scholarly journals Transcriptomic analysis of melon/squash graft junction reveals molecular mechanisms potentially underlying the graft union development

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12569
Author(s):  
Chuanqiang Xu ◽  
Ying Zhang ◽  
Mingzhe Zhao ◽  
Yiling Liu ◽  
Xin Xu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Healing Process ◽  
Signal Transduction Pathway ◽  
Lignin Biosynthesis ◽  
Graft Healing ◽  
Oriental Melon ◽  
Future Production ◽  
Grafting Technique ◽  
Phenylpropanoid Biosynthesis ◽  
Transcriptional Changes

Oriental melon (Cucumis melo var. makuwa Makino) has become a widely planted horticultural crop in China especially in recent years and has been subjected to the grafting technique for the improvement of cultivation and stress resistance. Although grafting has a long history in horticulture, there is little known about the molecular mechanisms of the graft healing process in oriental melon. This study aims to reveal the molecular changes involved in the graft healing process. In the present work, anatomical observations indicated that the 2, 6, and 9 DAG were three critical stages for the graft healing and therefore, were selected for the subsequent high-throughput RNA-seq analysis. A total of 1,950 and 1,313 DEGs were identified by comparing IL vs. CA and CA vs. VB libraries, respectively. More DEGs in the melon scion exhibited abundant transcriptional changes compared to the squash rootstock, providing increased metabolic activity and thus more material basis for the graft healing formation in the scion. Several DEGs were enriched in the plant hormone signal transduction pathway, phenylpropanoid biosynthesis, and carbon metabolism. In addition, the results showed that concentrations of IAA, GA3, and ZR were induced in the graft junctions. In conclusion, our study determined that genes involved in the hormone-signaling pathway and lignin biosynthesis played the essential roles during graft healing. These findings expand our current understandings of the molecular basis of the graft junction formation and facilitate the improvement and success of melon grafting in future production.

scholarly journals Comparative Transcriptome Analysis of Storage Root Reveals Regulatory Mechanisms of Lignin Biosynthesis During Root Development in Two Sweetpotato Cultivars

2021 ◽  
Author(s):  
Fuyun Hou ◽  
Zhen Qin ◽  
Taifeng Du ◽  
Yuanyuan Zhou ◽  
Aixian Li ◽  
...  
Keyword(s):  
Root Development ◽  
Ipomoea Batatas ◽  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Lignin Biosynthesis ◽  
Storage Root ◽  
Storage Roots ◽  
Homologous Genes ◽  
Phenylpropanoid Biosynthesis ◽  
Storage Root Development

Abstract BackgroundSweetpotato(Ipomoea batatas (L.) Lam.) is one of the most important crops with high storage roots yield. Lignin affects the storage root formation. However, the molecular mechanisms of lignin biosynthesis in storage roots development have been lacking.ResultsTo reveal the molecular mechanism of lignin biosynthesis and identify new homologous genes in lignin biosynthesis during storage root development, the storage root (SR) at three different stages (D1, D2 and D3) in the two cultivars (Jishu25 and Jishu29) was investigated with full-length and second-generation transcriptome. A total of 52,137 transcripts and 21,148 unigenes were obtained after corrected with Hiseq2500 sequencing. Through the comparative analysis, 9577 unigenes were found to be differently expressed in the different stage in two cultivars. Among of them, 91 unigenes enriched in the phenylpropanoid biosynthesis, and 201 unigenes in hormone signal transduction pathway with KEGG analysis. Weighted gene co-expression network analysis of differentially expressed unigenes showed that lignin biosynthesis genes might be co-expressed with transcription factors such as AP2/ERF and MYB at the transcription level, and regulated by phytohormones auxin and GA3.ConclusionsTaken together, our findings will throw light on molecular regulatory mechanism of lignin biosynthesis involved in storage root development.

scholarly journals RNA-Seq analysis of differential gene expression in Betula luminifera xylem during the early stages of tension wood formation

