), cellular inhibitor of apoptosis protein (CIAP)1, CIAP2, glutathione peroxidase-4 (GPX4), cyclophilin D (CYPD), CASP1, NLRP3 and poly(ADP-ribose) polymerase-1 (PARP1) in human and mouse solid organs. We observed significant differences in expression of these molecules between human and mice. In addition, we characterized their expression profiles in acute as well as persistent tissue injury and chronic tissue remodelling using acute and chronic kidney injury models. We observed that the degree and pattern of induction of RN-related molecules were highly dependent on the trigger and disease pathogenesis. Furthermore, we studied their expression patterns in mice with lupus-like systemic autoimmunity, which revealed that the expression of MLKL, GPX4 and PARP1 significantly increased in the spleen along disease progression and CASP1, RIPK1, RIPK3 and CYPD were higher at the earlier stages but were significantly decreased in the later stages. In contrast, in the kidney, the expression of genes involved in pyroptosis, e.g. NLRP3 and CASP1 were significantly increased and TNFR1, RIPK1, RIPK3, CIAP1/2 and GPX4 were significantly decreased along the progression of lupus nephritis (LN). Thus, the organ- and species-specific expression of RN-related molecules should be considered during designing experiments, interpreting the results as well as extrapolating the conclusions from one species or organ to another species or organ respectively.

scholarly journals The pineapple MADS-box gene family and the evolution of early monocot flower

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Juan Hu ◽  
Xiaojun Chang ◽  
Ying Zhang ◽  
Xianxian Yu ◽  
Yuan Qin ◽  
...  
Keyword(s):  
Fruit Development ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Ananas Comosus ◽  
Specific Gene ◽  
Type I ◽  
Mads Box ◽  
Specific Expression ◽  
Floral Organs ◽  
Species Specific

AbstractUnlike the flower of the model monocot rice, which has diverged greatly from the ancestral monocot flower, the pineapple (Ananas comosus) flower is more typical of monocot flowers. Here, we identified 43 pineapple genes containing MADS-box domains, including 11 type I and 32 type II genes. RNA-seq expression data generated from five pineapple floral organs (sepals, petals, stamens, pistils, and ovules) and quantitative real-time PCR revealed tissue-specific expression patterns for some genes. We found that AcAGL6 and AcFUL1 were mainly expressed in sepals and petals, suggesting their involvement in the regulation of these floral organs. A pineapple ‘ABCDE’ model was proposed based on the phylogenetic analysis and expression patterns of MADS-box genes. Unlike rice and orchid with frequent species-specific gene duplication and subsequent expression divergence, the composition and expression of the ABCDE genes were conserved in pineapple. We also found that AcSEP1/3, AcAG, AcAGL11a/b/c, and AcFUL1 were highly expressed at different stages of fruit development and have similar expression profiles, implicating these genes’ role in fruit development and ripening processes. We propose that the pineapple flower can be used as a model for studying the ancestral form of monocot flowers to investigate their development and evolutionary history.

Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽  
2018 ◽  
Vol 61 (2) ◽  
pp. 121-130 ◽  
Author(s):  
Chenghao Zhang ◽  
Wenqi Dong ◽  
Zong-an Huang ◽  
MyeongCheoul Cho ◽  
Qingcang Yu ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Environmental Stresses ◽  
Transcriptional Level ◽  
Specific Expression ◽  
Capsicum Annuum L ◽  
Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

scholarly journals Genome-Wide Analysis of Basic Helix–Loop–Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.)

