Salinity stress reveals three types of RNA editing sites in mitochondrial Nad7 gene of wild barley both in silico and in qRT-PCR experiments

2021 ◽  
Author(s):  
Ahmed M. Ramadan ◽  
Osama A. M. Said ◽  
Asmaa M. Abushady
Keyword(s):  
Rna Editing ◽  
Salinity Stress ◽  
In Silico ◽  
Wild Barley ◽  
Qrt Pcr

scholarly journals Análisis in silico y expresión génica del factor de transcripción TgNAC01 implicado en xilogénesis y estrés abiótico en Tectona grandis.

2017 ◽  
Vol 22 (3) ◽  
pp. 359-369 ◽  
Author(s):  
Vladimir Camel Paucar ◽  
Esteban Galeano ◽  
Helaine Carrer
Keyword(s):  
In Silico ◽  
Tectona Grandis ◽  
Qrt Pcr ◽  
Expresión Génica ◽  
R Project

El xilema secundario es el componente más abundante de la biomasa vegetal. Por tanto, conocer los genes que regulan su formación ayudaría a diseñar estrategias para el mejoramiento genético de la madera. Así, el objetivo de este trabajo fue realizar el análisis computacional de la estructura primaria y secundaria del factor de transcripción (FT) TgNAC01 de Tectona grandis, además de evaluar su historia evolutiva, dominios conservados y expresión génica en tejidos lignificados de árboles de 12 y 60 años. Para ello, se realizó una evaluación del potencial de interacción ion-electrón (PIIE), mediante el método del espectro de la información (MEI) utilizando la librería SFAPS de R-Project, seguido del modelamiento estructural utilizando el software MODELLER y visualizado mediante PyMol. Además, el análisis de alineamiento de secuencia múltiple y filogenia fue mediante el software Bioedit y MrBayes respectivamente. También se evaluó los niveles de síntesis del FT TgNAC01 mediante qRT-PCR. Como resultados, se evidencio que el FT mantiene una estructura β-hoja antiparalela retorcida, que se compacta contra una α-hélice en la región N-terminal, teniendo así tres dominios α hélice y siete dominios β plegada. Asimismo, mediante el MEI se demostró que tiene alrededor de cinco funciones biológicas y mutaciones sobre los aminoácidos con mayor PIIE, lo que conlleva a evoluciones sobre las redes de regulación genética. Finalmente, el FT TgNAC01 juega un papel fundamental en la organización y desarrollo de las partes que componen la albura, como las células radiales de la zona cambial, los vasos, fibras y los anillos de crecimiento.

scholarly journals The Barley S-Adenosylmethionine Synthetase 3 Gene HvSAMS3 Positively Regulates the Tolerance to Combined Drought and Salinity Stress in Tibetan Wild Barley

Cells ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1530
Author(s):  
Imrul Mosaddek Ahmed ◽  
Umme Aktari Nadira ◽  
Cheng-Wei Qiu ◽  
Fangbin Cao ◽  
Zhong-Hua Chen ◽  
...  
Keyword(s):  
Salinity Stress ◽  
Wild Barley ◽  
Leaf Tissue ◽  
Secretory Protein ◽  
Antioxidant Enzyme Activities ◽  
Virus Induced Gene Silencing ◽  
Salt Tolerant ◽  
Tibetan Wild Barley ◽  
Drought Tolerant ◽  
Adenosylmethionine Synthetase

Drought and salinity are two of the most frequently co-occurring abiotic stresses. Despite recent advances in the elucidation of the effects of these stresses individually during the vegetative stage of plants, significant gaps exist in our understanding of the combined effects of these two frequently co-occurring stresses. Here, Tibetan wild barley XZ5 (drought tolerant), XZ16 (salt tolerant), and cultivated barley cv. CM72 (salt tolerant) were subjected to drought (D), salinity (S), or a combination of both treatments (D+S). Protein synthesis is one of the primary activities of the green part of the plant. Therefore, leaf tissue is an important parameter to evaluate drought and salinity stress conditions. Sixty differentially expressed proteins were identified by mass spectrometry (MALDI-TOF/TOF) and classified into 9 biological processes based on Gene Ontology annotation. Among them, 21 proteins were found to be expressed under drought or salinity alone; however, under D+S, 7 proteins, including S-adenosylmethionine synthetase 3 (SAMS3), were exclusively upregulated in drought-tolerant XZ5 but not in CM72. HvSAMS3 carries both N-terminal and central domains compared with Arabidopsis and activates the expression of several ethylene (ET)-responsive transcription factors. HvSAMS3 is mainly expressed in the roots and stems, and HvSAMS3 is a secretory protein located in the cell membrane and cytoplasm. Barley stripe mosaic virus-based virus-induced gene silencing (BSMV-VIGS) of HvSAMS3 in XZ5 severely compromised its tolerance to D+S and significantly reduced plant growth and K+ uptake. The reduced tolerance to the combined stress was associated with the inhibition of polyamines such as spermidine and spermine, polyamine oxidase, ethylene, biotin, and antioxidant enzyme activities. Furthermore, the exogenous application of ethylene and biotin improved the tolerance to D+S in BSMV-VIGS:HvSAMS3-inoculated plants. Our findings highlight the significance of HvSAMS3 in the tolerance to D+S in XZ5.

