scholarly journals Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis Seeds

2020 ◽  
Author(s):  
Dongxing Li ◽  
Yingchao Li ◽  
Jialian Qian ◽  
Xiaojuan Liu ◽  
Huihui Xu ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Molecular Regulation ◽  
Regulation Mechanism ◽  
Hormone Synthesis ◽  
Quercus Variabilis ◽  
Desiccation Sensitivity ◽  
Work Model

Abstract Background: Chinese cork oak (Quercus variabilis) is a widely distributed and highly valuable deciduous broadleaf tree from both ecological and economic perspectives. Seeds of Q. variabilis are recalcitrant, i.e., sensitive to desiccation, which affects their storage and long-term preservation of germplasm. However, little is known about the underlying mechanism of desiccation sensitivity of Q. variabilis seeds. Results: In this study, the seeds were desiccated with silica gel for 0 day (control, CK), one day (T1) to 15 days (T15). After desiccation, the transcriptomic profiles of these different desiccation stages were compared using the Quercus suber genome as a reference, as well four key stages (CK, T2, T4 and T11) of desiccation sensitivity of Q. variabilis seeds through germination test were identified. A total of 4405, 4441, and 5907 differentially expressed genes (DEGs) were identified in T2 vs CK, T4 vs CK, and T11 vs CK, respectively. Among them, 2219 DEGs were overlapped in the three comparison groups. KEGG (Kyoto Encyclopaedia of Genes and Genomes) enrichment analysis showed that these DEGs were enriched into 124 pathways, such as "plant hormone signal transduction" and "glycerophospholipid metabolism". DEGs related to hormone synthesis and signal transduction (ZEP, YUC, PYR, ABI5, ERF1B, etc), stress response proteins (LEA D-29, HSP70, etc), and phospholipase D (PLD1) were detected during seed desiccation. These genes and their interactions may regulate the desiccation sensitivity of Q. variabilis seeds. Finally, a possible work model was proposed to show the molecular regulation mechanism of desiccation sensitivity in recalcitrant Q. variabilis seedsConclusions: Our study is the first on the molecular regulation mechanism of desiccation sensitivity of Q. variabilis seeds by using RNA-Seq and propose a possible work model. Our findings could make a great contribute to seed storage and long-term conservation of germplasm resources of recalcitrant seeds in the future.

scholarly journals Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis Seeds

2021 ◽  
Vol 12 ◽  
Author(s):  
Dongxing Li ◽  
Yingchao Li ◽  
Jialian Qian ◽  
Xiaojuan Liu ◽  
Huihui Xu ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Enrichment Analysis ◽  
Seed Storage ◽  
Germination Percentage ◽  
Molecular Regulation ◽  
Regulation Mechanism ◽  
Quercus Variabilis ◽  
Desiccation Sensitivity ◽  
Comparison Groups

Chinese cork oak (Quercus variabilis) is a widely distributed and highly valuable deciduous broadleaf tree from both ecological and economic perspectives. Seeds of this species are recalcitrant, i.e., sensitive to desiccation, which affects their storage and long-term preservation of germplasm. However, little is known about the underlying molecular mechanism of desiccation sensitivity of Q. variabilis seeds. In this study, the seeds were desiccated with silica gel for certain days as different treatments from 0 (Control) to 15 days (T15) with a gradient of 1 day. According to the seed germination percentage, four key stages (Control, T2, T4, and T11) were found. Then the transcriptomic profiles of these four stages were compared. A total of 4,405, 4,441, and 5,907 differentially expressed genes (DEGs) were identified in T2 vs. Control, T4 vs. Control, and T11 vs. Control, respectively. Among them, 2,219 DEGs were overlapped in the three comparison groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these DEGs were enriched into 124 pathways, such as “Plant hormone signal transduction” and “Glycerophospholipid metabolism”. DEGs related to hormone biosynthesis and signal transduction (ZEP, YUC, PYR, ABI5, ERF1B, etc.), stress response proteins (LEA D-29, HSP70, etc.), and phospholipase D (PLD1) were detected during desiccation. These genes and their interactions may determine the desiccation sensitivity of seeds. In addition, group specific DEGs were also identified in T2 vs. Control (PP2C62, UNE12, etc.), T4 vs. Control (WRKY1-like, WAK10, etc.), and T11 vs. Control (IBH1, bZIP44, etc.), respectively. Finally, a possible work model was proposed to show the molecular regulation mechanism of desiccation sensitivity in Q. variabilis seeds. This is the first report on the molecular regulation mechanism of desiccation sensitivity of Q. variabilis seeds using RNA-Seq. The findings could make a great contribution to seed storage and long-term conservation of recalcitrant seeds in the future.

