scholarly journals RNA sequencing-based exploration of the effects of far-red light on lncRNAs involved in the shade-avoidance response of D. officinale

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10769
Author(s):  
Hansheng Li ◽  
Wei Ye ◽  
Yaqian Wang ◽  
Xiaohui Chen ◽  
Yan Fang ◽  
...  
Keyword(s):  
Avoidance Response ◽  
Rna Sequencing ◽  
Production Efficiency ◽  
Stem Elongation ◽  
Red Light ◽  
Differentially Expressed ◽  
Control Group ◽  
Shade Avoidance ◽  
Biochemical Analyses ◽  
Experimental Group

Dendrobium officinale (D. officinale) is a valuable medicinal plant with a low natural survival rate, and its shade-avoidance response to far-red light is as an important strategy used by the plant to improve its production efficiency. However, the lncRNAs that play roles in the shade-avoidance response of D. officinale have not yet been investigated. This study found that an appropriate proportion of far-red light can have several effects, including increasing the leaf area and accelerating stem elongation, in D. officinale. The effects of different far-red light treatments on D. officinale were analysed by RNA sequencing technology, and a total of 69 and 78 lncRNAs were differentially expressed in experimental group 1 (FR1) versus the control group (CK) (FR1-CK) and in experimental group 4 (FR4) versus the CK (FR4-CK), respectively. According to GO and KEGG analyses, most of the differentially expressed lncRNA targets are involved in the membrane, some metabolic pathways, hormone signal transduction, and O-methyltransferase activity, among other functions. Physiological and biochemical analyses showed that far-red light promoted the accumulation of flavonoids, alkaloids, carotenoids and polysaccharides in D. officinale. The effect of far-red light on D. officinalemight be closely related to the cell membrane and Ca2+ transduction. Based on a Cytoscape analysis and previous research, this study also found that MSTRG.38867.1, MSTRG.69319.1, and MSTRG.66273.1, among other components, might participate in the far-red light signalling network through their targets and thus regulate the shade-avoidance response of D. officinale. These findings will provide new insights into the shade-avoidance response of D. officinale.

Proteomic analysis of tears and serum for dry eye disease using ovariectomized cynomolgus monkey

2020 ◽  
Author(s):  
xiaolong yang ◽  
Yue Xu ◽  
Yun Wang ◽  
Chang Li ◽  
Xiaofeng Zhang
Keyword(s):  
Gene Ontology ◽  
Growth Factor ◽  
Dry Eye ◽  
Cynomolgus Monkey ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Control Group ◽  
Differentially Expressed Proteins ◽  
Dry Eyes ◽  
Experimental Group

Abstract Background Ovariectomized cynomolgus monkey 30 months after surgery was selected as the research object to identify protein changes in tears and serum to provide a reference for the diagnosis and pathogenesis of dry eye in menopausal women. Methods Six cynomolgus monkey were randomly divided into an experimental group and a control group (3 in each group). The experimental group underwent bilateral ovariectomy, while the control group underwent sham surgery with their ovaries reserved. Proteomic analysis was performed by LC-MS/MS on tears and serum collected from two groups. Differentially expressed proteins were identified and were performed cluster analysis, which included gene ontology, the Kyoto Encyclopedia of Genes and Genomes pathway and protein-protein interaction. Results 33 differentially expressed proteins have been identified in tears and17 differentially expressed proteins have been identified in serum. Kyoto Encyclopedia of Genes and Genomes enrichment analysis in tears has discovered Glucagon signaling pathway and neurotrophin signaling pathway may play an important role in the pathogenesis of dry eye. Gene ontology enrichment analysis in serum has discovered insulin-like growth factor binding and growth factor binding in molecular function probably make effort in pathogenesis of dry eye. KEGG analysis in serum has discovered salivary secretion may be the key pathway in pathogenesis of dry eye. Conclusions Protein G7PCH4, Q2PG17 and G7PT55 in tears may be the key protein in pathogenesis of dry eyes. Protein G7P1T1, G7PUN9 and G8F302 in serum may play an important role in pathogenesis of dry eyes.