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 914
Author(s):  
Shan ◽  
Zhang ◽  
Yu ◽  
Wang ◽  
Li ◽  
...  
Keyword(s):  
Brassica Oleracea ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Chilling Stress ◽  
Expression Patterns ◽  
Comprehensive Analysis ◽  
Bhlh Transcription Factor ◽  
Specific Expression ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix

Basic helix–loop–helix (bHLH) transcription factor (TF) family is commonly found in eukaryotes, which is one of the largest families of regulator proteins. It plays an important role in plant growth and development, as well as various biotic and abiotic stresses. However, a comprehensive analysis of the bHLH family has not been reported in Brassica oleracea. In this study, we systematically describe the BobHLHs in the phylogenetic relationships, expression patterns in different organs/tissues, and in response to chilling stress, and gene and protein characteristics. A total of 234 BobHLH genes were identified in the B. oleracea genome and were further clustered into twenty-three subfamilies based on the phylogenetic analyses. A large number of BobHLH genes were unevenly located on nine chromosomes of B. oleracea. Analysis of RNA-Seq expression profiles revealed that 21 BobHLH genes exhibited organ/tissue-specific expression. Additionally, the expression of six BobHLHs (BobHLH003, -048, -059, -093, -109, and -148) were significantly down-regulated in chilling-sensitive cabbage (CS-D9) and chilling-tolerant cabbage (CT-923). At 24h chilling stress, BobHLH054 was significantly down-regulated and up-regulated in chilling-treated CS-D9 and CT-923. Conserved motif characterization and exon/intron structural patterns showed that BobHLH genes had similar structures in the same subfamily. This study provides a comprehensive analysis of BobHLH genes and reveals several candidate genes involved in chilling tolerance of B. oleracea, which may be helpful to clarify the roles of bHLH family members and understand the regulatory mechanisms of BobHLH genes in response to the chilling stress of cabbage.

KVα1 channels in murine arterioles: differential cellular expression and regulation of diameter

2001 ◽  
Vol 281 (3) ◽  
pp. H1057-H1065 ◽  
Author(s):  
A. Cheong ◽  
A. M. Dedman ◽  
S. Z. Xu ◽  
D. J. Beech
Keyword(s):  
Smooth Muscle ◽  
Smooth Muscle Cells ◽  
Expression Profiles ◽  
Second Messengers ◽  
Expression Patterns ◽  
Muscle Cells ◽  
Cell Types ◽  
Specific Expression ◽  
Major Function ◽  
Cellular Expression

The primary objectives of this study were to reveal cell-specific expression patterns and functions of voltage-gated K+ channel (KVα1) subunits in precapillary arterioles of the murine cerebral circulation. KVα1 were detected using peptide-specific antibodies in immunofluorescence and Western blotting assays. KV1.2 was localized almost exclusively to endothelial cells, whereas KV1.5 was discretely localized to the nerves and nerve terminals that innervate the arterioles. KV1.5 also localized specifically to arteriolar nerves in human pial membrane. KV1.5 was notable for its absence from smooth muscle cells. KV1.3, KV1.4, and KV1.6 were localized to endothelial and smooth muscle cells, although KV1.4 had a low expression level. KV1.1 was not expressed. Therefore, we show that different cell types of pial arterioles have distinct physiological expression profiles of KVα1, conferring the possibility of differential modulation by extracellular and second messengers. Furthermore, we show recombinant agitoxin-2 and margatoxin are potent vasoconstrictors, suggesting that KVα1 subunits have a major function in determining arteriolar resistance to blood flow.

scholarly journals Systematic Analysis of Gibberellin Pathway Components in Medicago truncatula Reveals the Potential Application of Gibberellin in Biomass Improvement

2020 ◽  
Vol 21 (19) ◽  
pp. 7180
Author(s):  
Hongfeng Wang ◽  
Hongjiao Jiang ◽  
Yiteng Xu ◽  
Yan Wang ◽  
Lin Zhu ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Feedback Regulation ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Model Legume ◽  
Genome Wide ◽  
A Genome

