scholarly journals Transcriptome analysis reveals different responses and tolerance mechanisms of EPSPS and GAT genes in transgenic soybeans

2021 ◽  
Author(s):  
Bingfu Guo ◽  
Hui-Long Hong ◽  
Yong Guo ◽  
Li-Juan Qiu
Keyword(s):  
Molecular Basis ◽  
Biosynthetic Pathway ◽  
Early Stage ◽  
Transcriptional Level ◽  
Similar Response ◽  
Rna Seq ◽  
Tolerance Mechanisms ◽  
Glyphosate Tolerance ◽  
Before And After ◽  
Soybean Genotypes

Abstract Background: Glyphosate is a broad-spectrum and non-selective systemic herbicide. Introduction of glyphosate tolerance genes like EPSPS or detoxification genes like GAT could confer glyphosate tolerance to plants. Our previous study revealed that co-expression of EPSPS and GAT genes conferred higher glyphosate tolerance with no “yellow flashing” phenomenon. However, the tolerance mechanisms response to glyphosate at transcriptional level was still unknown. Methods and Results: To investigate glyphosate tolerance mechanisms in different GM soybeans, RNA-seq analysis was conducted using four soybean genotypes, including two non-transgenic (NT) soybeans ZH10, MD12, and two GM soybeans HJ698 and ZH10-6. A total of 90.72 Gb clean reads were generated and differentially expressed genes (DEGs) were identified in these soybeans before and after glyphosate treatments. The similar response of glyphosate in NT soybeans and the different effect of glyphosate to two GM soybeans were identified. The number of DEGs involved in shikimate biosynthetic pathway and herbicide targeted cross-pathways was continuously increased in NT soybeans, and slightly increased in HJ698 as the increasing of treat time. However, it was only significantly increased at 12hpt but tended to recover to levels of 0 hpt at 72 hpt in ZH10-6, which can explain the higher glyphosate tolerance of ZH10-6.Conclusions: All these results suggested that GAT and EPSPS genes associated play a crucial role in response to glyphosate, and the former might work at the early stage of glyphosate exposure while the latter might be activated after the uptake of glyphosate uptake. These findings will provide valuable sights for understanding of the molecular basis underlying glyphosate tolerance.

scholarly journals Transcriptome of peanut kernel and shell reveals the mechanism of calcium on peanut pod development

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sha Yang ◽  
Jianguo Wang ◽  
Zhaohui Tang ◽  
Feng Guo ◽  
Ye Zhang ◽  
...  
Keyword(s):  
Early Stage ◽  
Central Element ◽  
Abnormal Development ◽  
Transcriptional Level ◽  
Peanut Kernel ◽  
Rna Seq ◽  
Embryo Abortion ◽  
Genes Encoding ◽  
Pod Development ◽  
The Relationship

Abstract Calcium is not only a nutrient necessary for plant growth but also a ubiquitous central element of different signaling pathways. Ca2+ deficiency in soil may cause embryo abortion, which can eventually lead to abnormal development of peanut pods during the harvest season. To further study the mechanisms by which Ca2+ affects the shells and kernels of peanuts, transcriptome sequencing was used to explore the genes differentially expressed in shells and kernels during the early stage of peanut pod development between Ca2+ sufficient and deficient treatments. In this study, 38,894 expressed genes were detected. RNA-seq based gene expression profiling showed a large number of genes at the transcriptional level that changed significantly in shells and kernels between the Ca2+ sufficient and deficient treatments, respectively. Genes encoding key proteins involved in Ca2+ signal transduction, hormones, development, ion transport, and nutrition absorption changed significantly. Meanwhile, in the early stage of pod development, calcium first promoted nutrient absorption and development of shells, which has less effect on the formation of seed kernels. These results provide useful information for understanding the relationship between Ca2+ absorption and pod development.

scholarly journals Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant–Bacteria Interactions

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1802
Author(s):  
Tongda Li ◽  
Ross Mann ◽  
Jatinder Kaur ◽  
German Spangenberg ◽  
Timothy Sawbridge
Keyword(s):  
Plant Growth ◽  
Nutrient Uptake ◽  
Molecular Basis ◽  
Early Stage ◽  
Rna Seq ◽  
Bacterial Strains ◽  
Paenibacillus Sp ◽  
Plant Growth Promoting ◽  
Growth Promoting ◽  
Uptake And Metabolism