Maximum elongation growth promoted as a shade-avoidance response by blue light is related to deactivated phytochrome: a comparison with red light in four microgreen species

2020 ◽  
Vol 100 (3) ◽  
pp. 314-326 ◽  
Author(s):  
Yun Kong ◽  
Katherine Schiestel ◽  
Youbin Zheng
Keyword(s):  
Avoidance Response ◽  
Blue Light ◽  
Plant Traits ◽  
Red Light ◽  
Elongation Growth ◽  
Extension Rate ◽  
Shade Avoidance ◽  
Maximum Elongation ◽  
Hypocotyl Length ◽  
Response Sensitivity

To clarify detailed patterns of responses to blue light associated with decreasing phytochrome activity, the growth and morphology traits of arugula, cabbage, mustard, and kale microgreens were compared under the treatments: (1) R, pure red light; (2) B, pure blue light; (3) BRF0, (4) BRF2, (5) BRF4, and (6) BRF6: unpure blue lights created by mixing B with low-level (6%) R, and further adding 0, 2, 4, and 6 μmol m−2 s−1 of far-red light, respectively. The calculated phytochrome photostationary state (PPS) value, indicating phytochrome activity, gradually decreased in the order of R (0.89), BRF0 (0.69), BRF2 (0.65), BRF4 (0.63), BRF6 (0.60), and B (0.50). Generally, the elongation growth (including stem extension rate, hypocotyl length, or petiole length) under blue lights increased with the decreasing PPS values, showing the highest and lowest sensitivity for arugula and mustard, respectively. However, the elongation promoted by blue lights gradually became saturated once the PPS values decreased below 0.60, a level which deactivates phytochrome. Other plant traits, such as biomass allocation and plant color, varied with increasing shade-avoidance responses to blue lights with decreasing PPS values relative to R, and these traits reached saturation at a similar PPS value as elongation. The response sensitivity was highest in elongation growth for arugula and cabbage, and highest in plant color for kale and mustard. This suggests that deactivated phytochrome contributes to the maximum elongation promotion as a shade-avoidance response induced by blue light, although the response sensitivity varies with plant traits and species.

Influence of Water Activated by Far Infrared Porous Ceramics on Nitrogen Absorption in the Pig Feed

2016 ◽  
Vol 16 (4) ◽  
pp. 3977-3980 ◽  
Author(s):  
Junping Meng ◽  
Jie Liu ◽  
Jinsheng Liang ◽  
Hongchen Zhang ◽  
Yan Ding
Keyword(s):  
Drinking Water ◽  
Protein Content ◽  
Production Efficiency ◽  
Animal Husbandry ◽  
Far Infrared ◽  
Porous Ceramics ◽  
Control Group ◽  
The Sustainable Development ◽  
Pig Feed ◽  
Experimental Group

Under modern and intensive feeding livestock and poultry density has increased, and brought a deterioration of the farm environment. The livestock and their excrement generate harmful gases such as ammonia, etc. which restricted the sustainable development and improvement of production efficiency of animal husbandry. In this paper, a new kind of far infrared porous ceramics was prepared to activate the animal drinking water. The activated water and common water were then supplied to pigs, and the fresh pig feces of experimental group and control group were collected on a regular basis. The residual protein content in feces was tested by Kjeldahl nitrogen method to study the influence law of the porous ceramics on absorbing nitrogen element in animal feces. The results showed that compared with the control group, the protein content in the experimental group decreased on average by 39.2%. The activated drinking water was conducive to the absorption of nitrogen in pig feed. The clusters of water molecules became smaller under the action of the porous ceramics. Hence, they were easy to pass through the water protein channel on the cell membrane for speeding up the metabolism.

scholarly journals Phytochrome contributes to blue-light-mediated stem elongation and associated shade-avoidance response in mature Arabidopsis plants

2020 ◽  
Author(s):  
Yun Kong ◽  
Youbin Zheng
Keyword(s):  
Avoidance Response ◽  
Blue Light ◽  
Stem Elongation ◽  
Growth Trait ◽  
Stem Length ◽  
Photon Flux ◽  
Photon Flux Density ◽  
Shade Avoidance ◽  
Wild Type ◽  
Avoidance Responses