scholarly journals Cancer-associated fibroblasts promote the survival of irradiated nasopharyngeal carcinoma cells via the NF-κB pathway

2021 ◽  
Vol 40 (1) ◽  
Author(s):  
Weiqiang Huang ◽  
Longshan Zhang ◽  
Mi Yang ◽  
Xixi Wu ◽  
Xiaoqing Wang ◽  
...  
Keyword(s):  
Dna Damage ◽  
Nasopharyngeal Carcinoma ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Gene Set Enrichment Analysis ◽  
Cancer Associated Fibroblasts ◽  
Western Blot Assay ◽  
Damage Level ◽  
Radiation Resistant

Abstract Background Irradiation has emerged as a valid tool for nasopharyngeal carcinoma (NPC) in situ treatment; however, NPC derived from tissues treated with irradiation is a main cause cancer-related death. The purpose of this study is to uncover the underlying mechanism regarding tumor growth after irradiation and provided potential therapeutic strategy. Methods Fibroblasts were extracted from fresh NPC tissue and normal nasopharyngeal mucosa. Immunohistochemistry was conducted to measure the expression of α-SMA and FAP. Cytokines were detected by protein array chip and identified by real-time PCR. CCK-8 assay was used to detect cell proliferation. Radiation-resistant (IRR) 5-8F cell line was established and colony assay was performed to evaluate tumor cell growth after irradiation. Signaling pathways were acquired via gene set enrichment analysis (GSEA). Comet assay and γ-H2AX foci assay were used to measure DNA damage level. Protein expression was detected by western blot assay. In vivo experiment was performed subcutaneously. Results We found that radiation-resistant NPC tissues were constantly infiltrated with a greater number of cancer-associated fibroblasts (CAFs) compared to radiosensitive NPC tissues. Further research revealed that CAFs induced the formation of radioresistance and promoted NPC cell survival following irradiation via the IL-8/NF-κB pathway to reduce irradiation-induced DNA damage. Treatment with Tranilast, a CAF inhibitor, restricted the survival of CAF-induced NPC cells and attenuated the of radioresistance properties. Conclusions Together, these data demonstrate that CAFs can promote the survival of irradiated NPC cells via the NF-κB pathway and induce radioresistance that can be interrupted by Tranilast, suggesting the potential value of Tranilast in sensitizing NPC cells to irradiation.

scholarly journals Uncovering Statistical Links Between Gene Expression and Structural Connectivity Patterns in the Mouse Brain

2021 ◽  
Author(s):  
Nestor Timonidis ◽  
Alberto Llera ◽  
Paul H. E. Tiesinga
Keyword(s):  
Gene Expression ◽  
Mouse Brain ◽  
Structural Connectivity ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Synaptic Function ◽  
Reticular Nucleus ◽  
Sources Of Information ◽  
Independent Components ◽  
Brain Connectome