Plant growth-promoting bacteria can improve host plant traits including nutrient uptake and metabolism and tolerance to biotic and abiotic stresses. Understanding the molecular basis of plant–bacteria interactions using dual RNA-seq analyses provides key knowledge of both host and bacteria simultaneously, leading to future enhancements of beneficial interactions. In this study, dual RNA-seq analyses were performed to provide insights into the early-stage interactions between barley seedlings and three novel bacterial strains (two Paenibacillus sp. strains and one Erwinia gerundensis strain) isolated from the perennial ryegrass seed microbiome. Differentially expressed bacterial and barley genes/transcripts involved in plant–bacteria interactions were identified, with varying species- and strain-specific responses. Overall, transcriptome profiles suggested that all three strains improved stress response, signal transduction, and nutrient uptake and metabolism of barley seedlings. Results also suggested potential improvements in seedling root growth via repressing ethylene biosynthesis in roots. Bacterial secondary metabolite gene clusters producing compounds that are potentially associated with interactions with the barley endophytic microbiome and associated with stress tolerance of plants under nutrient limiting conditions were also identified. The results of this study provided the molecular basis of plant growth-promoting activities of three novel bacterial strains in barley, laid a solid foundation for the future development of these three bacterial strains as biofertilisers, and identified key differences between bacterial strains of the same species in their responses to plants.

scholarly journals The long noncoding RNA MALAT1 modulates adipose loss in cancer-associated cachexia by suppressing adipogenesis through PPAR-γ

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Jun Han ◽  
Lei Shen ◽  
Zheng Zhan ◽  
Yuguo Liu ◽  
Chang Zhang ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Reporter Gene ◽  
Noncoding Rna ◽  
Early Stage ◽  
Interaction Network ◽  
Reporter Gene Assay ◽  
Transcriptional Level ◽  
Rna Seq ◽  
Ppar Γ ◽  
Gene Assay

Abstract Background Cancer-associated cachexia is a multifactorial syndrome defined by progressive weight loss with ongoing loss of adipose tissue and skeletal muscle. Adipose loss occurs in the early stage of cachexia and is associated with reduced quality of life and survival time. Although numerous lncRNAs are regarded as novel regulators in adipose metabolism, the role of lncRNAs that selectively modulate the development of adipose loss in cachexia remains limited. Methods In this study, we analyzed microarray data of lncRNAs in adipose loss and further explored the function and mechanism of MALAT1 in adipose loss. First, we explored the expression and function of MALAT1 in adipose cell by quantitative PCR and RNA knockdown. Subsequently, the mechanism of MALAT1 involvement in adipose loss was analyzed via RNA-seq, bioinformatics analysis and reporter gene assay. Finally, we explored the clinical significance of MALAT1 through correlation analysis. Results Cellular experiments revealed that knocking down MALAT1 significantly inhibited the process of adipogenesis. RNA-seq data showed that numerous adipogenic genes were downregulated upon MALAT1 knockdown. A protein–protein interaction network analysis identified PPAR-γ as the central node transcription factor, the inhibition of which explains the downregulation of numerous adipogenic genes. A reporter gene assay suggested that MALAT1 can regulate the gene expression of PPAR-γ at the transcriptional level. Moreover, MALAT1 was weakly expressed in the subcutaneous white adipose tissue of cancer-associated cachexia patients and was related to low fat mass index and poor prognosis in cancer patients. Conclusions This study indicated that MALAT1 is associated with adipose loss in cancer-associated cachexia by regulating adipogenesis through PPAR-γ, which may potentially be a novel target for the diagnosis and treatment of cancer-associated cachexia in the clinic.

