Isolation of potential vertebrate limb-identity genes

Development ◽  
1989 ◽  
Vol 105 (4) ◽  
pp. 813-820 ◽  
Author(s):  
C.J. Tabin
Keyword(s):  
Sequence Analysis ◽  
Differentially Express ◽  
Limb Regeneration ◽  
Differential Screening ◽  
Differentially Expressed ◽  
Vertebrate Limb ◽  
Differentially Express Genes ◽  
The Difference ◽  
Morphological Patterns ◽  
Mesodermal Tissue

Forelimbs and hindlimbs of tetrapods have different morphological patterns. One plausible explanation for the difference is that the cells that give rise to the limbs differentially express genes which control their pattern of development. Amphibian limb regeneration is an excellent system to test this hypothesis, since the same ultimate morphology is attained in regeneration as through embryogenesis. Using a combination of homeobox probes and differential screening, I have isolated two newt genes which are differentially expressed in regenerating forelimbs and hindlimbs. One of these genes displays properties expected of a gene involved in controlling limb morphology, including expression in mesodermal tissue and constancy of expression upon transplantation. Based on sequence analysis, this gene appears to be homologous to a homeobox-containing gene previously isolated from frog and human libraries.

Ultrastructural analysis of the apical ectodermal ridge during vertebrate limb morphogenesis

Development ◽  
1977 ◽  
Vol 41 (1) ◽  
pp. 223-232
Author(s):  
John F. Fallon ◽  
Robert O. Kelley
Keyword(s):  
Electron Microscopy ◽  
Gap Junctions ◽  
Freeze Fracture ◽  
Apical Ectodermal Ridge ◽  
Structural Requirements ◽  
Limb Morphogenesis ◽  
Vertebrate Limb ◽  
The Difference ◽  
Freeze Fracture Electron Microscopy ◽  
Fracture Electron

The fine structure of the apical ectodermal ridge of five phylogenetically divergent orders of mammals and two orders of birds was examined using transmission and freeze fracture electron microscopy. Numerous large gap junctions were found in all apical ectodermal ridges studied. This was in contrast to the dorsal and ventral limb ectoderms where gap junctions were always very small and sparsely distributed. Thus, gap junctions distinguish the inductively active apical epithelium from the adjacent dorsal and ventral ectoderms. The distribution of gap junctions in the ridge was different between birds and mammals but characteristic within the two classes. Birds, with a pseudostratified columnar apical ridge, had the heaviest concentration of gap junctions at the base of each ridge cell close to the point where contact was made with the basal lamina. Whereas mammals, with a stratified cuboidal to squamous apical ridge, had a more uniform distribution of gap junctions throughout the apical epithelium. The difference in distribution for each class may reflect structural requirements for coupling of cells in the entire ridge. We propose that all cells of the apical ridges of birds and mammals are electrotonically and/or metabolically coupled and that this may be a requirement for the integrated function of the ridge during limb morphogenesis.

scholarly journals MicroRNA sequence analysis identifies microRNAs associated with peri-implantitis in dogs

2017 ◽  
Vol 37 (5) ◽  
Author(s):  
Xiaolin Wu ◽  
Xipeng Chen ◽  
Wenxiang Mi ◽  
Tingting Wu ◽  
Qinhua Gu ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Target Genes ◽  
Alveolar Bone ◽  
Biological Effects ◽  
Bone Destruction ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Mitogen Activated Protein Kinase ◽  
Mirna Sequence ◽  
Differentially Expressed Mirnas

Peri-implantitis, which is characterized by dense inflammatory infiltrates and increased osteoclast activity, can lead to alveolar bone destruction and implantation failure. miRNAs participate in the regulation of various inflammatory diseases, such as periodontitis and osteoporosis. Therefore, the present study aimed to investigate the differential expression of miRNAs in canine peri-implantitis and to explore the functions of their target genes. An miRNA sequence analysis was used to identify differentially expressed miRNAs in peri-implantitis. Under the criteria of a fold-change >1.5 and P<0.01, 8 up-regulated and 30 down-regulated miRNAs were selected for predictions of target genes and their biological functions. Based on the results of Gene Ontology (GO) and KEGG pathway analyses, these miRNAs may fine-tune the inflammatory process in peri-implantitis through an intricate mechanism. The results of quantitative real-time PCR (qRT-PCR) revealed that let-7g, miR-27a, and miR-145 may play important roles in peri-implantitis and are worth further investigation. The results of the present study provide insights into the potential biological effects of the differentially expressed miRNAs, and specific enrichment of target genes involved in the mitogen-activated protein kinase (MAPK) signaling pathway was observed. These findings highlight the intricate and specific roles of miRNAs in inflammation and osteoclastogenesis, both of which are key aspects of peri-implantitis, and thus may contribute to future investigations of the etiology, underlying mechanism, and treatment of peri-implantitis.

