scholarly journals Transcriptomic Analysis Provides Insights into Grafting Union Development in Pecan (Carya illinoinensis)

2017 ◽  
Author(s):  
Zhenghai Mo ◽  
Gang Feng ◽  
Wenchuan Su ◽  
Zhuangzhuang Liu ◽  
Fangren Peng
Keyword(s):  
Secondary Cell Wall ◽  
Developmental Process ◽  
Carya Illinoinensis ◽  
Differentially Expressed ◽  
Vascular Bundles ◽  
Oxygen Species ◽  
Hormone Signaling ◽  
Graft Union ◽  
Time Points ◽  
Cell Wall Deposition

Pecan (Carya illinoinensis), as a popular nut tree, is widely planted in China in recent years. Grafting is an important technique for its cultivation. For a successful grafting, graft union development generally involves the formation of callus and vascular bundles at the graft union. To explore the molecular mechanism of graft union development, we applied high through-put RNA sequencing to investigate transcriptomic profiles of graft union at four time points (0d, 8d, 15d, and 30d) during pecan grafting process. We identified a total of 12,180 differentially expressed genes. In addition, we found that the content of auxin, cytokinin and gibberellin were accumulated at the graft unions during the grafting process. Correspondingly, genes involved in those hormone signaling were found to be differentially expressed. Interestingly, we found that most genes associated with cell division were up-regulated at callus formative stages, while genes related to cell elongation, secondary cell wall deposition, and programmed cell death were generally up-regulated at vascular bundle formative stages. In the meantime, genes responsible for reactive oxygen species were highly up-regulated across the graft union developmental process. These results will aid in our understanding of successful grafting in the future.

scholarly journals Knockout of Auxin Response Factor SlARF4 Improves Tomato Resistance to Water Deficit

2021 ◽  
Vol 22 (7) ◽  
pp. 3347
Author(s):  
Mengyi Chen ◽  
Xiaoyang Zhu ◽  
Xiaojuan Liu ◽  
Caiyu Wu ◽  
Canye Yu ◽  
...  
Keyword(s):  
Water Stress ◽  
Water Deficit ◽  
Vascular Bundle ◽  
Plant Resistance ◽  
Quantitative Polymerase Chain Reaction ◽  
Photochemical Efficiency ◽  
Differentially Expressed ◽  
Vascular Bundles ◽  
Aba Signaling ◽  
Auxin Response

Auxin response factors (ARFs) play important roles in various plant physiological processes; however, knowledge of the exact role of ARFs in plant responses to water deficit is limited. In this study, SlARF4, a member of the ARF family, was functionally characterized under water deficit. Real-time fluorescence quantitative polymerase chain reaction (PCR) and β-glucuronidase (GUS) staining showed that water deficit and abscisic acid (ABA) treatment reduced the expression of SlARF4. SlARF4 was expressed in the vascular bundles and guard cells of tomato stomata. Loss of function of SlARF4 (arf4) by using Clustered Regularly Interspaced Short Palindromic Repeats/Cas 9 (CRISPR/Cas 9) technology enhanced plant resistance to water stress and rehydration ability. The arf4 mutant plants exhibited curly leaves and a thick stem. Malondialdehyde content was significantly lower in arf4 mutants than in wildtype plants under water stress; furthermore, arf4 mutants showed higher content of antioxidant substances, superoxide dismutase, actual photochemical efficiency of photosystem II (PSII), and catalase activities. Stomatal and vascular bundle morphology was changed in arf4 mutants. We identified 628 differentially expressed genes specifically expressed under water deficit in arf4 mutants; six of these genes, including ABA signaling pathway-related genes, were differentially expressed between the wildtype and arf4 mutants under water deficit and unlimited water supply. Auxin responsive element (AuxRE) elements were found in these genes’ promoters indicating that SlARF4 participates in ABA signaling pathways by regulating the expression of SlABI5/ABF and SCL3, thereby influencing stomatal morphology and vascular bundle development and ultimately improving plant resistance to water deficit.

Dynamic plasma extracellular vesicle long RNA profiling changes during the peri-operative period

2020 ◽  
Author(s):  
qing hua ◽  
wenhao xu ◽  
xuefang shen ◽  
xi tian ◽  
Peng Wang ◽  
...  
Keyword(s):  
Immune Cell ◽  
Surgical Stress ◽  
Distant Metastases ◽  
Cell Types ◽  
R Package ◽  
Extracellular Vesicle ◽  
Differentially Expressed ◽  
Dynamic Changes ◽  
Rna Profiling ◽  
Time Points