A Comparative Study of Amalaki Choorna along with Madhu and Vata Twak Kashaya Yoni Pichu Dharana in the Management of Shweta Pradara

2017 ◽  
Vol 2 (4) ◽  
Author(s):  
Renuka M. Tenahalli
Keyword(s):  
Vitamin C ◽  
Early Stage ◽  
Pathological Condition ◽  
Before And After ◽  
Group A ◽  
Phosphorus Iron ◽  
Group B ◽  
Busy Schedule ◽  
Iron And Calcium

Shweta Pradara (Leucorrhoea) is the disease which is characterized by vaginal white discharge. Vaginal white discharge this symptom is present in both physiological and pathological condition, when it becomes pathological it disturbs routine life style of the woman. Most of the women in the early stage will not express the symptoms because of hesitation and their busy schedule. If it is not treated it may leads to chronic diseases like PID (Garbhashaya Shotha etc.) Charaka mentioned Amalaki Choorna along with Madhu and Vata Twak Kashaya Yoni Pichu Dharana. This treatment is used in Shweta Pradara shown positive results, hence a study was under taken to assess its clinical efficacy. 30 diagnosed patients of Shweta Pradara were randomly selected, allocated in three groups. Group A and Group B received Amalaki Choorna with Madhu and Vata Twak Kashaya Yoni Pichu Dharana respectively and Group C received Amalaki Choorna with Madhu followed by Vata Twak Kashaya Yoni Pichu Dharana for 15 days. The patients were assessed for the severity of the symptoms subjectively and objectively before and after the treatment and at the end of the follow up. Data from each group were statistically analyzed and were compared. No side effects were noted and it may be considered as an effective alternative medicine in Shweta Pradara (leucorrhea). Amalaki is rich in natural source of vitamin C and contains phosphorus, iron and calcium. Honey contains carbohydrate, vitamin C, phosphorus iron and calcium. All together these help to increase Hb% and immunity. Vata Twak Kashaya contains tannin which helps to maintain normal pH of the vagina.

scholarly journals OP0286 PROTEOMICS AND RNA SEQUENCING APPROACHES HIGHLIGHT THE ROLE OF ENDOTHELIAL CELL DYSREGULATION IN IL-1 AND IFN MEDIATED AUTOINFLAMMATORY DISEASES, NOMID AND CANDLE

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 178-179
Author(s):  
S. Alehashemi ◽  
M. Garg ◽  
B. Sellers ◽  
A. De Jesus ◽  
A. Biancotto ◽  
...  
Keyword(s):  
Endothelial Cell ◽  
Whole Blood ◽  
Cell Activation ◽  
Immune Cell ◽  
Differentially Expressed ◽  
Neutrophilic Dermatosis ◽  
Healthy Controls ◽  
Differentially Expressed Proteins ◽  
Rna Seq ◽  
Before And After