scholarly journals A comparative analysis of differentially expressed mRNAs, miRNAs and circRNAs provides insights into the key genes involved in the high-altitude adaptation of yaks

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qianyun Ge ◽  
Yongbo Guo ◽  
Wangshan Zheng ◽  
Yuan Cai ◽  
Xuebin Qi ◽  
...  
Keyword(s):  
High Altitude ◽  
Molecular Mechanisms ◽  
Regulation Of Gene Expression ◽  
Differentially Expressed ◽  
The Tibetan Plateau ◽  
The Core ◽  
Processing Pathways ◽  
Genetic Information Processing ◽  
Altitude Adaptation ◽  
The Difference

Abstract Background Yaks that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from cattle and have adapted well to the extreme conditions on the plateau. However, the mechanisms used by these animals for the regulation of gene expression at high altitude are not fully understood. Results Here, we sequenced nine lung transcriptomes of yaks at altitudes of 3400, 4200 and 5000 m, and low-altitude Zaosheng cattle, which is a closely related species, served as controls. The analysis identified 21,764 mRNAs, 1377 circRNAs and 1209 miRNAs. By comparing yaks and cattle, 4975 mRNAs, 252 circRNAs and 75 miRNAs were identified differentially expressed. By comparing yaks at different altitudes, we identified 756 mRNAs, 64 circRNAs and 83 miRNAs that were differentially expressed (fold change ≥2 and P-value < 0.05). The pathways enriched in the mRNAs, circRNAs and miRNAs identified from the comparison of yaks and cattle were mainly associated with metabolism, including ‘glycosaminoglycan degradation’, ‘pentose and glucuronate interconversions’ and ‘flavone and flavonol biosynthesis’, and the mRNAs, circRNAs and miRNAs identified from the comparison of yaks at different altitude gradients were significantly enriched in metabolic pathways and immune and genetic information processing pathways. The core RNAs were identified from the mRNA-miRNA-circRNA networks constructed using the predominant differentially expressed RNAs. The core genes specific to the difference between yaks and cattle were associated with the endoplasmic reticulum and fat deposition, but those identified from the comparison among yaks at different altitude gradients were associated with maintenance of the normal biological functions of cells. Conclusions This study enhances our understanding of the molecular mechanisms involved in hypoxic adaptation in yaks and might contribute to improvements in the understanding and prevention of hypoxia-related diseases.

scholarly journals Identification of Potential Therapeutic Targets and Molecular Regulatory Mechanisms for Osteoporosis by Bioinformatics Methods

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Li Zhang ◽  
Yunlong Yang ◽  
Dechun Geng ◽  
Yonghua Wu
Keyword(s):  
Immune Cell ◽  
Therapeutic Targets ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Differential Analysis ◽  
Ppi Network ◽  
The Difference ◽  
And Control

Background. Osteoporosis is characterized by low bone mass, deterioration of bone tissue structure, and susceptibility to fracture. New and more suitable therapeutic targets need to be discovered. Methods. We collected osteoporosis-related datasets (GSE56815, GSE99624, and GSE63446). The methylation markers were obtained by differential analysis. Degree, DMNC, MCC, and MNC plug-ins were used to screen the important methylation markers in PPI network, then enrichment analysis was performed. ROC curve was used to evaluate the diagnostic effect of osteoporosis. In addition, we evaluated the difference in immune cell infiltration between osteoporotic patients and control by ssGSEA. Finally, differential miRNAs in osteoporosis were used to predict the regulators of key methylation markers. Results. A total of 2351 differentially expressed genes and 5246 differentially methylated positions were obtained between osteoporotic patients and controls. We identified 19 methylation markers by PPI network. They were mainly involved in biological functions and signaling pathways such as apoptosis and immune inflammation. HIST1H3G, MAP3K5, NOP2, OXA1L, and ZFPM2 with higher AUC values were considered key methylation markers. There were significant differences in immune cell infiltration between osteoporotic patients and controls, especially dendritic cells and natural killer cells. The correlation between MAP3K5 and immune cells was high, and its differential expression was also validated by other two datasets. In addition, NOP2 was predicted to be regulated by differentially expressed hsa-miR-3130-5p. Conclusion. Our efforts aim to provide new methylation markers as therapeutic targets for osteoporosis to better treat osteoporosis in the future.

scholarly journals Melanocortin Receptor 4 Signaling Regulates Vertebrate Limb Regeneration

2018 ◽  
Vol 46 (4) ◽  
pp. 397-409.e5 ◽  
Author(s):  
Mengshi Zhang ◽  
Youwei Chen ◽  
Hanqian Xu ◽  
Li Yang ◽  
Feng Yuan ◽  
...  
Keyword(s):  
Limb Regeneration ◽  
Melanocortin Receptor ◽  
Vertebrate Limb