Abstract Background: Surgery remains the most important treatment strategy for solid tumors, such as colorectal cancer (CRC); However, a number of studies have suggested that surgical stress contributes to tumor recurrence or distant metastases. Extracellular vesicles (EVs), which contain a rich variety of RNAs with specialized functions and clinical applications, have been shown to be an indicator for diagnosis and prognosis of cancers. The effect of surgical stress on the landscape and characteristics of EV long RNA (exLR) in human blood, however, remains largely unknown.Methods: We present an optimized strategy for exLR sequencing (exLR-seq) the plasma from three patients with CRC at 4 time points (before surgery [T0], after extubation [T1], 1 day after surgery [T2], and 3 days after surgery [T4]). The “Limma” R package was used to evaluate the dynamic changes of mRNAs and long non-coding (lnc)RNAs from EVs. We also constructed a protein–protein interaction (PPI) network of hub genes and predicted biological processes, cellular components, and molecular functions of gene ontology (GO) functional analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Results: We observed a sufficient number of exLRs, including 12,924 mRNAs and 2196 lncRNAs. Both mRNAs and lncRNAs underwent dynamic changes during the peri-operative period. Compared with T0, there were 110 mRNAs differentially expressed after extubation, 60 differentially expressed genes（DEGs）1 day after surgery, and 50 DEGs 3 days after surgery. A total of 11 genes changed at all 3 time points and were related to regulation of the membrane potential, receptor complex, and passive transmembrane transporter activity. In addition, 22 lncRNAs were differentially expressed after extubation (T1). Nineteen lncRNAs were differentially expressed between T0 and T2, and 38 lncRNAs were differentially expressed between T0 and T3. In addition, we found that only 3 lncRNAs changed at 3 time points. Interestingly, blood exLRs reflected the tissue origins and relative fractions of different immune cell types. EVs from CD8+ T，CD4+ memory T, and NK cells decreased after surgery and the absolute quality of EVs from immune cells decreased as well. Conclusion: In summary, this study demonstrated abundant exLRs in human plasma and the dynamic changes of these exLRs and exLRs originating from CD8+ T and CD4+ memory T cells were reduced during the peri-operative period.

scholarly journals DHA reduces oxidative stress following hypoxia-ischemia in newborn piglets: a study of lipid peroxidation products in urine and plasma

2018 ◽  
Vol 46 (2) ◽  
pp. 209-217 ◽  
Author(s):  
Marianne Ullestad Huun ◽  
Håvard T. Garberg ◽  
Javier Escobar ◽  
Consuelo Chafer ◽  
Maximo Vento ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Reactive Oxygen Species ◽  
Lipid Peroxidation ◽  
Oxygen Species ◽  
Major Contributor ◽  
Time Points ◽  
Newborn Piglets ◽  
Hypoxia Group ◽  
Hypoxia Ischemia ◽  
Anti Oxidant

AbstractBackground:Lipid peroxidation mediated by reactive oxygen species is a major contributor to oxidative stress. Docosahexaenoic acid (DHA) has anti-oxidant and neuroprotective properties. Our objective was to assess how oxidative stress measured by lipid peroxidation was modified by DHA in a newborn piglet model of hypoxia-ischemia (HI).Methods:Fifty-five piglets were randomized to (i) hypoxia, (ii) DHA, (iii) hypothermia, (iv) hypothermia+DHA or (v) sham. All groups but sham were subjected to hypoxia by breathing 8% O2. DHA was administered 210 min after end of hypoxia and the piglets were euthanized 9.5 h after end of hypoxia. Urine and blood were harvested at these two time points and analyzed for F4-neuroprostanes, F2-isoprostanes, neurofuranes and isofuranes using UPLC-MS/MS.Results:F4-neuroprostanes in urine were significantly reduced (P=0.006) in groups receiving DHA. Hypoxia (median, IQR 1652 nM, 610–4557) vs. DHA (440 nM, 367–738, P=0.016) and hypothermia (median, IQR 1338 nM, 744–3085) vs. hypothermia+DHA (356 nM, 264–1180, P=0.006). The isoprostane compound 8-iso-PGF2α was significantly lower (P=0.011) in the DHA group compared to the hypoxia group. No significant differences were found between the groups in blood.Conclusion:DHA significantly reduces oxidative stress by measures of lipid peroxidation following HI in both normothermic and hypothermic piglets.

scholarly journals The Impacts of Tumorigenic and Nontumorigenic Agrobacterium vitis Strains on Graft Strength and Growth of Grapevines

Plant Disease ◽  
2018 ◽  
Vol 102 (2) ◽  
pp. 375-381 ◽  
Author(s):  
Lingyun Hao ◽  
David J. Kemmenoe ◽  
Didem Canik Orel ◽  
Thomas Burr
Keyword(s):  
Crown Gall ◽  
Shoot Growth ◽  
Callus Formation ◽  
Aqueous Suspension ◽  
Water Control ◽  
Agrobacterium Vitis ◽  
Graft Union ◽  
Time Points ◽  
Graft Interface ◽  
Grafting Procedure