Gibberellins (GAs), a class of phytohormones, act as an essential natural regulator of plant growth and development. Many studies have shown that GA is related to rhizobial infection and nodule organogenesis in legume species. However, thus far, GA metabolism and signaling components are largely unknown in the model legume Medicago truncatula. In this study, a genome-wide analysis of GA metabolism and signaling genes was carried out. In total 29 components, including 8 MtGA20ox genes, 2 MtGA3ox genes, 13 MtGA2ox genes, 3 MtGID1 genes, and 3 MtDELLA genes were identified in M. truncatula genome. Expression profiles revealed that most members of MtGAox, MtGID1, and MtDELLA showed tissue-specific expression patterns. In addition, the GA biosynthesis and deactivation genes displayed a feedback regulation on GA treatment, respectively. Yeast two-hybrid assays showed that all the three MtGID1s interacted with MtDELLA1 and MtDELLA2, suggesting that the MtGID1s are functional GA receptors. More importantly, M. truncatula exhibited increased plant height and biomass by ectopic expression of the MtGA20ox1, suggesting that enhanced GA response has the potential for forage improvement.

Tissue- and species-specific expression patterns of class I, III, and IV Adh and Aldh1 mRNAs in rodent embryos

2005 ◽  
Vol 322 (2) ◽  
pp. 227-236 ◽  
Author(s):  
Marie Westerlund ◽  
Dagmar Galter ◽  
Andrea Carmine ◽  
Lars Olson
Keyword(s):  
Expression Patterns ◽  
Class I ◽  
Specific Expression ◽  
Species Specific

scholarly journals Genome-wide and expression analysis of B-box gene family in pepper

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jing Ma ◽  
Jia-xi Dai ◽  
Xiao-wei Liu ◽  
Duo Lin
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Transient Expression Assay ◽  
Specific Expression ◽  
Tissue Specific ◽  
Duplication Events ◽  
Onion Inner Epidermis

Abstract Background BBX transcription factors are a kind of zinc finger transcription factors with one or two B-box domains, which partilant in plant growth, development and response to abiotic or biotic stress. The BBX family has been identified in Arabidopsis, rice, tomato and some other model plant genomes. Results Here, 24 CaBBX genes were identified in pepper (Capsicum annuum L.), and the phylogenic analysis, structures, chromosomal location, gene expression patterns and subcellular localizations were also carried out to understand the evolution and function of CaBBX genes. All these CaBBXs were divided into five classes, and 20 of them distributed in 11 of 12 pepper chromosomes unevenly. Most duplication events occurred in subgroup I. Quantitative RT-PCR indicated that several CaBBX genes were induced by abiotic stress and hormones, some had tissue-specific expression profiles or differentially expressed at developmental stages. Most of CaBBX members were predicated to be nucleus-localized in consistent with the transient expression assay by onion inner epidermis of the three tested CaBBX members (CaBBX5, 6 and 20). Conclusion Several CaBBX genes were induced by abiotic stress and exogenous phytohormones, some expressed tissue-specific and variously at different developmental stage. The detected CaBBXs act as nucleus-localized transcription factors. Our data might be a foundation in the identification of CaBBX genes, and a further understanding of their biological function in future studies.

scholarly journals Gene expression patterns associated with neurological disease in HIV infection

2016 ◽  
Author(s):  
Pietro Paolo Sanna ◽  
Vez Repunte-Canonigo ◽  
Eliezer Masliah ◽  
Celine Lefebvre
Keyword(s):  
Gene Expression ◽  
White Matter ◽  
Hiv Infection ◽  
Immune Activation ◽  
Tissue Injury ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Distinct Pattern ◽  
Gene Set Enrichment Analysis ◽  
Hiv Encephalitis

AbstractTo provide new insight into the pathogenesis of neurocognitive impairments (NCI) in HIV infection, we used the Gene Set Enrichment Analysis (GSEA) algorithm to analyze pathway dysregulations in gene expression profiles of HIV-infected patients with or without NCI and HIV encephalitis (HIVE). While HIVE was characterized by widespread inflammation and tissue damage, gene expression evidence of induction of interferon (IFN), cytokines and tissue injury was apparent in all brain regions studied before the emergence of NCI. Various degrees of white matter changes were present in all HIV-infected subjects and were the primary manifestation in patients with NCI in the absence of HIVE. The latter showed a distinct pattern of immune activation with induction of chemokines, cytokines, β-defensins, and limited IFN induction.Altogether results indicate that significant neuroinflammation and neuronal suffering precede NCI. Patients with NCI without HIVE showed a predominantly white matter dysfunction with a distinct pattern of immune activation.