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5427 ◽  
Author(s):  
Miaomiao Cai ◽  
Huahong Huang ◽  
Fei Ni ◽  
Zaikang Tong ◽  
Erpei Lin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Tension Wood ◽  
Molecular Mechanisms ◽  
Southern China ◽  
Lignin Biosynthesis ◽  
Wood Formation ◽  
Cellulose Synthesis ◽  
Early Stages ◽  
Transcriptional Changes ◽  
Betula Luminifera

Background Betula luminifera H. Winkler, which is widely distributed in southern China, is an economically important broadleaf tree species. However, little genomic information of B. luminifera is available, and little is known about the molecular mechanisms of wood formation in this species. Meanwhile, few efforts have focused on investigating the early transcriptional changes during tension wood formation in woody plants. Results A reference transcriptome dataset was first generated containing 45,700 Unigenes, and 35,135 (76.9%) Unigenes were annotated by a BLAST similarity search against four public databases. Then, based on an anatomical investigation, the global gene expression changes during the early stages of tension wood formation were analyzed. Gene expression profiling showed that a total of 13,273 Unigenes were differentially regulated during the early stages of tension wood formation. Most genes involved in cellulose and lignin biosynthesis were highlighted to reveal their biological importance in tension wood formation. In addition, the transcription levels of many genes involved in the auxin response pathway were significantly changed during the early stages of tension wood formation. Furthermore, 18 TFs co-expressed with key enzymes of cellulose synthesis were identified. Conclusions Our results revealed the transcriptional changes associated with TW formation and identified potential key genes in the regulation of this process. These results will help to dissect the molecular mechanism of wood formation and provide key candidate genes for marker-assisted selection in B. luminifera.

scholarly journals Full-length transcriptome and targeted metabolome analyses provide insights into defense mechanisms of Malus sieversii against Agrilus mali

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8992
Author(s):  
Chuang Mei ◽  
Jie Yang ◽  
Peng Yan ◽  
Ning Li ◽  
Kai Ma ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Full Length ◽  
Metabolome Analysis ◽  
Insect Feeding ◽  
Illumina Hiseq ◽  
Malus Sieversii ◽  
Long Reads ◽  
Transcriptional Changes

Malus sieversii is the wild progenitor for many cultivars of domesticated apple and an important germplasm resource for breeding. However, this valuable species faces a significant threat in the areas north of the Tianshan Mountains in China, by the invasion of Agrilus mali, a destructive pest of apple trees belonging to the family Buprestidae. Our preliminary study has has shown that there may be resistance to this insect in M. sieversii plants in the field, but the corresponding molecular mechanisms remain unclear. In this study, we compared the response of insect-resistant and insect-susceptible plants of M. sieversii to insect feeding using full-length transcriptome and targeted metabolome. 112,103 non-chimeric full-length reads (FLNC) totaling 10.52 Gb of data were generating with Pacific Biosciences SingleMolecule, Real-Time (PacBio SMRT) sequencing. A total of 130.06 Gb data of long reads were acquired with an Illumina HiSeq. Function annotation indicated that the different expressed genes (DEGs) were mainly involved in signal transduction pathway of plant hormones and in the synthesis of compounds such as terpenes, quinones, flavonoids, and jasmonic acid. Through targeted metabolome analysis resistant strains showed higher levels of trans-cinnamic acid, caffeine and ferulic acid after pest infestation. This study helps to decipher the transcriptional changes and related signaling paths in M. sieversii after an insect feeding, which lays a foundation for further research on molecular mechanisms of insect resistance in apples.

Comparative transcriptome profiling provides insights into endocarp lignification of walnut (Juglans Regia L.)