Genetic variation in the root growth response of barley genotypes to salinity stress

2013 ◽  
Vol 40 (5) ◽  
pp. 516 ◽  
Author(s):  
Megan C. Shelden ◽  
Ute Roessner ◽  
Robert E. Sharp ◽  
Mark Tester ◽  
Antony Bacic
Keyword(s):  
Genetic Variation ◽  
Salt Stress ◽  
Root Growth ◽  
Salinity Stress ◽  
Early Phase ◽  
Root Elongation ◽  
Wild Barley ◽  
Seminal Root ◽  
Biochemical Characterisation ◽  
Barley Genotypes

We aimed to identify genetic variation in root growth in the cereal crop barley (Hordeum vulgare L.) in response to the early phase of salinity stress. Seminal root elongation was examined at various concentrations of salinity in seedlings of eight barley genotypes consisting of a landrace, wild barley and cultivars. Salinity inhibited seminal root elongation in all genotypes, with considerable variation observed between genotypes. Relative root elongation rates were 60–90% and 30–70% of the control rates at 100 and 150 mM NaCl, respectively. The screen identified the wild barley genotype CPI71284–48 as the most tolerant, maintaining root elongation and biomass in response to salinity. Root elongation was most significantly inhibited in the landrace Sahara. Root and shoot Na+ concentrations increased and K+ concentrations decreased in all genotypes in response to salinity. However, the root and shoot ion concentrations did not correlate with root elongation rates, suggesting that the Na+ and K+ concentrations were not directly influencing root growth, at least during the early phase of salt stress. The identification of genetic diversity in root growth responses to salt stress in barley provides important information for future genetic, physiological and biochemical characterisation of mechanisms of salinity tolerance.

scholarly journals Evaluation of potential reference genes for quantitative RT-PCR analysis in spotted sea bass (Lateolabrax maculatus) under normal and salinity stress conditions

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5631 ◽  
Author(s):  
Haolong Wang ◽  
Haishen Wen ◽  
Yun Li ◽  
Kaiqiang Zhang ◽  
Yang Liu
Keyword(s):  
Salinity Stress ◽  
Reference Genes ◽  
18S Rrna ◽  
Sea Bass ◽  
Stress Conditions ◽  
Pcr Analysis ◽  
Stable Gene ◽  
Qrt Pcr ◽  
Lateolabrax Maculatus ◽  
Suitable Reference

The aim of this study was to select the most suitable reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) of spotted sea bass (Lateolabrax maculatus), an important commercial marine fish in Pacific Asia, under normal physiological and salinity stress conditions. A total of 9 candidate reference genes (HPRT, GAPDH, EF1A, TUBA, RPL7, RNAPol II, B2M, ACTB and 18S rRNA) were analyzed by qRT-PCR in 10 tissues (intestine, muscle, stomach, brain, heart, liver, gill, kidney, pectoral fins and spleen) of L. maculatus. Four algorithms, geNorm, NormFinder, BestKeeper, and comparative ΔCt method, were used to evaluate the expression stability of the candidate reference genes. The results showed the 18S rRNA was most stable in different tissues under normal conditions. During salinity stress, RPL7 was the most stable gene according to overall ranking and the best combination of reference genes was RPL7 and RNAPol II. In contrast, GAPDH was the least stable gene which was not suitable as reference genes. The study showed that different algorithms might generate inconsistent results. Therefore, the combination of several reference genes should be selected to accurately calibrate system errors. The present study was the first to select reference genes of L. maculatus by qRT-PCR and provides a useful basis for selecting the appropriate reference gene in L. maculatus. The present study also has important implications for gene expression and functional genomics research in this species or other teleost species.

scholarly journals Evaluation of WHO listed COVID-19 qPCR primers and probe in silico with 375 SERS-CoV-2 full genome sequences