The effects of tumorigenic and nontumorigenic strains of Agrobacterium vitis on graft strength and growth of grapevines was studied. A procedure was developed for inoculating graft interface surfaces with A. vitis and for measuring the force required to break grafts at different time points. Cuttings were soaked in an aqueous suspension of bacteria, about 106 CFU/ml, and bacteria were spread onto the graft interface during the grafting procedure. Tumorigenic strain CG49 caused reduced bud germination and increased callus (crown gall) at the graft union and at the base of cuttings at 30 days postinoculation (dpi) and significantly reduced shoot growth by 60 dpi whereas, at the same time points, nontumorigenic strain F2/5 inhibited callus formation but did not affect bud germination or shoot growth. Graft strength was enhanced at 30 dpi with CG49, presumably because the crown gall callus served to secure the union; graft strength was weakened by F2/5 over the same period. Between 30 and 60 dpi, the greatest increase in graft strength was observed in the water control. Following graft union inoculations, the A. vitis population increased more than 1,000-fold within 5 days.

Effects of short- and medium-term calorie restriction on muscle mitochondrial proton leak and reactive oxygen species production

2004 ◽  
Vol 286 (5) ◽  
pp. E852-E861 ◽  
Author(s):  
Lisa Bevilacqua ◽  
Jon J. Ramsey ◽  
Kevork Hagopian ◽  
Richard Weindruch ◽  
Mary-Ellen Harper
Keyword(s):  
Reactive Oxygen Species ◽  
Oxidative Phosphorylation ◽  
Metabolic Control ◽  
Calorie Restriction ◽  
Reactive Oxygen ◽  
Proton Leak ◽  
Ros Production ◽  
Oxygen Species ◽  
Medium Term ◽  
Time Points

Reductions in cellular oxygen consumption (V̇o2) and reactive oxygen species (ROS) production have been proposed as mechanisms underlying the anti-aging effects of calorie restriction (CR). Mitochondria are a cell's greatest “sink” for oxygen and also its primary source of ROS. The mitochondrial proton leak pathway is responsible for 20–30% of V̇o2 in resting cells. We hypothesized that CR leads to decreased proton leak with consequential decreases in V̇o2, ROS production, and cellular damage. Here, we report the effects of short-term (2-wk, 2-mo) and medium-term (6-mo) CR (40%) on rat muscle mitochondrial proton leak, ROS production, and whole animal V̇o2. Whole body V̇o2 decreased with CR at all time points, whereas mass-adjusted V̇o2 was normal until the 6-mo time point, when it was 40% lower in CR compared with control rats. At all time points, maximal leak-dependent V̇o2 was lower in CR rats compared with controls. Proton leak kinetics indicated that mechanisms of adaptation to CR were different between short- and medium-term treatments, with the former leading to decreases in protonmotive force (Δp) and state 4 V̇o2 and the latter to increases in Δp and decreases in state 4 V̇o2. Results from metabolic control analyses of oxidative phosphorylation are consistent with the idea that short- and medium-term responses are distinct. Mitochondrial H2O2 production was lower in all three CR groups compared with controls. Overall, this study details the rapid effects of short- and medium-term CR on proton leak, ROS production, and metabolic control of oxidative phosphorylation. Results indicate that a reduction in mitochondrial V̇o2 and ROS production may be a mechanism for the actions of CR.

scholarly journals Transcriptomic profiling of neonatal mouse granulosa cells reveals new insights into primordial follicle activation

2021 ◽  
Author(s):  
Emmalee A Ford ◽  
Emily R Frost ◽  
Emma L Beckett ◽  
Shaun D Roman ◽  
Eileen A McLaughlin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Granulosa Cells ◽  
Expression Profiles ◽  
Primordial Follicle ◽  
Differentially Expressed ◽  
Primary Follicle ◽  
Primordial Follicles ◽  
Time Points ◽  
Primordial Follicle Activation ◽  
Follicle Activation