2020 ◽  
Author(s):  
Xiaoting Wu ◽  
Zechao Zhang ◽  
Mintao Sun ◽  
Xiuhong An ◽  
Shugang Zhao ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Juglans Regia ◽  
Expression Patterns ◽  
Lignin Biosynthesis ◽  
Transcriptome Profiling ◽  
Phenotypic Differences ◽  
Phenylpropanoid Biosynthesis ◽  
Key Genes ◽  
Main Component

Abstract Background Lignin is the main component of walnut endocarp, although we know little about the molecular mechanism of lignin formation in walnut endocarp. To understand the molecular mechanisms behind the two kinds of walnut phenotype and explore the genes involved into lignin formation, transcriptome sequencing was conducted in the walnut endocarp of the ‘Zanmei’ (ZM) and ‘Liaoning 7’ (L7) cultivars, which have different endocarp thicknesses. Compared with L7 walnut endocarp, the endocarp of ZM walnut is thicker, which decreases dehiscent nuts and compromised kernels.Results There are more differentially expressed genes (DEGs) in the ZM walnut cultivar. The DEGs involved in the phenylpropanoid biosynthesis were significantly upregulated in both cultivars 45 days after full bloom (DAFB), but more genes were upregulated in ZM than in L7. Moreover, the same DEGs showed different expression levels in the two cultivars. Most of the key genes in ZM had more different multiples than those in L7. Interestingly, when qRT-PCR was used to determine the expression of the key genes in different development stages of the two varieties, the expression patterns were different from those known in other species. Furthermore, transcription factors regulating secondary cell wall and lignin biosynthesis were identified. Quantitative real-time PCR results were consistent with transcriptome data.Conclusion In this study, transcriptome analysis was used to understand the molecular mechanisms of lignin formation in two walnut cultivars with different shell thickness. Several important key genes in the phenylpropanoid biosynthesis pathway were significantly different in the two cultivars, which may be the reason for the phenotypic differences. The analysis of transcription factors revealed that the regulation network in endocarp of walnut may be different from that of drupe such as apricot or peach. This study provides important candidate genes for exploring the complicated metabolic processes involved in the formation of walnut lignin.

scholarly journals Integrated transcriptomic and proteomic analysis reveals the complex molecular mechanisms underlying stone cell formation in Korla pear

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aisajan Mamat ◽  
Kuerban Tusong ◽  
Juan Xu ◽  
Peng Yan ◽  
Chuang Mei ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Proteomic Analysis ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Cell Formation ◽  
Parenchyma Cell ◽  
Lignin Biosynthesis ◽  
Cell Content ◽  
Stone Cell ◽  
Fruit Samples

AbstractKorla pear (Pyrus sinkiangensis Yü) is a landrace selected from a hybrid pear species in the Xinjiang Autonomous Region in China. In recent years, pericarp roughening has been one of the major factors that adversely affects fruit quality. Compared with regular fruits, rough-skin fruits have a greater stone cell content. Stone cells compose sclerenchyma tissue that is formed by secondary thickening of parenchyma cell walls. In this work, we determined the main components of stone cells by isolating them from the pulp of rough-skin fruits at the ripening stage. Stone cell staining and apoptosis detection were then performed on fruit samples that were collected at three different developmental stages (20, 50 and 80 days after flowering (DAF)) representing the prime, late and stationary stages of stone cell differentiation, respectively. The same batches of samples were used for parallel transcriptomic and proteomic analysis to identify candidate genes and proteins that are related to SCW biogenesis in Korla pear fruits. The results showed that stone cells are mainly composed of cellulose (52%), hemicellulose (23%), lignin (20%) and a small amount of polysaccharides (3%). The periods of stone cell differentiation and cell apoptosis were synchronous and primarily occurred from 0 to 50 DAF. The stone cell components increased abundantly at 20 DAF but then decreased gradually. A total of 24,268 differentially expressed genes (DEGs) and 1011 differentially accumulated proteins (DAPs) were identified from the transcriptomic and proteomic data, respectively. We screened the DEGs and DAPs that were enriched in SCW-related pathways, including those associated with lignin biosynthesis (94 DEGs and 31 DAPs), cellulose and xylan biosynthesis (46 DEGs and 18 DAPs), S-adenosylmethionine (SAM) metabolic processes (10 DEGs and 3 DAPs), apoplastic ROS production (16 DEGs and 2 DAPs), and cell death (14 DEGs and 6 DAPs). Among the identified DEGs and DAPs, 63 significantly changed at both the transcript and protein levels during the experimental periods. In addition, the majority of these identified genes and proteins were expressed the most at the prime stage of stone cell differentiation, but their levels gradually decreased at the later stages.

