scholarly journals Evolutionary Understanding of Aquaporin Transport System in the Basal Eudicot Model Species Aquilegia coerulea

Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 799 ◽  
Author(s):  
Shweta Singh ◽  
Vacha Bhatt ◽  
Virender Kumar ◽  
Surbhi Kumawat ◽  
Praveen Khatri ◽  
...  
Keyword(s):  
Floral Development ◽  
Bioinformatics Analysis ◽  
Cellular Transport ◽  
Pore Morphology ◽  
Rna Seq ◽  
Model Species ◽  
Protein Structure Analysis ◽  
Single Clade ◽  
Plasma Membrane Intrinsic Proteins ◽  
Influx Transporter

Aquaporins (AQPs) play a pivotal role in the cellular transport of water and many other small solutes, influencing many physiological and developmental processes in plants. In the present study, extensive bioinformatics analysis of AQPs was performed in Aquilegia coerulea L., a model species belonging to basal eudicots, with a particular focus on understanding the AQPs role in the developing petal nectar spur. A total of 29 AQPs were identified in Aquilegia, and their phylogenetic analysis performed with previously reported AQPs from rice, poplar and Arabidopsis depicted five distinct subfamilies of AQPs. Interestingly, comparative analysis revealed the loss of an uncharacterized intrinsic protein II (XIP-II) group in Aquilegia. The absence of the entire XIP subfamily has been reported in several previous studies, however, the loss of a single clade within the XIP family has not been characterized. Furthermore, protein structure analysis of AQPs was performed to understand pore diversity, which is helpful for the prediction of solute specificity. Similarly, an AQP AqcNIP2-1 was identified in Aquilegia, predicted as a silicon influx transporter based on the presence of features such as the G-S-G-R aromatic arginine selectivity filter, the spacing between asparagine-proline-alanine (NPA) motifs and pore morphology. RNA-seq analysis showed a high expression of tonoplast intrinsic proteins (TIPs) and plasma membrane intrinsic proteins (PIPs) in the developing petal spur. The results presented here will be helpful in understanding the AQP evolution in Aquilegia and their expression regulation, particularly during floral development.

scholarly journals Transcriptome Analysis of Responses to Dengue Virus 2 Infection in Aedes albopictus (Skuse) C6/36 Cells

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 343
Author(s):  
Manjin Li ◽  
Dan Xing ◽  
Duo Su ◽  
Di Wang ◽  
Heting Gao ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Aedes Albopictus ◽  
Bioinformatics Analysis ◽  
Interaction Mechanism ◽  
Transcriptional Analysis ◽  
Functional Verification ◽  
Mosquito Vector ◽  
Rna Seq ◽  
Sequencing Data ◽  
Qrt Pcr

Dengue virus (DENV), a member of the Flavivirus genus of the Flaviviridae family, can cause dengue fever (DF) and more serious diseases and thus imposes a heavy burden worldwide. As the main vector of DENV, mosquitoes are a serious hazard. After infection, they induce a complex host–pathogen interaction mechanism. Our goal is to further study the interaction mechanism of viruses in homologous, sensitive, and repeatable C6/36 cell vectors. Transcriptome sequencing (RNA-Seq) technology was applied to the host transcript profiles of C6/36 cells infected with DENV2. Then, bioinformatics analysis was used to identify significant differentially expressed genes and the associated biological processes. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was performed to verify the sequencing data. A total of 1239 DEGs were found by transcriptional analysis of Aedes albopictus C6/36 cells that were infected and uninfected with dengue virus, among which 1133 were upregulated and 106 were downregulated. Further bioinformatics analysis showed that the upregulated DEGs were significantly enriched in signaling pathways such as the MAPK, Hippo, FoxO, Wnt, mTOR, and Notch; metabolic pathways and cellular physiological processes such as autophagy, endocytosis, and apoptosis. Downregulated DEGs were mainly enriched in DNA replication, pyrimidine metabolism, and repair pathways, including BER, NER, and MMR. The qRT-PCR results showed that the concordance between the RNA-Seq and RT-qPCR data was very high (92.3%). The results of this study provide more information about DENV2 infection of C6/36 cells at the transcriptome level, laying a foundation for further research on mosquito vector–virus interactions. These data provide candidate antiviral genes that can be used for further functional verification in the future.