AbstractOur recent studies on ornamental plants and microgreens indicate that blue-light-mediated stem elongation is related to phytochrome activity, which was based on the calculated phytochrome photoequilibrium. To examine whether phytochromes really contribute to the blue light’s effect, plant phenotypic responses were investigated in wild type Arabidopsis (Col-0), and its quintuple phytochrome (phyA phyB phyC phyD phyE) mutant plants under the following light treatments: (1) R, a pure red light from 660-nm LED; (2) B, a pure blue light from 455-nm LED; (3) BR, a impure blue light from LED combination of 94% B and 6% R; and (4) BRF, another impure blue light from LED combination of BR and 6 µmol m−2 s−1 of FR (735 nm). For all the light treatments, a photosynthetic photon flux density of ≈100 μmol m−2 s−1 were provided by 24-h lighting daily inside a walk-in growth chamber, which had an air temperature of ≈ 23 °C. The calculated phytochrome photoequilibrium was 0.89, 0.50, 0.69, and 0.60 for R, B, BR, and BRF, respectively, indicating a higher phytochrome activity under R and BR than B and BRF. After 18 days of light treatment, B or BRF increased main stem length in wild-type plants compared with R, but BR had an inhibition effect similar to R. Also, B and BRF relative to R or BR induced earlier flowering and reduced leaf size in wild type plants, showing typical shade-avoidance responses. In phytochrome-deficient mutant plants, the above shade-avoidance responses were inhibited under B or BRF, and induced under BR. However, as an exception, hypocotyl length, a growth trait during the de-etiolation stage, was reduced under B, BR and BRF vs. R regardless of phytochrome absence. It suggests that for mature Arabidopsis plants, phytochrome plays an active role in blue-light-mediated stem elongation and associated shade-avoidance response.

scholarly journals The bacteriostatic effect and mechanism of berberine on Methicillin resistant Staphylococcus aureus in vitro

2020 ◽  
Author(s):  
Lei Wang ◽  
Fangfang Zhou ◽  
Minyi Xu ◽  
Pei Lu ◽  
Ming Lin ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Cell Wall ◽  
Rna Sequencing ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Differentially Expressed ◽  
Control Group ◽  
High Concentration ◽  
Bacteriostatic Effect ◽  
Low Concentration ◽  
Cell Wall Hydrolysis

Abstract Background: To observe the bacteriostatic effect of berberine (BBR) and BBR combined with gentamicin (GEN), levofloxacin (LEV) and amikacin (AMI) on Methicillin resistant Staphylococcus aureus (MRSA), while also exploring the bacteriostatic mechanism of BBR on MRSA. Results: The MICs range of BBR on 26 strains of MRSA was 32-256 µg/mL. BBR combined with GEN, LEV and AMI had obvious bacteriostatic effect on MRSA. After co-culturing MRSA with BBR at 512 µg/mL, 64 µg/mL and 8 µg/mL, respectively, the electrical conductivity increased, compared with the control group, by 8.14%, 13.08% and 12.01%, respectively. Using transmission electron microscopy, we found that low concentration of BBR (8 µg/mL; 1/8 MIC) caused no significant damage to MRSA, and the bacterial structure of MRSA remained intact, while high concentration of BBR (512 µg/mL; 8 MIC) induced the destruction and dissolution of MRSA cell wall structure and the leakage of bacterial contents, leading to bacterial lysis. RNA-sequencing results showed that there were 754 differentially expressed genes in the high concentration group compared with the normal control group. Compared with the low concentration group, there were 590 differentially expressed genes in the high concentration group. Compared with the control group, only 19 genes were differentially expressed in the low concentration group. The up-regulated genes are mainly related to the cell wall hydrolysis regulatory genes, while the down-regulated genes are mainly related to the serine protease family. Conclusions: BBR displayed an excellent bacteriostatic effect on MRSA. BBR combined with GEN and AMI significantly enhanced the bacteriostatic effect on MRSA, while BBR combined with LEV showed no significant change in the bacteriostatic effect on MRSA. BBR inhibited bacteria by destroying and dissolving the structure of MRSA cell wall. RNA-sequencing results further demonstrated that the expression of cell wall hydrolysis genes ssaA, lytM and virulence factor serine protease genes were significantly differentially expressed when high concentration BBR treated on MRSA.