Abstract The dormant population of ovarian primordial follicles is determined at birth and serves as the reservoir for future female fertility. Yet our understanding of the molecular, biochemical, and cellular processes underpinning primordial follicle activation remains limited. The survival of primordial follicles relies on the correct complement and morphology of granulosa cells, which provide signalling factors essential for oocyte and follicular survival. To investigate the contribution of granulosa cells in the primordial-to-primary follicle transition, gene expression profiles of granulosa cells undergoing early differentiation were assessed in a murine model. Ovaries from C57Bl/6 mice were enzymatically dissociated at time-points spanning the initial wave of primordial follicle activation. Post-natal day (PND) 1 ovaries yielded primordial granulosa cells, and PND4 ovaries yielded a mixed population of primordial and primary granulosa cells. The comparative transcriptome of granulosa cells at these time-points was generated via Illumina NextSeq 500 system which identified 131 significantly differentially expressed transcripts. The differential expression of eight of the transcripts was confirmed by RT-qPCR Following biological network mapping via Ingenuity Pathway Analysis, the functional expression of the protein products of three of the differentially expressed genes, namely FRZB, POD1 and ZFX, was investigated with in-situ immunolocalisation in PND4 mouse ovaries was investigated. Finally, evidence was provided that Wnt pathway antagonist, secreted frizzled-related protein 3 (FRZB), interacts with a suppressor of primordial follicle activation WNT3A and may be involved in promoting primordial follicle activation. This study highlights the dynamic changes in gene expression of granulosa cells during primordial follicle activation and provides evidence for a renewed focus into the Wnt signalling pathway’s role in primordial follicle activation.

scholarly journals Multi-organ transcriptomic landscape of Ambystoma velasci metamorphosis

2020 ◽  
Author(s):  
Palacios-Martínez Janet ◽  
Caballero-Pérez Juan ◽  
Espinal-Centeno Annie ◽  
Marquez-Chavoya Gilberto ◽  
Lomelí Hilda ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Developmental Process ◽  
Global Analysis ◽  
Expression Patterns ◽  
Coronary Vessels ◽  
Aquatic Organisms ◽  
Gene Clusters ◽  
Differentially Expressed ◽  
Transcriptional Responses ◽  
Terrestrial Environment

Metamorphosis is a postembryonic developmental process that involves morphophysiological and behavioral changes, allowing organisms to adapt into a novel environment. In some amphibians, aquatic organisms undergo metamorphosis to adapt in a terrestrial environment. These organisms experience major changes in their circulatory, respiratory, digestive, excretory and reproductive systems. We performed a transcriptional global analysis of heart, lung and gills during diverse stages of Ambystoma velasci metamorphosis. In our analyses, we identified eight gene clusters for each organ, according to the expression patterns of differentially expressed genes. We found 4,064 differentially expressed genes in the heart, 4,107 in the lung and 8,265 in the gills. Among the differentially expressed genes in the heart, we observed genes involved in the differentiation of cardiomyocytes in the interatrial zone, vasculogenesis and in the maturation of coronary vessels. In the lung, we found genes differentially expressed related to angiogenesis, alveolarization and synthesis of the surfactant protein. In the case of the gills, the most prominent biological processes identified are degradation of extracellular matrix, apoptosis and keratin production. Our study sheds light on the transcriptional responses and the pathways involved in the transformation of the facultative metamorphic salamander A. velasci in an organ-specific manner.

scholarly journals Reactive oxygen species as important regulators of cell division

2020 ◽  
Author(s):  
Weiliang Qi ◽  
Li Ma ◽  
Fei Wang ◽  
Ping Wang ◽  
Junyan Wu ◽  
...  
Keyword(s):  
Reactive Oxygen Species ◽  
Cell Wall ◽  
Cell Division ◽  
Cold Stress ◽  
Reactive Oxygen ◽  
Vascular Bundles ◽  
Oxygen Species ◽  
Root Primordia ◽  
Lateral Root Primordia

AbstractCurrently, the role of reactive oxygen species (ROS) in plant growth is a topic of interest. In this study, we discuss the role of ROS in cell division. We analyzed ROS’ impact on the stiffness of plant cell walls and whether ROS play an important role in Brassica napus’ ability to adapt to cold stress. Cultivated sterile seedlings and calli of cold-tolerant cultivar 16NTS309 were subjected to cold stress at 25°C and 4°C, respectively. Under normal conditions, O2.− mainly accumulated in the leaf edges, shoot apical meristem, leaf primordia, root tips, lateral root primordia, calli of meristematic nodular tissues, cambia, vascular bundles and root primordia, which are characterized by high division rates. After exposure to cold stress, the malondialdehyde and ROS (O2.−) contents in roots, stems and leaves of cultivar 16NTS309 were significantly higher than under non-cold conditions (P < 0.05). ROS (O2.−) were not only distributed in these zones, but also in other cells, at higher levels than under normal conditions. A strong ROS-based staining appeared in the cell wall. The results support a dual role for apoplastic ROS, in which they have direct effects on the stiffness of the cell wall, because ROS cleave cell-wall, and act as wall loosening agents, thereby either promoting or restricting cellular division. This promotes the appearance of new shoots and a strong root system, allowing plants to adapt to cold stress.

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