AbstractFinding links between genes and structural connectivity is of the utmost importance for unravelling the underlying mechanism of the brain connectome. In this study we identify links between the gene expression and the axonal projection density in the mouse brain, by applying a modified version of the Linked ICA method to volumetric data from the Allen Institute for Brain Science for identifying independent sources of information that link both modalities at the voxel level. We performed separate analyses on sets of projections from the visual cortex, the caudoputamen and the midbrain reticular nucleus, and we determined those brain areas, injections and genes that were most involved in independent components that link both gene expression and projection density data, while we validated their biological context through enrichment analysis. We identified representative and literature-validated cortico-midbrain and cortico-striatal projections, whose gene subsets were enriched with annotations for neuronal and synaptic function and related developmental and metabolic processes. The results were highly reproducible when including all available projections, as well as consistent with factorisations obtained using the Dictionary Learning and Sparse Coding technique. Hence, Linked ICA yielded reproducible independent components that were preserved under increasing data variance. Taken together, we have developed and validated a novel paradigm for linking gene expression and structural projection patterns in the mouse mesoconnectome, which can power future studies aiming to relate genes to brain function.

scholarly journals Not BCL2 mutation but dominant mutation conversation contributed to acquired venetoclax resistance in acute myeloid leukemia

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Xiang Zhang ◽  
Jiejing Qian ◽  
Huafeng Wang ◽  
Yungui Wang ◽  
Yi Zhang ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Underlying Mechanism ◽  
Lymphocytic Leukemia ◽  
First Line ◽  
Dominant Mutation ◽  
First Line Therapy ◽  
Line Therapy ◽  
Acute Myeloid

AbstractVenetoclax (VEN) plus azacitidine has become the first-line therapy for elderly patients with acute myeloid leukemia (AML), and has a complete remission (CR) plus CR with incomplete recovery of hemogram rate of ≥70%. However, the 3-year survival rate of these patients is < 40% due to relapse caused by acquired VEN resistance, and this remains the greatest obstacle for the maintenance of long-term remission in VEN-sensitive patients. The underlying mechanism of acquired VEN resistance in AML remains largely unknown. Therefore, in the current study, nine AML patients with acquired VEN resistance were retrospectively analyzed. Our results showed that the known VEN resistance-associated BCL2 mutation was not present in our cohort, indicating that, in contrast to chronic lymphocytic leukemia, this BCL2 mutation is dispensable for acquired VEN resistance in AML. Instead, we found that reconstructed existing mutations, especially dominant mutation conversion (e.g., expanded FLT3-ITD), rather than newly emerged mutations (e.g., TP53 mutation), mainly contributed to VEN resistance in AML. According to our results, the combination of precise mutational monitoring and advanced interventions with targeted therapy or chemotherapy are potential strategies to prevent and even overcome acquired VEN resistance in AML.

scholarly journals Slc7a11 Modulated by POU2F1 is Involved in Pigmentation in Rabbit

2019 ◽  
Vol 20 (10) ◽  
pp. 2493 ◽  
Author(s):  
Yang Chen ◽  
Shuaishuai Hu ◽  
Lin Mu ◽  
Bohao Zhao ◽  
Manman Wang ◽  
...  
Keyword(s):  
Skin Color ◽  
Site Directed Mutagenesis ◽  
Molecular Regulation ◽  
Luciferase Reporter ◽  
Directed Mutagenesis ◽  
Regulation Mechanism ◽  
Solute Carrier Family ◽  
Depth Analysis ◽  
Solute Carrier ◽  
Fur Color

Solute carrier family 7 member 11 (Slc7a11) is a cystine/glutamate xCT transporter that controls the production of pheomelanin pigment to change fur and skin color in animals. Previous studies have found that skin expression levels of Slc7a11 varied significantly with fur color in Rex rabbits. However, the molecular regulation mechanism of Slc7a11 in pigmentation is unknown. Here, rabbit melanocytes were first isolated and identified. The distribution and expression pattern of Slc7a11 was confirmed in skin from rabbits with different fur colors. Slc7a11 affected the expression of pigmentation related genes and thus affected melanogenesis. Meanwhile, Slc7a11 decreased melanocyte apoptosis, but inhibition of Slc7a11 enhanced apoptosis. Furthermore, the POU2F1 protein was found to bind to the −713 to −703 bp region of Slc7a11 promoter to inhibit its activity in a dual-luciferase reporter and site-directed mutagenesis assay. This study reveals the function of the Slc7a11 in melanogenesis and provides in-depth analysis of the mechanism of fur pigmentation.