Memory and Ribonucleic Acid (Rna): Transfer of an Avoidance Response

1970 ◽  
Vol 27 (1) ◽  
pp. 99-103 ◽  
Author(s):  
Franco Lepore ◽  
Raymond Ducharme ◽  
Bruno Cardu
Keyword(s):  
Avoidance Response ◽  
Ribonucleic Acid ◽  
Avoidance Training ◽  
Control Group ◽  
Fourth Group ◽  
Experimental Group

4 groups of rats were used to test the hypothesis that learning can be “transferred” by means of “ribonucleic” acid (RNA). The experimental group was injected with RNA obtained from the brains of rats conditioned to an avoidance response. The control group received no RNA. A second control group was given RNA which came from the brains of non-conditioned rats. The fourth group received RNA extracted from the muscles of conditioned rats. The results did not confirm the transfer hypothesis since no RNA facilitating effect on subsequent avoidance training was observed.

scholarly journals Effect of thyme extract on fertility and survival of ISA F-15 broilers

2018 ◽  
pp. 74-80
Author(s):  
Е. A. Kishniaikina ◽  
К. V. Zhuchaev
Keyword(s):  
Weight Gain ◽  
Production Efficiency ◽  
Live Weight ◽  
Productivity Index ◽  
Feed Consumption ◽  
Control Group ◽  
Production Cycle ◽  
Feed Costs ◽  
Experimental Group ◽  
Different Doses

The paper highlights the research conducted in order to assess the effect of different doses of thyme extract on the productive properties and livability of broiler chickens. The experiment was conducted at a broiler poultry farm with a closed production cycle; the experiment assumed the control group and 5 experimental groups where each group contained 37 broilers at floor housing. The broilers of the 1st experimental group were fed with the extract of medicinal plant thyme dosed 2 mg/kg; broilers of the 2nd group received thyme extract dosed 4 mg/kg; 3rd group of broilers – 6 mg/kg, 4th group -8 mg/kg, and the dosage of the thyme extract was 10 mg/kg for broilers in the 5th experimental group. The authors controlled the live weight of broilers in each group by means of individual weighing every 7 days. Using this data the researchers calculated average daily body weight gain, absolute and relative gain; feed consumption was daily calculated. Feed consumption became the basis for calculating feed costs per a kilo of live weight gain. The authors recorded the number of daily fallen chickens. The data on poultry loss was the basis for calculating poultry livability. In order to assess production efficiency, the European productivity index was calculated. The research results indicate the efficiency of thyme extract application in different doses when feeding the broiler. Application of thyme extract in feeding meat poultry allowed to increase productive properties of broilers from experimental groups from 2.3 to 4.7%, reduce feed costs per a kilo by 1.1-8.1%, increase poultry livability on 2.7-8.1% and increase the European productivity index in the experimental groups on 0.2 21.3%.

scholarly journals Phytochrome-A as a Strategy to Control Internode Elongation in Crops Grown in Crowded Conditions

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 862E-862
Author(s):  
D.J. Tennessen
Keyword(s):  
Avoidance Response ◽  
Crop Production ◽  
Plant Density ◽  
Red Light ◽  
Shade Avoidance ◽  
Internode Elongation ◽  
Phytochrome A ◽  
Dark Green ◽  
Transformed Tobacco

Increased plant density can reduce the per-plant cost of ornamental and vegetable crop production, but also reduces the quality of the crop produced. Plants grown under these conditions exhibit internode elongation and yellow leaves. This response generally is described as a shade-avoidance response. Genetically transformed tobacco that express oat Phytochrome-A (Phy-A) grew short in white light but grew as tall as the nontransformed control (10 cm) in red light. When a mixture of red and 5% far-red (700 to 750 nm) was used, transformed tobacco remained short (5 cm) and dark green, whereas nontransformed grew taller (27 cm). The concept of masking the shade avoidance response was tested in transformed lines of tomato (Boylan and Quail 1989) that express elevated oat Phy-A. Transformed plants remained short and dark-green in shade-light. Phy-A may be a useful strategy to mask the shade-avoidance response.