scholarly journals Pre-transplant Transcriptional Signature in Peripheral Blood Mononuclear Cells of Acute Renal Allograft Rejection

2022 ◽  
Vol 8 ◽  
Author(s):  
Wenyu Xiang ◽  
Shuai Han ◽  
Cuili Wang ◽  
Hongjun Chen ◽  
Lingling Shen ◽  
...  
Keyword(s):  
Complement Activation ◽  
Allograft Rejection ◽  
Renal Allograft ◽  
Mononuclear Cells ◽  
Bioinformatics Analysis ◽  
Rna Seq ◽  
Peripheral Blood Mononuclear ◽  
Renal Allograft Rejection ◽  
Acute Renal Allograft Rejection ◽  
Blood Mononuclear Cells

Acute rejection (AR) is closely associated with renal allograft dysfunction. Here, we utilised RNA sequencing (RNA-Seq) and bioinformatic methods to characterise the peripheral blood mononuclear cells (PBMCs) of patients with acute renal allograft rejection. Pretransplant blood samples were collected from 32 kidney allograft donors and 42 corresponding recipients with biopsies classified as T cell-mediated rejection (TCMR, n = 18), antibody-mediated rejection (ABMR, n = 5), and normal/non-specific changes (non-AR, n = 19). The patients with TCMR and ABMR were assigned to the AR group, and the patients with normal/non-specific changes (n = 19) were assigned to the non-AR group. We analysed RNA-Seq data for identifying differentially expressed genes (DEGs), and then gene ontology (GO) analysis, Reactome, and ingenuity pathway analysis (IPA), protein—protein interaction (PPI) network, and cell-type enrichment analysis were utilised for bioinformatics analysis. We identified DEGs in the PBMCs of the non-AR group when compared with the AR, ABMR, and TCMR groups. Pathway and GO analysis showed significant inflammatory responses, complement activation, interleukin-10 (IL-10) signalling pathways, classical antibody-mediated complement activation pathways, etc., which were significantly enriched in the DEGs. PPI analysis showed that IL-10, VEGFA, CXCL8, MMP9, and several histone-related genes were the hub genes with the highest degree scores. Moreover, IPA analysis showed that several proinflammatory pathways were upregulated, whereas antiinflammatory pathways were downregulated. The combination of NFSF14+TANK+ANKRD 33 B +HSPA1B was able to discriminate between AR and non-AR with an AUC of 92.3% (95% CI 82.8–100). Characterisation of PBMCs by RNA-Seq and bioinformatics analysis demonstrated gene signatures and biological pathways associated with AR. Our study may provide the foundation for the discovery of biomarkers and an in-depth understanding of acute renal allograft rejection.

scholarly journals Drought-Induced Root Pressure in Sorghum bicolor

2021 ◽  
Vol 12 ◽  
Author(s):  
Sarah Tepler Drobnitch ◽  
Louise H. Comas ◽  
Nora Flynn ◽  
Jorge Ibarra Caballero ◽  
Ryan W. Barton ◽  
...  
Keyword(s):  
Sorghum Bicolor ◽  
Biomass Production ◽  
Crop Production ◽  
Shoot Biomass ◽  
Cellular Transport ◽  
Rna Seq ◽  
Root Pressure ◽  
Coarse Root ◽  
Gene Transcripts

Root pressure, also manifested as profusive sap flowing from cut stems, is a phenomenon in some species that has perplexed biologists for much of the last century. It is associated with increased crop production under drought, but its function and regulation remain largely unknown. In this study, we investigated the initiation, mechanisms, and possible adaptive function of root pressure in six genotypes of Sorghum bicolor during a drought experiment in the greenhouse. We observed that root pressure was induced in plants exposed to drought followed by re-watering but possibly inhibited by 100% re-watering in some genotypes. We found that root pressure in drought stressed and re-watered plants was associated with greater ratio of fine: coarse root length and shoot biomass production, indicating a possible role of root allocation in creating root pressure and adaptive benefit of root pressure for shoot biomass production. Using RNA-Seq, we identified gene transcripts that were up- and down-regulated in plants with root pressure expression, focusing on genes for aquaporins, membrane transporters, and ATPases that could regulate inter- and intra-cellular transport of water and ions to generate positive xylem pressure in root tissue.

scholarly journals RNA-Seq analysis of gene expression for floral development in crested wheatgrass (Agropyron cristatum L.)