scholarly journals Nanocomposite scaffolds for accelerating chronic wound healing by enhancing angiogenesis

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Hamed Nosrati ◽  
Reza Aramideh Khouy ◽  
Ali Nosrati ◽  
Mohammad Khodaei ◽  
Mehdi Banitalebi-Dehkordi ◽  
...  
Keyword(s):  
Tissue Engineering ◽  
Wound Healing ◽  
Tissue Regeneration ◽  
Molecular Mechanisms ◽  
Healing Process ◽  
The Body ◽  
Key Factors ◽  
Potential Applications ◽  
Nanocomposite Scaffolds

AbstractSkin is the body’s first barrier against external pathogens that maintains the homeostasis of the body. Any serious damage to the skin could have an impact on human health and quality of life. Tissue engineering aims to improve the quality of damaged tissue regeneration. One of the most effective treatments for skin tissue regeneration is to improve angiogenesis during the healing period. Over the last decade, there has been an impressive growth of new potential applications for nanobiomaterials in tissue engineering. Various approaches have been developed to improve the rate and quality of the healing process using angiogenic nanomaterials. In this review, we focused on molecular mechanisms and key factors in angiogenesis, the role of nanobiomaterials in angiogenesis, and scaffold-based tissue engineering approaches for accelerated wound healing based on improved angiogenesis.

scholarly journals Integrated Transcriptomic and Un-Targeted Metabolomics Analysis Reveals Mulberry Fruit (Morus atropurpurea) in Response to Sclerotiniose Pathogen Ciboria shiraiana Infection

2020 ◽  
Vol 21 (5) ◽  
pp. 1789 ◽  
Author(s):  
Lijun Bao ◽  
Hongpeng Gao ◽  
Zelin Zheng ◽  
Xiaoxiao Zhao ◽  
Minjuan Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Early Stage ◽  
Metabolite Profile ◽  
Northwest China ◽  
Targeted Metabolomics ◽  
Mulberry Fruit ◽  
Phenylpropanoid Biosynthesis ◽  
Mapman Analysis ◽  
Mulberry Fruits ◽  
Prevention Methods

Mulberry sclerotiniose caused by Ciboria shiraiana is a devastating disease of mulberry (Morus alba L.) fruit in Northwest China. At present, no disease-resistant varieties are used in production, as the molecular mechanisms of this disease are not well understood. In this study, to explore new prevention methods and provide direction for molecular breeding, transcriptomic sequencing and un-targeted metabolomics were performed on healthy (CK), early-stage diseased (HB1), and middle-stage diseased (HB2) mulberry fruits. Functional annotation, gene ontology, a Kyoto encyclopedia of genes and genomes (KEGG) analysis, and a Mapman analysis of the differentially expressed genes revealed differential regulation of genes related to plant hormone signal transduction, transcription factors, and phenylpropanoid biosynthesis. A correspondence between the transcript pattern and metabolite profile was observed in the phenylpropanoid biosynthesis pathway. It should be noted that the log2 ratio of eugenol (isoeugenol) in HB1 and HB2 are 85 times and 23 times higher than CK, respectively. Our study shows that phenylpropanoid biosynthesis may play an essential role in response to sclerotiniose pathogen infection and eugenol(isoeugenol) enrichment in mulberry fruit, which may provide a novel method for mulberry sclerotiniose control.

scholarly journals Physical dissociation of the TCR-CD3 complex accompanies receptor ligation.

1995 ◽  
Vol 182 (6) ◽  
pp. 1997-2006 ◽  
Author(s):  
H Kishimoto ◽  
R T Kubo ◽  
H Yorifuji ◽  
T Nakayama ◽  
Y Asano ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Cell Surface ◽  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Surface Expression ◽  
Cell Surface Expression ◽  
Protein Levels ◽  
Before And After ◽  
Physical Dissociation ◽  
Receptor Ligation