15 Differentially Expressed Long Non-coding RNA Associated with Gastrointestinal Nematode Infection in Divergent Immune Response Sheep

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 7-8
Author(s):  
Maria Malane M Muniz ◽  
Mohammed Boareki ◽  
Samantha Dixon ◽  
Andrew S Peregrine ◽  
Paula Menzies ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Liver Tissue ◽  
Gastrointestinal Nematode ◽  
Nematode Infection ◽  
Differentially Expressed ◽  
Control Group ◽  
Non Coding Rna ◽  
And Control ◽  
Long Non Coding Rna ◽  
Transcript Discovery

Abstract Gastrointestinal nematode infection is one of the major production problems for sheep producers worldwide due its high incidence, morbidity, and mortality in affected flocks. The study of long non-coding RNA (lncRNA) in liver tissue of high (HIR) and low immune responder (LIR) sheep to GINs using RNA-Sequencing technology may provide a better understanding of the gene regulation mechanism associated with the host response to the infection. The aim of this study was to identify differentially expressed (DE) lncRNA between HIR and LIR natural infested sheep and control group. Liver tissue samples from the 13 divergent animals (out of a population of 211) based on their immunoglobulin G levels after vaccination using Hen Egg White (HEW) Lysozyme, and immature abomasum worm counts [HIR (> 4000) (n = 5), LIR (< 1500) (n=5) and control (no parasite challenge) (n=4) groups] were used to perform transcriptomic analysis using RNA-Sequencing. The “Large Gap read mapping “and “Transcript Discovery” tools from CLC Genomics Workbench 20.0.4 (CLC Bio, Aarhus, Denmark), were used to map reads to a reference genome (Oar_rambouillet_v1.0) and transcript discovery, respectively. The FEELnc software was used to identify, from predicted transcript model, potential lncRNAs and classify those transcripts into intro putative lncRNAs and protein coding RNAs. As preliminary results, 8 and 48 DE lncRNAs for HIR and LIR compared to control group were identified, respectively using an adjusted p-value False Discovery Rate (FDR) < 0.05 and Fold change (FC) abs > 2. Functional analyses using the list of DE lncRNAs identified metabolic pathways related to immune function. In depth analysis will help to better understand the physiological mechanisms of resilience of high immune sheep.

scholarly journals Identification and Characterization of Serum microRNAs as Biomarkers for Human Disc Degeneration: An RNA Sequencing Analysis

Diagnostics ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1063
Author(s):  
Shangbin Cui ◽  
Zhiyu Zhou ◽  
Xizhe Liu ◽  
Robert Geoff Richards ◽  
Mauro Alini ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Disc Degeneration ◽  
Lumbar Disc ◽  
Young Patients ◽  
Differentially Expressed ◽  
Control Group ◽  
Sequencing Analysis ◽  
Circulating Mirnas ◽  
Sequencing Data ◽  
Ivd Degeneration

Circulating microRNAs (miRNAs) have been associated with various degenerative diseases, including intervertebral disc (IVD) degeneration. Lumbar disc herniation (LDH) often occurs in young patients, although the underlying mechanisms are poorly understood. The aim of this work was to generate RNA deep sequencing data of peripheral blood samples from patients suffering from LDH, identify circulating miRNAs, and analyze them using bioinformatics applications. Serum was collected from 10 patients with LDH (Disc Degeneration Group); 10 patients without LDH served as the Control Group. RNA sequencing analysis identified 73 differential circulating miRNAs (p < 0.05) between the Disc Degeneration Group and Control Group. Gene ontology enrichment analysis (p < 0.05) showed that these differentially expressed miRNAs were associated with extracellular matrix, damage reactions, inflammatory reactions, and regulation of apoptosis. Kyoto Encyclopedia of Genes and Genomes analysis showed that the differentially expressed genes were involved in diverse signaling pathways. The profile of miR-766-3p, miR-6749-3p, and miR-4632-5p serum miRNAs was significantly enriched (p < 0.05) in multiple pathways associated with IVD degeneration. miR-766-3p, miR-6749-3p, and miR-4632-5p signature from serum may serve as a noninvasive diagnostic biomarker for LHD manifestation of IVD degeneration. Furthermore, several dysregulated miRNAs may be involved in the pathogenesis of IVD degeneration. Further study is needed to confirm the functional role of the identified miRNAs.

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