PLoS ONE ◽  
2017 ◽  
Vol 12 (5) ◽  
pp. e0177417 ◽  
Author(s):  
Fangqin Zeng ◽  
Bill Biligetu ◽  
Bruce Coulman ◽  
Michael P. Schellenberg ◽  
Yong-Bi Fu
Keyword(s):  
Gene Expression ◽  
Floral Development ◽  
Agropyron Cristatum ◽  
Rna Seq ◽  
Crested Wheatgrass

scholarly journals Deep RNA-Seq to Unlock the Gene Bank of Floral Development in Sinapis arvensis

PLoS ONE ◽  
2014 ◽  
Vol 9 (9) ◽  
pp. e105775 ◽  
Author(s):  
Jia Liu ◽  
Desheng Mei ◽  
Yunchang Li ◽  
Shunmou Huang ◽  
Qiong Hu
Keyword(s):  
Floral Development ◽  
Gene Bank ◽  
Rna Seq ◽  
Sinapis Arvensis

scholarly journals M1-like tumor-associated macrophages cascade a mesenchymal/stem-like phenotype of oral squamous cell carcinoma via the IL6/Stat3/THBS1 feedback loop

2022 ◽  
Vol 41 (1) ◽  
Author(s):  
Yuanhe You ◽  
Zhuowei Tian ◽  
Zhong Du ◽  
Kailiu Wu ◽  
Guisong Xu ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Feedback Loop ◽  
Molecular Mechanisms ◽  
Bioinformatics Analysis ◽  
Rna Seq ◽  
Stat3 Pathway ◽  
Functional Roles

Abstract Background Tumor-associated macrophages (TAMs) have a leading position in the tumor microenvironment. Previously, we have demonstrated that M1-like TAMs activated by exosome-transferred THBS1 promote malignant migration in oral squamous cell carcinoma (OSCC). However, the functional roles and associated molecular mechanisms of the activated M1-like TAMs need to be further clarified in OSCC. Methods Conditioned Media (CM) were harvested from the exosome activated M1-like TAMs. We measured the malignant behaviors of OSCC under the treatment of CM from M1-like TAMs by performing colony forming assays, invasion assays, wound-healing assays, spheroid forming assays and in vivo xenograft experiments. The underlying mechanisms were investigated by RNA-seq, cytokines analysis, intracellular signaling pathway analysis, ChIP assays, bioinformatics analysis and validation. Results M1-like TAMs significantly promoted the epithelial-mesenchymal transition (EMT) process, and induced the cancer-stem like cells (CSCs) by upregulating the expression of MME and MMP14 in OSCC cells. Cytokine analysis revealed a shark increase of IL6 secretion from M1-like TAMs. Blocking IL6 in the CM from M1-like TAMs could significantly weaken its effects on the colony forming, invasion, migration, microsphere forming and xenograft forming abilities of OSCC cells. Cellular signaling assays indicated the activation of Jak/Stat3 pathway in the OSCC cells treated by the CM from M1-like TAMs. Blocking the activation of the Jak/Stat3 pathway could significantly weaken the effects of M1-like TAMs on the colony forming, invasion, migration, microsphere forming and xenograft forming abilities of OSCC cells. Further RNA-seq analysis and bioinformatics analysis revealed an increased expression of THBS1 in the OSCC cells treated by M1-like TAMs. Bioinformatics prediction and ChIP assays revealed the activation of Stat3 by CM from M1-like TAMs could directly promote the transcription of THBS1 in OSCC cells. Conclusions We proposed that M1-like TAMs could cascade a mesenchymal/stem-like phenotype of OSCC via the IL6/Stat3/THBS1 feedback loop. A better understanding on the functional roles and associated molecular mechanisms of M1-like TAMs might facilitate the development of novel therapies for supplementing the current treatment strategies for OSCC patients.