Recent studies indicate that there may be functional uncoupling of the TCR-CD3 complex and suggest that the TCR-CD3 complex is composed of two parallel signal-transducing units, one made of gamma delta epsilon chains and the other of zeta chains. To elucidate the molecular mechanisms that may explain the functional uncoupling of TCR and CD3, we have analyzed their expression by using flow cytometry as well as immunochemical means both before and after stimulation with anti-TCR-beta, anti-CD3 epsilon, anti-CD2, staphylococcal enterotoxin B, and ionomycin. We present evidence that TCR physically dissociates from CD3 after stimulation of the TCR-CD3 complex. Stimulation with anti-CD3 resulted in down-modulation of TCR within 45 min whereas CD3 epsilon was still expressed on the cell surface as detected by flow cytometry. However, the cell surface expression of TCR and CD3 was not affected when cells were stimulated with anti-TCR-beta under the same conditions. In the case of anti-CD3 treatment of T cells, the TCR down-modulation appeared to be due to the internalization of TCR, as determined by immunoelectron microscopy. Immunochemical analysis of cells after stimulation with either anti-TCR or anti-CD3 mAbs revealed that the overall protein levels of TCR and CD3 were similar. More interestingly, the dissociation of the TCR-CD3 complex was observed with both treatments and occurred in a manner that the TCR and the associated TCR-zeta chain dissociated as a unit from CD3. These results provide the first report of physical dissociation of TCR and CD3 after stimulation through the TCR-CD3 complex. The results also suggest that the signal transduction pathway triggered by TCR may differ from that induced by CD3.

Identifying New Pathways and Targets for Wound Healing and Therapeutics from Natural Sources

2021 ◽  
Vol 18 ◽  
Author(s):  
Xinchi Feng ◽  
Jinsong Hao
Keyword(s):  
Wound Healing ◽  
Molecular Mechanisms ◽  
Chronic Wounds ◽  
Wound Care ◽  
Healing Process ◽  
Unmet Need ◽  
Wound Dressings ◽  
Wound Healing Process ◽  
Natural Sources ◽  
Viable Approach

: Chronic wounds remain a significant public problem and the development of wound treatments has been a research focus for the past few decades. Despite advances in the products derived from endogenous substances involved in a wound healing process (e.g. growth factors, stem cells, and extracellular matrix), effective and safe wound therapeutics are still limited. There is an unmet need to develop new therapeutics. Various new pathways and targets have been identified and could become a molecular target in designing novel wound agents. Importantly, many existing drugs that target these newly identified pathways could be repositioned for wound therapy, which will facilitate fast translation of research findings to clinical applications. This review discusses the newly identified pathways/targets and their potential uses in the development of wound therapeutics. Some herbs and amphibian skins have been traditionally used for wound repairs and their active ingredients have been found to act in these new pathways. Hence, screening these natural products for novel wound therapeutics remains a viable approach. The outcomes of wound care using natural wound therapeutics could be improved if we can better understand their cellular and molecular mechanisms and fabricate them in appropriate formulations, such as using novel wound dressings and nano-engineered materials. Therefore, we also provide an update on the advances in the wound therapeutics from natural sources. Overall, this review offers new insights into novel wound therapeutics.

Platelets in tissue repair: control of apoptosis and interactions with regenerative cells

Blood ◽  
2013 ◽  
Vol 122 (15) ◽  
pp. 2550-2554 ◽  
Author(s):  
Meinrad Gawaz ◽  
Sebastian Vogel
Keyword(s):  
Cell Survival ◽  
Tissue Repair ◽  
Molecular Mechanisms ◽  
Healing Process ◽  
Critical Role ◽  
Cellular Migration ◽  
Tissue Repair And Regeneration ◽  
Primary Hemostasis ◽  
Regenerative Cells ◽  
Insight Into

Abstract Besides mediating primary hemostasis and thrombosis, platelets play a critical role in tissue repair and regeneration. They regulate fundamental mechanisms involved in the healing process including cellular migration, proliferation, and angiogenesis. Control of apoptosis/cell survival and interaction with progenitor cells, which are clinically relevant but poorly understood aspects of platelets in tissue repair, will be highlighted in this review. Gaining deeper insight into the less well-characterized molecular mechanisms is necessary to develop new therapeutic platelet-based options.

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