T cell long-term hyporesponsiveness follows antigen receptor engagement and results from defective signal transduction

1994 ◽  
Vol 24 (2) ◽  
pp. 348-354 ◽  
Author(s):  
Patrice M. Dubois ◽  
Fabienne Andris ◽  
Jacques Urbain ◽  
Oberdan Leo ◽  
Marcelle Kaufman ◽  
...  
Keyword(s):  
Signal Transduction ◽  
T Cell ◽  
Antigen Receptor

Subjective Age and Late-Life Functional Status: Mediating and Moderating Effects

2021 ◽  
Author(s):  
Joel R Petashnick ◽  
Amit Shrira ◽  
Yaakov Hoffman ◽  
Yuval Palgi ◽  
Gitit Kavé ◽  
...  
Keyword(s):  
Older Adults ◽  
Depressive Symptoms ◽  
Functional Status ◽  
Objective Measure ◽  
Later Life ◽  
Underlying Mechanism ◽  
Integrative Model ◽  
Subjective Age ◽  
Longitudinal Relationships

Abstract Objectives The present study examined the longitudinal relationships between subjective age (SA) and future functional status in later life, via depressive symptoms. Additionally, we assessed the role of subjective nearness to death (SNtD) as a potential moderator within these pathways. Methods Older adults (average age 81.14 at T1) were interviewed once a year for three consecutive years (N=224 at T1, N=178 at T2, and N=164 at T3), Participants reported their SA, SNtD, depressive symptoms, and functional status. Additionally, grip strength was employed as an objective measure of functional status. Results Data analysis revealed distinct pathways leading from T1 SA to T3 functional status through T2 depressive symptoms. Moreover, T1 SNtD was found to significantly moderate most of these indirect pathways, so that the mediation model of T1 SA-T2 depressive symptoms-T3 functional status was mostly significant among those who felt closer to death. Discussion The findings contribute to our understanding of the underlying mechanism through which SA predicts long-term functioning sequelae by underscoring the indirect effect of depressive symptoms. They further indicate the importance of gauging the effects of SNtD on these longitudinal relationships. Present results may further contribute to establishing an integrative model for predicting long-term functional outcomes based on older adults' earlier subjective views of aging.

scholarly journals Emotional Tagging and Belief Formation: The Long-Lasting Effects of Experiencing Communism

2019 ◽  
Vol 109 ◽  
pp. 567-571 ◽  
Author(s):  
Christine Laudenbach ◽  
Ulrike Malmendier ◽  
Alexandra Niessen-Ruenzi
Keyword(s):  
Formation Process ◽  
Crucial Role ◽  
Underlying Mechanism ◽  
Memory Formation ◽  
Belief Formation ◽  
Long Term Effects ◽  
Long Run

Growing evidence in macrofinance suggests long-lasting effects of personally experienced outcomes on beliefs. To understand the underlying mechanism we turn to the neurological foundations of memory formation. We propose that emotional tagging plays a crucial role in assigning weights in the belief formation process. We use exposure to communism as well as variation in its emotional tagging to predict long-run beliefs. We show that living under communism has long-term effects on beliefs about its benefits. In addition, positive and negative emotional tags strongly affect the (pro- or anti-communist) direction of beliefs, providing anchors to memory that seem hard to reverse.

scholarly journals Effects of Long-Term Hydrogen Intervention on Plasma Metabolites and Gut Microbiome of Rats in Health Status

2021 ◽  
Author(s):  
Fei Xie ◽  
Xue Jiang ◽  
Yang Yi ◽  
Zi-Jia Liu ◽  
Chen Ma ◽  
...  
Keyword(s):  
Health Status ◽  
Gut Microbiota ◽  
Biological Effects ◽  
Enrichment Analysis ◽  
The Body ◽  
Plasma Metabolites ◽  
Control Group ◽  
Pathway Enrichment Analysis ◽  
Rrna Gene