scholarly journals Identification of Genes Involved in Low Temperature-Induced Senescence of Panicle Leaf in Litchi chinensis

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 111
Author(s):  
Congcong Wang ◽  
Hao Liu ◽  
Sheng Yu ◽  
Houbin Chen ◽  
Fuchu Hu ◽  
...  
Keyword(s):  
Low Temperature ◽  
Leaf Senescence ◽  
Molecular Breeding ◽  
Hot Springs ◽  
Floral Development ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Qrt Pcr ◽  
Digital Expression ◽  
Indole 3 Acetic Acid

Warm winters and hot springs may promote panicle leaf growing and repress floral development. To identify genes potentially involved in litchi panicle leaf senescence, eight RNA-sequencing (RNA-Seq) libraries of the senescing panicle leaves under low temperature (LT) conditions and the developing panicle leaves under high temperature (HT) conditions were constructed. For each library, 4.78–8.99 × 106 clean reads were generated. Digital expression of the genes was compared between the senescing and developing panicle leaves. A total of 6477 upregulated differentially expressed genes (DEGs) (from developing leaves to senescing leaves), and 6318 downregulated DEGs were identified, 158 abscisic acid (ABA)-, 68 ethylene-, 107 indole-3-acetic acid (IAA)-, 27 gibberellic acid (GA)-, 68 cytokinin (CTK)-, 37 salicylic acid (SA)-, and 23 brassinolide (BR)-related DEGs. Confirmation of the RNA-Seq data by quantitative real-time PCR (qRT-PCR) analysis suggested that expression trends of the 10 candidate genes using qRT-PCR were similar to those revealed by RNA-Seq, and a significantly positive correlation between the obtained data from qRT-PCR and RNA-Seq were found, indicating the reliability of our RNA-Seq data. The present studies provided potential genes for the future molecular breeding of new cultivars that can induce panicle leaf senescence and reduce floral abortion under warm climates.

scholarly journals Transcriptome profiling for floral development in reblooming cultivar ‘High Noon’ of Paeonia suffruticosa

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Yanting Chang ◽  
Tao Hu ◽  
Wenbo Zhang ◽  
Lin Zhou ◽  
Yan Wang ◽  
...  
Keyword(s):  
Flower Development ◽  
Floral Development ◽  
Developmental Stages ◽  
Transcriptome Profiling ◽  
Full Length ◽  
Rna Seq ◽  
Paeonia Suffruticosa ◽  
Tree Peony ◽  
Flower Bud ◽  
High Noon

Abstract Tree peony (Paeonia suffruticosa Andrew) is a popular ornamental plant due to its large, fragrant and colorful flowers. The floral development is the most important event in its lifecycle. To explore the mechanism that regulate flower development, we sequenced the flower bud transcriptomes of ‘High Noon’, a reblooming cultivar of P. suffruticosa × P. lutea, using both full-length isoform-sequencing (ISO-seq) and RNA-seq were sequenced. A total of 15.94 Gb raw data were generated in full-length transcriptome sequencing of the 3 floral developmental stages, resulting 0.11 M protein-coding transcripts. Over 457.0 million reads were obtained by RNA-seq in the 3 floral buds. Here, we openly released the full-length transcriptome database of ‘High Noon’ and RNA-seq database of floral development. These databases can provide a fundamental genetic information of tree peony to investigate its transcript structure, variants and evolution. Data will facilitate to deep analyses of the transcriptome for flower development.

Caspase-related apoptosis genes in gliomas by RNA-seq and bioinformatics analysis

2016 ◽  
Vol 33 ◽  
pp. 259-263
Author(s):  
Rui Wang ◽  
Bo Wei ◽  
Jun Wei ◽  
Zhaohui Li ◽  
Yu Tian ◽  
...  
Keyword(s):  
Bioinformatics Analysis ◽  
Rna Seq
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