scholarly journals Assessment of CircRNA Expression Profiles and Potential Functions in Brown Adipogenesis

2021 ◽  
Vol 12 ◽  
Author(s):  
Pengpeng Zhang ◽  
Mingxuan Sheng ◽  
Chunyu Du ◽  
Zhe Chao ◽  
Haixia Xu ◽  
...  
Keyword(s):  
Binding Sites ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Potential Functions ◽  
Rna Seq ◽  
Specific Expression ◽  
Protein Coding ◽  
Multiple Binding Sites ◽  
Brown Adipose ◽  
Brown Adipogenesis

Brown adipose tissue (BAT) is specialized for energy expenditure, thus a better understanding of the regulators influencing BAT development could provide novel strategies to defense obesity. Many protein-coding genes, miRNAs, and lncRNAs have been investigated in BAT development, however, the expression patterns and functions of circRNA in brown adipogenesis have not been reported yet. This study determined the circRNA expression profiles across brown adipogenesis (proliferation, early differentiated, and fully differentiated stages) by RNA-seq. We identified 3,869 circRNAs and 36.9% of them were novel. We found the biogenesis of circRNA was significantly related to linear mRNA transcription, meanwhile, almost 70% of circRNAs were generated by alternative back-splicing. Next, we examined the cell-specific and differentiation stage-specific expression of circRNAs. Compared to white adipocytes, nearly 30% of them were specifically expressed in brown adipocytes. Further, time-series expression analysis showed circRNAs were dynamically expressed, and 117 differential expression circRNAs (DECs) in brown adipogenesis were identified, with 77 upregulated and 40 downregulated. Experimental validation showed the identified circRNAs could be successfully amplified and the expression levels detected by RNA-seq were reliable. For the potential functions of the circRNAs, GO analysis suggested that the decreased circRNAs were enriched in cell proliferation terms, while the increased circRNAs were enriched in development and thermogenic terms. Bioinformatics predictions showed that DECs contained numerous binding sites of functional miRNAs. More interestingly, most of the circRNAs contained multiple binding sites for the same miRNA, indicating that they may facilitate functions by acting as microRNA sponges. Collectively, we characterized the circRNA expression profiles during brown adipogenesis and provide numerous novel circRNAs candidates for future brown adipogenesis regulating studies.

Differential expression of the closely linked KISS1, REN, and FLJ10761 genes in transgenic mice

2004 ◽  
Vol 17 (1) ◽  
pp. 4-10 ◽  
Author(s):  
Ravi Nistala ◽  
Xiaoji Zhang ◽  
Curt D. Sigmund
Keyword(s):  
Transgenic Mice ◽  
Human Chromosome ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Artificial Chromosome ◽  
Chromosome 1 ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression ◽  
Human Chromosome 1

We previously reported the development and characterization of transgenic mice containing a large 160-kb P1 artificial chromosome (PAC) encompassing the renin (REN) locus from human chromosome 1. Here we demonstrate that PAC160 not only encodes REN, but also complete copies of the next upstream (KISS1) and downstream ( FLJ10761 ) gene along human chromosome 1. Incomplete copies of the second upstream (PEPP3) and downstream (SOX13) genes are also present. The gene order PEPP3-KISS1-REN-FLJ10761-SOX13 is conserved in mice containing either one or two copies of the REN locus. Despite the close localization of KISS1, REN, and FLJ10761 , they each exhibit distinct, yet overlapping tissue-specific expression profiles in humans. The tissue-specific expression patterns of REN and FLJ10761 were retained in transgenic mice containing PAC160. Expression of REN and FLJ10761 were also proportional to copy number. Expression of KISS1 in PAC160 mice showed both similarities and differences to humans. These data suggest that expression of gene blocks encoded on large genomic clones are retained when the clones are used to generate transgenic mice. Genomic elements which act to insulate genes from their neighbors are also apparently retained.

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