Participation of grafted nerves in amphibian limb regeneration

Development ◽  
1973 ◽  
Vol 29 (3) ◽  
pp. 559-570
Author(s):  
B. M. Wallace ◽  
H. Wallace
Keyword(s):  
Limb Regeneration ◽  
Normal Sequence ◽  
Histological Transformation ◽  
The Difference

Irradiated axolotl arms bearing grafts of brachial nerves can regenerate, albeit imperfectly. The origin of the regenerated tissues has been traced by means of the difference between dark and white genotypes. Although the origin of the melanophores cannot be decided in this way, their abundance identifies the genotype of the tissue they occupy. Sections of nine regenerates provide consistent evidence for the following conclusions. (1) The epidermis of the regenerate is probably an extension of the irradiated host epidermis. (2) All other tissues of the regenerate which differentiate from a mesenchymal blastema originate from the non-irradiated graft. Regeneration thus involves a true dedifferentiation and redifferentiation (i.e. a loss of determination and equivalent gain in potency for histological transformation). Irradiated cells apparently also dedifferentiate but cannot undergo the normal sequence of proliferation and redifferentiation, and so are not found in the mesodermal component of the regenerate.

scholarly journals Comparative proteomics analysis reveals the difference during antler regeneration stage between red deer and sika deer

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7299 ◽  
Author(s):  
Hang Su ◽  
Xiaolei Tang ◽  
Xiaocui Zhang ◽  
Li Liu ◽  
Li Jing ◽  
...  
Keyword(s):  
Red Deer ◽  
Sika Deer ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Deer Antler ◽  
Biological Difference ◽  
Regeneration Stage ◽  
The Difference ◽  
Antler Tip ◽  
Antler Development

Deer antler, as the only mammalian regenerative appendage, provides an optimal model to study regenerative medicine. Antler harvested from red deer or sika deer were mainly study objects used to disclose the mechanism underlying antler regeneration over past decades. A previous study used proteomic technology to reveal the signaling pathways of antler stem cell derived from red deer. Moreover, transcriptome of antler tip from sika deer provide us with the essential genes, which regulated antler development and regeneration. However, antler comparison between red deer and sika deer has not been well studied. In our current study, proteomics were employed to analyze the biological difference of antler regeneration between sika deer and red deer. The proteomics profile was completed by searching the UniProt database, and differentially expressed proteins were identified by bioinformatic software. Thirty-six proteins were highly expressed in red deer antler, while 144 proteins were abundant in sika deer. GO and KEGG analysis revealed that differentially expressed proteins participated in the regulation of several pathways including oxidative phosphorylation, ribosome, extracellular matrix interaction, and PI3K-Akt pathway.

scholarly journals Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Suxiang Lu ◽  
Qian Xiong ◽  
Kang Du ◽  
Xiaoni Gan ◽  
Xuzhen Wang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Multiple Reaction Monitoring ◽  
Limb Regeneration ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Differentially Expressed Proteins ◽  
Absolute Quantitation ◽  
Bioinformatics Analyses ◽  
Fin Regeneration ◽  
Early Stages

Abstract Background Polypterus senegalus can fully regenerate its pectoral lobed fins, including a complex endoskeleton, with remarkable precision. However, despite the enormous potential of this species for use in medical research, its regeneration mechanisms remain largely unknown. Methods To identify the differentially expressed proteins (DEPs) during the early stages of lobed fin regeneration in P. senegalus, we performed a differential proteomic analysis using isobaric tag for relative and absolute quantitation (iTRAQ) approach based quantitative proteome from the pectoral lobed fins at 3 time points. Furthermore, we validated the changes in protein expression with multiple-reaction monitoring (MRM) analysis. Results The experiment yielded a total of 3177 proteins and 15,091 unique peptides including 1006 non-redundant (nr) DEPs. Of these, 592 were upregulated while 349 were downregulated after lobed fin amputation when compared to the original tissue. Bioinformatics analyses showed that the DEPs were mainly associated with Ribosome and RNA transport, metabolic, ECM-receptor interaction, Golgi and endoplasmic reticulum, DNA replication, and Regulation of actin cytoskeleton. Conclusions To our knowledge, this is the first proteomic research to investigate alterations in protein levels and affected pathways in bichirs’ lobe-fin/limb regeneration. In addition, our study demonstrated a highly dynamic regulation during lobed fin regeneration in P. senegalus. These results not only provide a comprehensive dataset on differentially expressed proteins during the early stages of lobe-fin/limb regeneration but also advance our understanding of the molecular mechanisms underlying lobe-fin/limb regeneration.

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