Background:Systemic Autoinflammatory diseases present with sterile inflammation. NOMID (Neonatal-Onset Multisystem Inflammatory Disease) is caused by gain-of-function mutations inNLRP3and excess IL-1 production, presents with fever, neutrophilic dermatosis, aseptic meningitis, hearing loss and eye inflammation; CANDLE (Chronic Atypical Neutrophilic Dermatosis, Lipodystrophy and Elevated Temperature) is caused by loss-of-function mutations in proteasome genes that lead to type-1 interferon signaling, characterized by fever, panniculitis, lipodystrophy, cytopenia, systemic and pulmonary hypertension and basal ganglia calcification. IL-1 blockers are approved for NOMID and JAK-inhibitors show efficacy in CANDLE treatment.Objectives:We used proteomic analysis to compare differentially expressed proteins in active NOMID and CANDLE compared to healthy controls before and after treatment, and whole blood bulk RNA seq to identify the immune cell signatures.Methods:Serum samples from active NOMID (n=12) and CANDLE (n=7) before and after treatment (table 1) and age matched healthy controls (HC) (n=7) were profiled using the SomaLogic platform (n=1125 proteins). Differentially expressed proteins in NOMID and CANDLE were ranked after non-parametric tests for unpaired (NOMIDp<0.05, CANDLE,p<0.1) and paired (p<0.05) analysis and assessed by enriched Gene Ontology pathways and network visualization. Whole blood RNA seq was performed (NOMID=7, CANDLE=7, Controls =5) and RPKM values were used to assess immune cells signatures.Table 1.Patient’s characteristicsNOMIDN=12, Male =6CANDLEN=7, Male =6AgeMedian (range)12 (2, 28)16 (3, 20)Ethnicity%White (Hispanic)80 (20)100 (30)GeneticsNLRP3mutation(2 Somatic, 10 Germline)mutations in proteasome component genes(1 digenic, 6 Homozygous/compound Heterozygous)Before treatmentAfter treatmentBefore treatmentAfter treatmentCRPMedian (range) mg/L52 (16-110)5 (0-23)5 (0-101)1 (0-4)IFN scoremedian (range)0NA328 (211-1135)3 (0-548)Results:Compared to control, 205 proteins (127 upregulated, 78 downregulated) were significantly different at baseline in NOMID, compared to 163 proteins (101 upregulated, and 62 downregulated) in CANDLE. 134 dysregulated proteins (85 upregulated, 49 downregulated) overlapped in NOMID and CANDLE (Figure 1). Pathway analysis identified neutrophil and monocyte chemotaxis signature in both NOMID and CANDLE. NOMID patients had neutrophilia and active neutrophils. CANDLE patients exhibited active neutrophils in whole blood RNA. Endothelial cell activation was the most prominent non-hematopoietic signature and suggest distinct endothelial cell dysregulation in NOMID and CANDLE. In NOMID, the signature included neutrophil transmigration (SELE) endothelial cell motility in response to angiogenesis (HGF, VEGF), while in CANDLE the endothelial signatures included extracellular matrix protein deposition (COL8A) suggesting increased vascular stiffness. CANDLE patients had higher expression of Renin, 4 out of 7 had hypertension, NOMID patients did not have hypertension. Treatment with anakinra and baricitinib normalized 143 and 142 of dysregulated proteins in NOMID and CANDLE respectively.Conclusion:Differentially expressed proteins in NOMID and CANDLE are consistent with innate immune cell activation. Distinct endothelial cell signatures in NOMID and CANDLE may provide mechanistic insight into differences in vascular phenotypes. Treatment with anakinra and Baricitinib in NOMID and CANDLE leaves 30% and 13% of the dysregulated proteins unchanged.Acknowledgments:This work was supported by Intramural Research atNational Institute of Allergy Immunology and Infectious Diseases of National Institutes of Health, Bethesda, Maryland, the Center of Human Immunology and was approved by the IRB.Disclosure of Interests:None declared

scholarly journals Lamin A/C Is Dispensable to Mechanical Repression of Adipogenesis

2021 ◽  
Vol 22 (12) ◽  
pp. 6580
Author(s):  
Matthew Goelzer ◽  
Amel Dudakovic ◽  
Melis Olcum ◽  
Buer Sen ◽  
Engin Ozcivici ◽  
...  
Keyword(s):  
Cell Structure ◽  
Nuclear Architecture ◽  
Focal Adhesions ◽  
Protein Translation ◽  
Lamin A ◽  
Transcriptional Level ◽  
Rna Seq ◽  
Interferon Signaling ◽  
Regulate Protein ◽  
Low Intensity Vibration

Mesenchymal stem cells (MSCs) maintain the musculoskeletal system by differentiating into multiple lineages, including osteoblasts and adipocytes. Mechanical signals, including strain and low-intensity vibration (LIV), are important regulators of MSC differentiation via control exerted through the cell structure. Lamin A/C is a protein vital to the nuclear architecture that supports chromatin organization and differentiation and contributes to the mechanical integrity of the nucleus. We investigated whether lamin A/C and mechanoresponsiveness are functionally coupled during adipogenesis in MSCs. siRNA depletion of lamin A/C increased the nuclear area, height, and volume and decreased the circularity and stiffness. Lamin A/C depletion significantly decreased markers of adipogenesis (adiponectin, cellular lipid content) as did LIV treatment despite depletion of lamin A/C. Phosphorylation of focal adhesions in response to mechanical challenge was also preserved during loss of lamin A/C. RNA-seq showed no major adipogenic transcriptome changes resulting from LIV treatment, suggesting that LIV regulation of adipogenesis may not occur at the transcriptional level. We observed that during both lamin A/C depletion and LIV, interferon signaling was downregulated, suggesting potentially shared regulatory mechanism elements that could regulate protein translation. We conclude that the mechanoregulation of adipogenesis and the mechanical activation of focal adhesions function independently from those of lamin A/C.