Abstract The potential for preventive and therapeutic applications of H2 have now been confirmed in various disease. However, the effects of H2 on health status have not been fully elucidated. Our previous study reported changes in the body weight and 13 serum biochemical parameters during the six-month hydrogen intervention. To obtain a more comprehensive understanding of the effects of long-term hydrogen consumption, the plasma metabolome and gut microbiota were investigated in this study. Compared with the control group, 14 and 10 differential metabolites (DMs) were identified in hydrogen-rich water (HRW) and hydrogen inhalation (HI) group, respectively. Pathway enrichment analysis showed that HRW intake mainly affected starch and sucrose metabolism, and DMs in HI group were mainly enriched in arginine biosynthesis. 16S rRNA gene sequencing showed that HRW intake induced significant changes in the structure of gut microbiota, while no marked bacterial community differences was observed in HI group. HRW intake mainly induced significant increase in the abundance of Lactobacillus, Ruminococcus, Clostridium XI, and decrease in Bacteroides. HI mainly induced decreased abundances of Blautia and Paraprevotella. The results of this study provide basic data for further research on hydrogen medicine. Determination of the effects of hydrogen intervention on microbiota profiles could also shed light on identification of mechanism underlying the biological effects of molecular hydrogen.

scholarly journals Network Pharmacology-Based Strategy for the Investigation of the Anti-Osteoporosis Effects and Underlying Mechanism of Zhuangguguanjie Formulation

2021 ◽  
Vol 12 ◽  
Author(s):  
Wang Gong ◽  
Xingren Chen ◽  
Tianshu Shi ◽  
Xiaoyan Shao ◽  
Xueying An ◽  
...  
Keyword(s):  
Bone Resorption ◽  
Bone Formation ◽  
Bone Mass ◽  
Signaling Pathway ◽  
Osteoclast Differentiation ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Network Pharmacology ◽  
Biological Processes

As the society is aging, the increasing prevalence of osteoporosis has generated huge social and economic impact, while the drug therapy for osteoporosis is limited due to multiple targets involved in this disease. Zhuangguguanjie formulation (ZG) is extensively used in the clinical treatment of bone and joint diseases, but the underlying mechanism has not been fully described. This study aimed to examine the therapeutic effect and potential mechanism of ZG on postmenopausal osteoporosis. The ovariectomized (OVX) mice were treated with normal saline or ZG for 4 weeks after ovariectomy following a series of analyses. The bone mass density (BMD) and trabecular parameters were examined by micro-CT. Bone remodeling was evaluated by the bone histomorphometry analysis and ELISA assay of bone turnover biomarkers in serum. The possible drug–disease common targets were analyzed by network pharmacology. To predict the potential biological processes and related pathways, GO/KEGG enrichment analysis was performed. The effects of ZG on the differentiation phenotype of osteoclasts and osteoblasts and the predicted pathway were verified in vitro. The results showed that ZG significantly improved the bone mass and micro-trabecular architecture in OVX mice compared with untreated OVX mice. ZG could promote bone formation and inhibit bone resorption to ameliorate ovariectomy-induced osteoporosis as evidenced by increased number of osteoblast (N.Ob/Tb.Pm) and decreased number of osteoclast (N.Oc/Tb.Pm) in treated group compared with untreated OVX mice. After identifying potential drug–disease common targets by network pharmacology, GO enrichment analysis predicted that ZG might affect various biological processes including osteoblastic differentiation and osteoclast differentiation. The KEGG enrichment analysis suggested that PI3K/Akt and mTOR signaling pathways could be the possible pathways. Furthermore, the experiments in vitro validated our findings. ZG significantly down-regulated the expression of osteoclast differentiation markers, reduced osteoclastic resorption, and inhibited the phosphorylation of PI3K/Akt, while ZG obviously up-regulated the expression of osteogenic biomarkers, promoted the formation of calcium nodules, and hampered the phosphorylation of 70S6K1/mTOR, which can be reversed by the corresponding pathway activator. Thus, our study suggested that ZG could inhibit the PI3K/Akt signaling pathway to reduce osteoclastic bone resorption as well as hamper the mTORC1/S6K1 signaling pathway to promote osteoblastic bone formation.

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