2020 ◽  
Author(s):  
Derek Toms ◽  
Julang Li ◽  
Hugh Y. Cai
Keyword(s):  
In Silico ◽  
Sequence Data ◽  
World Health ◽  
Sequence Information ◽  
Genome Sequences ◽  
Qrt Pcr ◽  
Reverse Transcription Pcr ◽  
Successful Design ◽  
Pcr Assays ◽  
Health Organization

AbstractQuantitative reverse-transcription PCR (qRT-PCR) assays remains the gold standard for detection of the SARS-CoV-2 virus because of its sensitivity and specificity. However, successful design of qRT-PCR assays requires accurate viral genome sequences. With mutations accumulating as the virus is transmitted globally, we sought to compare current assays recommended by the World Health Organization with available SARS-CoV-2 genomic sequences in silico. While most sequences were conserved, there were notable mismatches, particularly in assays developed using early sequences when compared to more recent isolates. We recommend that any assay being evaluated for diagnostic tests be compared with prevalent sequence data from the region of proposed testing and that continued publicly accessible sequence information continue to be provided by the research community.

scholarly journals Computational and in vitro Investigation of miRNA-Gene Regulations in Retinoblastoma Pathogenesis: miRNA Mimics Strategy

2015 ◽  
Vol 9 ◽  
pp. BBI.S21742 ◽  
Author(s):  
Nalini Venkatesan ◽  
Perinkulam Ravi Deepa ◽  
Vikas Khetan ◽  
Subramanian Krishnakumar
Keyword(s):  
Cell Cycle ◽  
In Silico ◽  
Apoptotic Cell ◽  
Minimum Energy ◽  
Mirna Gene ◽  
Stem Cell Markers ◽  
Qrt Pcr ◽  
Mirna Mimic ◽  
In Vitro Investigation

Purpose Retinoblastoma (RB), a primary pediatric intraocular tumor, arises from primitive retinal layers. Several novel molecular strategies are being developed for the clinical management of RB. miRNAs are known to regulate cancer-relevant biological processes. Here, the role of selected miRNAs, namely, miR-532-5p and miR-486-3p, has been analyzed for potential therapeutic targeting in RB. Methods A comprehensive bioinformatic analysis was performed to predict the posttranscriptional regulators (miRNAs) of the select panel of genes [Group 1: oncogenes (HMGA2, MYCN, SYK, FASN); Group 2: cancer stem cell markers (TACSTD, ABCG2, CD133, CD44, CD24) and Group 3: cell cycle regulatory proteins (p53, MDM2)] using Microcosm, DIANALAB, miRBase v 18, and REFSEQ database, and RNA hybrid. The expressions of five miRNAs, namely, miR-146b-5p, miR-532-5p, miR-142-5p, miR-328, and miR-486-3p, were analyzed by qRT-PCR on primary RB tumor samples (n = 30; including 17 invasive RB tumors and 13 noninvasive RB tumors). Detailed complementary alignment between 5’ seed sequence of differentially expressed miRNAs and the sequence of target genes was determined. Based on minimum energy level and piCTAR scores, the gene targets were selected. Functional roles of these miRNA clusters were studied by using mimics in cultured RB (Y79, Weri Rb-1) cells in vitro. The gene targets (SYK and FASN) of the studied miRNAs were confirmed by qRT-PCR and western blot analysis. Cell proliferation and apoptotic studies were performed. Results Nearly 1948 miRNAs were identified in the in silico analysis, From this list, only 9 upregulated miRNAs (miR-146b-5p, miR-305, miR-663b, miR-299, miR-532-5p, miR-892b, miR-501, miR-142-5p, and miR-513b) and 10 downregulated miRNAs (miR-1254, miR-328, miR-133a, miR-1287, miR-1299, miR-375, miR-486-3p, miR-720, miR-98, and miR-122*) were found to be common with the RB serum miRNA profile. Downregulation of five miRNAs (miR-146b-5p, miR-532-5p, miR-142-5p, miR-328, and miR-486-3p) was confirmed experimentally. Predicted common oncogene targets (SYK and FASN) of miR-486-3p and miR-532-5p were evaluated for their mRNA and protein expression in these miRNA mimic-treated RB cells. Experimental overexpression of these miRNAs mediated apoptotic cell death without significantly altering the cell cycle in RB cells. Conclusion Key miRNAs in RB pathogenesis were identified by an in silico approach. Downregulation of miR-486-3p and miR-532-5p in primary retinoblastoma tissues implicates their role in tumorigenesis. Prognostic and therapeutic potential of these miRNA was established by the miRNA mimic strategy.

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