scholarly journals Triterpenoid Saponin Biosynthetic Pathway Profiling and Candidate Gene Mining of the Ilex asprella Root Using RNA-Seq

2014 ◽  
Vol 15 (4) ◽  
pp. 5970-5987 ◽  
Author(s):  
Xiasheng Zheng ◽  
Hui Xu ◽  
Xinye Ma ◽  
Ruoting Zhan ◽  
Weiwen Chen
Keyword(s):  
Candidate Gene ◽  
Biosynthetic Pathway ◽  
Triterpenoid Saponin ◽  
Rna Seq ◽  
Gene Mining

scholarly journals Rearing Drones in Queen Cells of Apis mellifera Honey Bees

2016 ◽  
Vol 60 (2) ◽  
pp. 119-128
Author(s):  
Georgios Goras ◽  
Chrysoula Tananaki ◽  
Sofia Gounari ◽  
Elissavet Lazaridou ◽  
Dimitrios Kanelis ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Larval Development ◽  
Honey Bees ◽  
Royal Jelly ◽  
Early Stage ◽  
Egg Laying ◽  
Horizontal Position ◽  
Before And After ◽  
Queen Larvae ◽  
As If

Abstract We investigated the rearing of drone larvae grafted in queen cells. From the 1200 drone larvae that were grafted during spring and autumn, 875 were accepted (72.9%) and reared as queens. Drone larvae in false queen cells received royal jelly of the same composition and of the same amounts as queen larvae. Workers capped the queen cells as if they were drones, 9-10 days after the egg laying. Out of 60 accepted false queen cells, 21 (35%) were capped. The shape of false queen cells with drone larvae is unusually long with a characteristically elongate tip which is probably due to the falling of larvae. Bees start the destruction of the cells when the larvae were 3 days old and maximised it before and after capping. Protecting false queen cells in the colony by wrapping, reversing them upside down, or placing in a horizontal position, did not help. The only adult drones that emerged from the false queen cells were those protected in an incubator and in push-in cages. Adult drones from false queen cells had smaller wings, legs, and proboscis than regular drones. The results of this study verify previous reports that the bees do not recognise the different sex of the larvae at least at the early stage of larval development. The late destruction of false queen cells, the similarity in quality and quantity of the produced royal jelly, and the bigger drone cells, allow for the use of drone larvae in cups for the production of royal jelly.

Antecedents of growth-oriented entrepreneurship before and during the Greek economic crisis

2017 ◽  
Vol 24 (3) ◽  
pp. 528-544 ◽  
Author(s):  
Ioannis Giotopoulos ◽  
Alexandra Kontolaimou ◽  
Aggelos Tsakanikas
Keyword(s):  
Work Experience ◽  
Early Stage ◽  
New Ventures ◽  
High Growth ◽  
Content Type ◽  
Crisis Period ◽  
Individual Level ◽  
Level Data ◽  
The Social ◽  
Before And After

Purpose The purpose of this paper is to explore potential drivers of high-growth intentions of early-stage entrepreneurs in Greece before and after the onset of the financial crisis of 2008. Design/methodology/approach To this end, the authors use individual-level data retrieved from Global Entrepreneurship Monitor annual surveys (2003-2015). Findings The results show that high-growth intentions of Greek entrepreneurs are driven by different factors in the crisis compared to the non-crisis period. Male entrepreneurs and entrepreneurs with significant work experience seem to be more likely to be engaged in growth-oriented new ventures during the crisis period. The same appears to hold for entrepreneurs who are motivated by an opportunity and also perceive future business opportunities in adverse economic conditions. On the other hand, the educational level and the social contacts of founders with other entrepreneurs are found to drive ambitious Greek entrepreneurship in the years before the crisis, while they were insignificant after the crisis outbreak. Originality/value Based on the concept of ambitious entrepreneurship, this study contributes to the literature by investigating the determinants of entrepreneurial high-growth expectations in the Greek context emphasizing the crisis period in comparison to the pre-crisis years.

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